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toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8 in error's stderr message

Listed in descending order by number of error of each type

Tool error	Number of error like this	Date of this error
--ERROR: Could not access created dir /tco/ [FATAL:T-COFFEE] --ERROR: Could not access created dir /tco/ [FATAL:T-COFFEE] ... SLURM_JOB_NODELIST=slurm.test.usegalaxy.no _=/usr/bin/env --ERROR: Could not access created dir /tco/ [FATAL:T-COFFEE] [this line in 2 times] ------------------------- Extended error ------------------------- --ERROR: Could not access created dir /tco/ [FATAL:T-COFFEE] --ERROR: Could not access created dir /tco/ [FATAL:T-COFFEE] SHELL=/bin/bash SLURM_JOB_USER=galaxy SLURM_TASKS_PER_NODE=1 SLURM_JOB_UID=1024 SLURM_TASK_PID=12528 SLURM_LOCALID=0 SLURM_SUBMIT_DIR=/srv/galaxy/server HOSTNAME=slurm.test.usegalaxy.no SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 SLURMD_NODENAME=slurm.test.usegalaxy.no JAVA_HOME=/usr/local/lib/jvm GALAXY_SLOTS=1 JAVA_LD_LIBRARY_PATH=/usr/local/lib/jvm/lib/server SLURM_NODE_ALIASES=(null) SLURM_CLUSTER_NAME=usegalaxy SLURM_CPUS_ON_NODE=1 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_JOB_CPUS_PER_NODE=1 PWD=/data/part0/tmp/jobs/001/1223/working SLURM_GTIDS=0 GSETTINGS_SCHEMA_DIR=/usr/local/share/glib-2.0/schemas LOGNAME=galaxy CONDA_PREFIX=/usr/local SLURM_JOB_PARTITION=usegalaxy_testing GSETTINGS_SCHEMA_DIR_CONDA_BACKUP= SLURM_JOB_NUM_NODES=1 SLURM_JOBID=1970 SLURM_JOB_QOS=normal USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin HOME=/srv/galaxy/ LANG=C.UTF-8 _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1223/home SLURM_PROCID=0 VIRTUAL_ENV=/srv/galaxy/venv SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 GALAXY_MEMORY_MB=4096 TMPDIR=/data/part0/tmp/jobs/001/1223/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SLURM_NTASKS=1 SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no JAVA_LD_LIBRARY_PATH_BACKUP= SLURM_TOPOLOGY_ADDR_PATTERN=node GEM_HOME=/usr/local/share/rubygems/ SLURM_MEM_PER_NODE=4096 SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 PYTHONPATH=/srv/galaxy/dynamic_rules GALAXY_CONFIG_SERVER_NAME=handler_0 USER=galaxy LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: SLURM_NODELIST=slurm.test.usegalaxy.no ENVIRONMENT=BATCH TEMP=/data/part0/tmp/jobs/001/1223/tmp SLURM_PRIO_PROCESS=0 SLURM_NPROCS=1 SHLVL=3 SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 APPTAINER_CACHEDIR=/var/tmp/containers SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1223/working:/data/part0/tmp/jobs/001/1223/working,/data/part0/tmp/jobs/001/1223:/data/part0/tmp/jobs/001/1223,/data/part0/tmp/jobs/001/1223/tmp:/tmp,/cvmfs/:/cvmfs/:ro SLURM_SUBMIT_HOST=test.usegalaxy.no DIR_4_TCOFFEE= LD_LIBRARY_PATH=/.singularity.d/libs SLURM_JOB_ID=1970 SLURM_NODEID=0 TMP_4_TCOFFEE= JAVA_HOME_CONDA_BACKUP= GALAXY_MEMORY_MB_PER_SLOT=4096 LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1223/tmp TMP=/data/part0/tmp/jobs/001/1223/tmp SLURM_CONF=/etc/slurm/slurm.conf PATH=/usr/local/share/rubygems/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin CACHE_4_TCOFFEE= APPTAINER_TMPDIR=/var/tmp PYTHONWARNINGS=ignore MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: SINGULARITY_COMMAND=exec SLURM_JOB_GID=1024 OLDPWD=/data/part0/tmp/jobs/001/1223 SLURM_JOB_NODELIST=slurm.test.usegalaxy.no _=/usr/bin/env --ERROR: Could not access created dir /tco/ [FATAL:T-COFFEE] [this line in 2 times] ------------------------------------------------------------------	1	2024-05-24
--ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] ... SINGULARITY_COMMAND=exec _=/usr/bin/env --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] [this line in 2 times] ------------------------- Extended error ------------------------- --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 JAVA_HOME=/usr/local/lib/jvm GALAXY_SLOTS=1 JAVA_LD_LIBRARY_PATH=/usr/local/lib/jvm/lib/server SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh PWD=/data/part0/tmp/jobs/001/1217/working GSETTINGS_SCHEMA_DIR=/usr/local/share/glib-2.0/schemas CONDA_PREFIX=/usr/local GSETTINGS_SCHEMA_DIR_CONDA_BACKUP= HOME=/srv/galaxy/ LANG=C.UTF-8 _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1217/home SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 GALAXY_MEMORY_MB=2048 TMPDIR=/data/part0/tmp/jobs/001/1217/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND JAVA_LD_LIBRARY_PATH_BACKUP= GEM_HOME=/usr/local/share/rubygems/ TEMP=/data/part0/tmp/jobs/001/1217/tmp SHLVL=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1217/working:/data/part0/tmp/jobs/001/1217/working,/data/part0/tmp/jobs/001/1217:/data/part0/tmp/jobs/001/1217,/data/part0/tmp/jobs/001/1217/tmp:/tmp,/cvmfs/:/cvmfs/:ro LD_LIBRARY_PATH=/.singularity.d/libs JAVA_HOME_CONDA_BACKUP= GALAXY_MEMORY_MB_PER_SLOT=2048 _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1217/tmp TMP=/data/part0/tmp/jobs/001/1217/tmp PATH=/usr/local/share/rubygems/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SINGULARITY_COMMAND=exec _=/usr/bin/env --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] [this line in 2 times] ------------------------------------------------------------------	1	2024-04-26
--ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] ... SINGULARITY_COMMAND=exec _=/usr/bin/env --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] [this line in 2 times] ------------------------- Extended error ------------------------- --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 JAVA_HOME=/usr/local/lib/jvm GALAXY_SLOTS=1 JAVA_LD_LIBRARY_PATH=/usr/local/lib/jvm/lib/server SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh PWD=/data/part0/tmp/jobs/001/1199/working GSETTINGS_SCHEMA_DIR=/usr/local/share/glib-2.0/schemas CONDA_PREFIX=/usr/local GSETTINGS_SCHEMA_DIR_CONDA_BACKUP= HOME=/srv/galaxy/ LANG=C.UTF-8 _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1199/home SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 GALAXY_MEMORY_MB=2048 TMPDIR=/data/part0/tmp/jobs/001/1199/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND JAVA_LD_LIBRARY_PATH_BACKUP= GEM_HOME=/usr/local/share/rubygems/ TEMP=/data/part0/tmp/jobs/001/1199/tmp SHLVL=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1199/working:/data/part0/tmp/jobs/001/1199/working,/data/part0/tmp/jobs/001/1199:/data/part0/tmp/jobs/001/1199,/data/part0/tmp/jobs/001/1199/tmp:/tmp,/cvmfs/:/cvmfs/:ro LD_LIBRARY_PATH=/.singularity.d/libs JAVA_HOME_CONDA_BACKUP= GALAXY_MEMORY_MB_PER_SLOT=2048 _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1199/tmp TMP=/data/part0/tmp/jobs/001/1199/tmp PATH=/usr/local/share/rubygems/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SINGULARITY_COMMAND=exec _=/usr/bin/env --ERROR: Could not access created dir /var/tmp//tco/ [FATAL:T-COFFEE] [this line in 2 times] ------------------------------------------------------------------	1	2024-04-11
SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no ... *********************************************************************************************** # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 10411 ppid 10410 #CL: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method muscle_msa -output clustalw_aln -n_core 1 -run_name t_coffee_out -quiet ------------------------- Extended error ------------------------- SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no SLURMD_NODENAME=slurm.test.usegalaxy.no HOSTNAME=slurm.test.usegalaxy.no SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) GALAXY_CONFIG_SERVER_NAME=handler_0 SHELL=/bin/bash SLURM_JOB_QOS=normal GALAXY_MEMORY_MB_PER_SLOT=2048 APPTAINER_TMPDIR=/var/tmp TMPDIR=/data/part0/tmp/jobs/001/1197/tmp SLURM_TOPOLOGY_ADDR_PATTERN=node LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1197/home SINGULARITY_COMMAND=exec LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1197/tmp USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin USER=galaxy SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 TEMP=/data/part0/tmp/jobs/001/1197/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PYTHONWARNINGS=ignore SLURM_JOBID=1947 SLURM_NTASKS=1 VIRTUAL_ENV=/srv/galaxy/venv APPTAINER_CACHEDIR=/var/tmp/containers SLURM_TASKS_PER_NODE=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 SLURM_CONF=/etc/slurm/slurm.conf SLURM_JOB_ID=1947 KJETIL=942 SLURM_JOB_USER=galaxy PWD=/data/part0/tmp/jobs/001/1197/working MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: DIR_4_TCOFFEE=/data/part0/tmp/jobs/001/1197/tmp GALAXY_SLOTS=1 CACHE_4_TCOFFEE=/data/part0/tmp/jobs/001/1197/tmp LANG=en_US.UTF-8 SLURM_JOB_UID=1024 SLURM_NODEID=0 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_SUBMIT_DIR=/srv/galaxy/server GALAXY_MEMORY_MB=2048 SLURM_TASK_PID=10342 SLURM_NPROCS=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1197/working:/data/part0/tmp/jobs/001/1197/working,/data/part0/tmp/jobs/001/1197:/data/part0/tmp/jobs/001/1197,/data/part0/tmp/jobs/001/1197/tmp:/tmp,/cvmfs/:/cvmfs/:ro SLURM_CPUS_ON_NODE=1 SLURM_PROCID=0 ENVIRONMENT=BATCH SLURM_JOB_NODELIST=slurm.test.usegalaxy.no SHLVL=3 HOME=/srv/galaxy/ SLURM_LOCALID=0 SLURM_JOB_GID=1024 SLURM_JOB_CPUS_PER_NODE=1 SLURM_CLUSTER_NAME=usegalaxy SLURM_SUBMIT_HOST=test.usegalaxy.no SLURM_GTIDS=0 SLURM_JOB_PARTITION=usegalaxy_testing TMP=/data/part0/tmp/jobs/001/1197/tmp PYTHONPATH=/srv/galaxy/dynamic_rules LOGNAME=galaxy SLURM_JOB_NUM_NODES=1 PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 SLURM_MEM_PER_NODE=2048 TMP_4_TCOFFEE=/data/part0/tmp/jobs/001/1197/tmp _=/usr/bin/env #************************************************************* --ERROR: # [FATAL:T-COFFEE] # The Program muscle Needed by T-COFFEE Could not be found # If muscle is installed on your system: # -Make sure muscle is in your $path: # If muscle is NOT installed obtain a copy from: # http://www.drive5.com/muscle/ # [this line in 3 times] and install it manualy ************************************************************** *********************************************************************************************** * FULL TRACE BACK PID: 10411 10411 -- ERROR: # [FATAL:T-COFFEE] 10411 -- COM: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method muscle_msa -output clustalw_aln -n_core 1 -run_name t_coffee_out -quiet 10411 -- STACK: 10410 -> 10411 ************************************************************************************************* # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 10411 ppid 10410 #CL: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method muscle_msa -output clustalw_aln -n_core 1 -run_name t_coffee_out -quiet ------------------------------------------------------------------	1	2024-04-11
SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no ... *********************************************************************************************** # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 9941 ppid 9940 #CL: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method clustalw_pair -output clustalw_aln -n_core 1 -run_name t_coffee_out -quiet ------------------------- Extended error ------------------------- SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no SLURMD_NODENAME=slurm.test.usegalaxy.no HOSTNAME=slurm.test.usegalaxy.no SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) GALAXY_CONFIG_SERVER_NAME=handler_1 SHELL=/bin/bash SLURM_JOB_QOS=normal GALAXY_MEMORY_MB_PER_SLOT=2048 APPTAINER_TMPDIR=/var/tmp TMPDIR=/data/part0/tmp/jobs/001/1196/tmp SLURM_TOPOLOGY_ADDR_PATTERN=node LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1196/home SINGULARITY_COMMAND=exec LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1196/tmp USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin USER=galaxy SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 TEMP=/data/part0/tmp/jobs/001/1196/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PYTHONWARNINGS=ignore SLURM_JOBID=1946 SLURM_NTASKS=1 VIRTUAL_ENV=/srv/galaxy/venv APPTAINER_CACHEDIR=/var/tmp/containers SLURM_TASKS_PER_NODE=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 SLURM_CONF=/etc/slurm/slurm.conf SLURM_JOB_ID=1946 KJETIL=942 SLURM_JOB_USER=galaxy PWD=/data/part0/tmp/jobs/001/1196/working MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: DIR_4_TCOFFEE=/data/part0/tmp/jobs/001/1196/tmp GALAXY_SLOTS=1 CACHE_4_TCOFFEE=/data/part0/tmp/jobs/001/1196/tmp LANG=en_US.UTF-8 SLURM_JOB_UID=1024 SLURM_NODEID=0 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_SUBMIT_DIR=/srv/galaxy/server GALAXY_MEMORY_MB=2048 SLURM_TASK_PID=9885 SLURM_NPROCS=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1196/working:/data/part0/tmp/jobs/001/1196/working,/data/part0/tmp/jobs/001/1196:/data/part0/tmp/jobs/001/1196,/data/part0/tmp/jobs/001/1196/tmp:/tmp,/cvmfs/:/cvmfs/:ro SLURM_CPUS_ON_NODE=1 SLURM_PROCID=0 ENVIRONMENT=BATCH SLURM_JOB_NODELIST=slurm.test.usegalaxy.no SHLVL=3 HOME=/srv/galaxy/ SLURM_LOCALID=0 SLURM_JOB_GID=1024 SLURM_JOB_CPUS_PER_NODE=1 SLURM_CLUSTER_NAME=usegalaxy SLURM_SUBMIT_HOST=test.usegalaxy.no SLURM_GTIDS=0 SLURM_JOB_PARTITION=usegalaxy_testing TMP=/data/part0/tmp/jobs/001/1196/tmp PYTHONPATH=/srv/galaxy/dynamic_rules LOGNAME=galaxy SLURM_JOB_NUM_NODES=1 PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 SLURM_MEM_PER_NODE=2048 TMP_4_TCOFFEE=/data/part0/tmp/jobs/001/1196/tmp _=/usr/bin/env #************************************************************* --ERROR: # [FATAL:T-COFFEE] # The Program clustalw Needed by T-COFFEE Could not be found # If clustalw is installed on your system: # -Make sure clustalw is in your $path: # If clustalw is NOT installed obtain a copy from: # http://www.clustal.org # [this line in 3 times] and install it manualy ************************************************************** *********************************************************************************************** * FULL TRACE BACK PID: 9941 9941 -- ERROR: # [FATAL:T-COFFEE] 9941 -- COM: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method clustalw_pair -output clustalw_aln -n_core 1 -run_name t_coffee_out -quiet 9941 -- STACK: 9940 -> 9941 ************************************************************************************************* # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 9941 ppid 9940 #CL: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method clustalw_pair -output clustalw_aln -n_core 1 -run_name t_coffee_out -quiet ------------------------------------------------------------------	1	2024-04-11
SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no ... *********************************************************************************************** # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 9259 ppid 9258 #CL: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method t_coffee_msa clustalw_msa -output clustalw_aln fasta_seq fasta_aln -n_core 1 -run_name t_coffee_out -quiet ------------------------- Extended error ------------------------- SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no SLURMD_NODENAME=slurm.test.usegalaxy.no HOSTNAME=slurm.test.usegalaxy.no SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) GALAXY_CONFIG_SERVER_NAME=handler_0 SHELL=/bin/bash SLURM_JOB_QOS=normal GALAXY_MEMORY_MB_PER_SLOT=2048 APPTAINER_TMPDIR=/var/tmp TMPDIR=/data/part0/tmp/jobs/001/1194/tmp SLURM_TOPOLOGY_ADDR_PATTERN=node LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1194/home SINGULARITY_COMMAND=exec LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1194/tmp USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin USER=galaxy SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 TEMP=/data/part0/tmp/jobs/001/1194/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PYTHONWARNINGS=ignore SLURM_JOBID=1944 SLURM_NTASKS=1 VIRTUAL_ENV=/srv/galaxy/venv APPTAINER_CACHEDIR=/var/tmp/containers SLURM_TASKS_PER_NODE=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 SLURM_CONF=/etc/slurm/slurm.conf SLURM_JOB_ID=1944 KJETIL=942 SLURM_JOB_USER=galaxy PWD=/data/part0/tmp/jobs/001/1194/working MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: DIR_4_TCOFFEE=/data/part0/tmp/jobs/001/1194/tmp GALAXY_SLOTS=1 CACHE_4_TCOFFEE=/data/part0/tmp/jobs/001/1194/tmp LANG=en_US.UTF-8 SLURM_JOB_UID=1024 SLURM_NODEID=0 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_SUBMIT_DIR=/srv/galaxy/server GALAXY_MEMORY_MB=2048 SLURM_TASK_PID=9203 SLURM_NPROCS=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1194/working:/data/part0/tmp/jobs/001/1194/working,/data/part0/tmp/jobs/001/1194:/data/part0/tmp/jobs/001/1194,/data/part0/tmp/jobs/001/1194/tmp:/tmp,/cvmfs/:/cvmfs/:ro SLURM_CPUS_ON_NODE=1 SLURM_PROCID=0 ENVIRONMENT=BATCH SLURM_JOB_NODELIST=slurm.test.usegalaxy.no SHLVL=3 HOME=/srv/galaxy/ SLURM_LOCALID=0 SLURM_JOB_GID=1024 SLURM_JOB_CPUS_PER_NODE=1 SLURM_CLUSTER_NAME=usegalaxy SLURM_SUBMIT_HOST=test.usegalaxy.no SLURM_GTIDS=0 SLURM_JOB_PARTITION=usegalaxy_testing TMP=/data/part0/tmp/jobs/001/1194/tmp PYTHONPATH=/srv/galaxy/dynamic_rules LOGNAME=galaxy SLURM_JOB_NUM_NODES=1 PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 SLURM_MEM_PER_NODE=2048 TMP_4_TCOFFEE=/data/part0/tmp/jobs/001/1194/tmp _=/usr/bin/env #************************************************************* --ERROR: # [FATAL:T-COFFEE] # The Program clustalw Needed by T-COFFEE Could not be found # If clustalw is installed on your system: # -Make sure clustalw is in your $path: # If clustalw is NOT installed obtain a copy from: # http://www.clustal.org # [this line in 3 times] and install it manualy ************************************************************** *********************************************************************************************** * FULL TRACE BACK PID: 9259 9259 -- ERROR: # [FATAL:T-COFFEE] 9259 -- COM: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method t_coffee_msa clustalw_msa -output clustalw_aln fasta_seq fasta_aln -n_core 1 -run_name t_coffee_out -quiet 9259 -- STACK: 9258 -> 9259 ************************************************************************************************* # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 9259 ppid 9258 #CL: /usr/local/lib/t_coffee-11.0.8/bin/t_coffee /data/part0/001/dataset_1434.dat -method t_coffee_msa clustalw_msa -output clustalw_aln fasta_seq fasta_aln -n_core 1 -run_name t_coffee_out -quiet ------------------------------------------------------------------	1	2024-04-11
sh: can't create /tmp/fileHADgxZ: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 6682 6682 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/fileHADgxZ: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 6676 6676 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no SLURMD_NODENAME=slurm.test.usegalaxy.no HOSTNAME=slurm.test.usegalaxy.no SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) GALAXY_CONFIG_SERVER_NAME=handler_1 SHELL=/bin/bash SLURM_JOB_QOS=normal GALAXY_MEMORY_MB_PER_SLOT=2048 APPTAINER_TMPDIR=/var/tmp TMPDIR=/data/part0/tmp/jobs/001/1188/tmp SLURM_TOPOLOGY_ADDR_PATTERN=node LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1188/home SINGULARITY_COMMAND=exec LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1188/tmp USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin USER=galaxy SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 TEMP=/data/part0/tmp/jobs/001/1188/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PYTHONWARNINGS=ignore SLURM_JOBID=1939 SLURM_NTASKS=1 VIRTUAL_ENV=/srv/galaxy/venv APPTAINER_CACHEDIR=/var/tmp/containers SLURM_TASKS_PER_NODE=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 SLURM_CONF=/etc/slurm/slurm.conf SLURM_JOB_ID=1939 KJETIL=942 SLURM_JOB_USER=galaxy PWD=/data/part0/tmp/jobs/001/1188/working MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: DIR_4_TCOFFEE=/data/part0/tmp/jobs/001/1188/tmp GALAXY_SLOTS=1 CACHE_4_TCOFFEE=/data/part0/tmp/jobs/001/1188/tmp LANG=en_US.UTF-8 SLURM_JOB_UID=1024 SLURM_NODEID=0 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_SUBMIT_DIR=/srv/galaxy/server GALAXY_MEMORY_MB=2048 SLURM_TASK_PID=6629 SLURM_NPROCS=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1188/working:/data/part0/tmp/jobs/001/1188/working,/data/part0/tmp/jobs/001/1188:/data/part0/tmp/jobs/001/1188,/cvmfs/:/cvmfs/:ro SLURM_CPUS_ON_NODE=1 SLURM_PROCID=0 ENVIRONMENT=BATCH SLURM_JOB_NODELIST=slurm.test.usegalaxy.no SHLVL=3 HOME=/srv/galaxy/ SLURM_LOCALID=0 SLURM_JOB_GID=1024 SLURM_JOB_CPUS_PER_NODE=1 SLURM_CLUSTER_NAME=usegalaxy SLURM_SUBMIT_HOST=test.usegalaxy.no SLURM_GTIDS=0 SLURM_JOB_PARTITION=usegalaxy_testing TMP=/data/part0/tmp/jobs/001/1188/tmp PYTHONPATH=/srv/galaxy/dynamic_rules LOGNAME=galaxy SLURM_JOB_NUM_NODES=1 PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 SLURM_MEM_PER_NODE=2048 TMP_4_TCOFFEE=/data/part0/tmp/jobs/001/1188/tmp _=/usr/bin/env sh: can't create /tmp/fileNMv0iv: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 6682 6682 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-11
sh: can't create /tmp/file30igNy: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 2959 2959 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/file30igNy: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 2950 2950 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no SLURMD_NODENAME=slurm.test.usegalaxy.no HOSTNAME=slurm.test.usegalaxy.no SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) GALAXY_CONFIG_SERVER_NAME=handler_1 SHELL=/bin/bash SLURM_JOB_QOS=normal GALAXY_MEMORY_MB_PER_SLOT=2048 APPTAINER_TMPDIR=/var/tmp TMPDIR=/data/part0/tmp/jobs/001/1187/tmp SLURM_TOPOLOGY_ADDR_PATTERN=node LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1187/home SINGULARITY_COMMAND=exec LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1187/tmp USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin USER=galaxy SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 TEMP=/data/part0/tmp/jobs/001/1187/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PYTHONWARNINGS=ignore SLURM_JOBID=1938 SLURM_NTASKS=1 VIRTUAL_ENV=/srv/galaxy/venv APPTAINER_CACHEDIR=/var/tmp/containers SLURM_TASKS_PER_NODE=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 SLURM_CONF=/etc/slurm/slurm.conf SLURM_JOB_ID=1938 KJETIL=942 SLURM_JOB_USER=galaxy PWD=/data/part0/tmp/jobs/001/1187/working MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: DIR_4_TCOFFEE=/data/part0/tmp/jobs/001/1187 GALAXY_SLOTS=1 CACHE_4_TCOFFEE=/data/part0/tmp/jobs/001/1187 LANG=en_US.UTF-8 SLURM_JOB_UID=1024 SLURM_NODEID=0 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_SUBMIT_DIR=/srv/galaxy/server GALAXY_MEMORY_MB=2048 SLURM_TASK_PID=2903 SLURM_NPROCS=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1187/working:/data/part0/tmp/jobs/001/1187/working,/data/part0/tmp/jobs/001/1187:/data/part0/tmp/jobs/001/1187,/cvmfs/:/cvmfs/:ro SLURM_CPUS_ON_NODE=1 SLURM_PROCID=0 ENVIRONMENT=BATCH SLURM_JOB_NODELIST=slurm.test.usegalaxy.no SHLVL=3 HOME=/srv/galaxy/ SLURM_LOCALID=0 SLURM_JOB_GID=1024 SLURM_JOB_CPUS_PER_NODE=1 SLURM_CLUSTER_NAME=usegalaxy SLURM_SUBMIT_HOST=test.usegalaxy.no SLURM_GTIDS=0 SLURM_JOB_PARTITION=usegalaxy_testing TMP=/data/part0/tmp/jobs/001/1187/tmp PYTHONPATH=/srv/galaxy/dynamic_rules LOGNAME=galaxy SLURM_JOB_NUM_NODES=1 PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 SLURM_MEM_PER_NODE=2048 TMP_4_TCOFFEE=/data/part0/tmp/jobs/001/1187 _=/usr/bin/env sh: can't create /tmp/file3hdC7Z: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 2959 2959 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-11
sh: can't create /tmp/filemqOZ3K: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 2269 2269 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/filemqOZ3K: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 2261 2261 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** GALAXY_MEMORY_MB_PER_SLOT=2048 TMPDIR=/data/part0/tmp/jobs/001/1185/tmp _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1185/home SINGULARITY_COMMAND=exec _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1185/tmp TEMP=/data/part0/tmp/jobs/001/1185/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/data/part0/tmp/jobs/001/1185/working GALAXY_SLOTS=1 LANG=C SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh GALAXY_MEMORY_MB=2048 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1185/working:/data/part0/tmp/jobs/001/1185/working,/data/part0/tmp/jobs/001/1185:/data/part0/tmp/jobs/001/1185,/cvmfs/:/cvmfs/:ro SHLVL=1 HOME=/srv/galaxy/ TMP=/data/part0/tmp/jobs/001/1185/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 _=/usr/bin/env sh: can't create /tmp/filetA2gMe: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 2269 2269 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-11
sh: can't create /tmp/file54K4pz: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 30768 30768 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/file54K4pz: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 30762 30762 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** SLURM_NODELIST=slurm.test.usegalaxy.no SLURM_TOPOLOGY_ADDR=slurm.test.usegalaxy.no SLURMD_NODENAME=slurm.test.usegalaxy.no HOSTNAME=slurm.test.usegalaxy.no SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) GALAXY_CONFIG_SERVER_NAME=handler_1 SHELL=/bin/bash SLURM_JOB_QOS=normal GALAXY_MEMORY_MB_PER_SLOT=2048 APPTAINER_TMPDIR=/var/tmp TMPDIR=/data/part0/tmp/jobs/001/1169/tmp SLURM_TOPOLOGY_ADDR_PATTERN=node LIBRARY_PATH=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic: _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1169/home SINGULARITY_COMMAND=exec LC_ALL=C _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1169/tmp USER_PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin USER=galaxy SLURM_NNODES=1 GALAXY_SLOTS_CONFIGURED=1 TEMP=/data/part0/tmp/jobs/001/1169/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PYTHONWARNINGS=ignore SLURM_JOBID=1924 SLURM_NTASKS=1 VIRTUAL_ENV=/srv/galaxy/venv APPTAINER_CACHEDIR=/var/tmp/containers SLURM_TASKS_PER_NODE=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin SLURM_WORKING_CLUSTER=usegalaxy:test.usegalaxy.no:6817:9216:101 SLURM_CONF=/etc/slurm/slurm.conf SLURM_JOB_ID=1924 KJETIL=942 SLURM_JOB_USER=galaxy PWD=/data/part0/tmp/jobs/001/1169/working MAGIC=/srv/galaxy/venv/lib/python3.8/site-packages/pylibmagic/magic.mgc: DIR_4_TCOFFEE=/data/part0/tmp/jobs/001/1169 GALAXY_SLOTS=1 CACHE_4_TCOFFEE=/data/part0/tmp/jobs/001/1169 LANG=en_US.UTF-8 SLURM_JOB_UID=1024 SLURM_NODEID=0 SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh SLURM_SUBMIT_DIR=/srv/galaxy/server GALAXY_MEMORY_MB=2048 SLURM_TASK_PID=30714 SLURM_NPROCS=1 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1169/working:/data/part0/tmp/jobs/001/1169/working,/data/part0/tmp/jobs/001/1169:/data/part0/tmp/jobs/001/1169,/cvmfs/:/cvmfs/:ro SLURM_CPUS_ON_NODE=1 SLURM_PROCID=0 ENVIRONMENT=BATCH SLURM_JOB_NODELIST=slurm.test.usegalaxy.no SHLVL=3 HOME=/srv/galaxy/ SLURM_LOCALID=0 SLURM_JOB_GID=1024 SLURM_JOB_CPUS_PER_NODE=1 SLURM_CLUSTER_NAME=usegalaxy SLURM_SUBMIT_HOST=test.usegalaxy.no SLURM_GTIDS=0 SLURM_JOB_PARTITION=usegalaxy_testing TMP=/data/part0/tmp/jobs/001/1169/tmp PYTHONPATH=/srv/galaxy/dynamic_rules LOGNAME=galaxy SLURM_JOB_NUM_NODES=1 PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 SLURM_MEM_PER_NODE=2048 TMP_4_TCOFFEE=/data/part0/tmp/jobs/001/1169 _=/usr/bin/env sh: can't create /tmp/fileLxHPAR: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 30768 30768 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-09
sh: can't create /tmp/fileR1JTkT: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 28686 28686 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/fileR1JTkT: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 28679 28679 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** GALAXY_MEMORY_MB_PER_SLOT=2048 TMPDIR=/data/part0/tmp/jobs/001/1163/tmp _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1163/home SINGULARITY_COMMAND=exec _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1163/tmp TEMP=/data/part0/tmp/jobs/001/1163/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/data/part0/tmp/jobs/001/1163/working GALAXY_SLOTS=1 LANG=C SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh GALAXY_MEMORY_MB=2048 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1163/working:/data/part0/tmp/jobs/001/1163/working,/data/part0/tmp/jobs/001/1163:/data/part0/tmp/jobs/001/1163,/cvmfs/:/cvmfs/:ro SHLVL=1 HOME=/srv/galaxy/ TMP=/data/part0/tmp/jobs/001/1163/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 _=/usr/bin/env sh: can't create /tmp/fileFQX7Gz: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 28686 28686 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-09
sh: can't create /tmp/fileUjaM4g: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 27758 27758 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/fileUjaM4g: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 27751 27751 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** GALAXY_MEMORY_MB_PER_SLOT=2048 TMPDIR=/data/part0/tmp/jobs/001/1161/tmp _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1161/home SINGULARITY_COMMAND=exec _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1161/tmp TEMP=/data/part0/tmp/jobs/001/1161/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/data/part0/tmp/jobs/001/1161/working GALAXY_SLOTS=1 LANG=C SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh GALAXY_MEMORY_MB=2048 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1161/working:/data/part0/tmp/jobs/001/1161/working,/data/part0/tmp/jobs/001/1161:/data/part0/tmp/jobs/001/1161,/cvmfs/:/cvmfs/:ro SHLVL=1 HOME=/srv/galaxy/ TMP=/data/part0/tmp/jobs/001/1161/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 _=/usr/bin/env sh: can't create /tmp/filewuhZST: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 27758 27758 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-09
sh: can't create /tmp/fileOSwJol: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 27194 27194 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/fileOSwJol: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 27188 27188 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** GALAXY_MEMORY_MB_PER_SLOT=4096 TMPDIR=/data/part0/tmp/jobs/001/1160/tmp _GALAXY_JOB_HOME_DIR=/data/part0/tmp/jobs/001/1160/home SINGULARITY_COMMAND=exec _GALAXY_JOB_TMP_DIR=/data/part0/tmp/jobs/001/1160/tmp TEMP=/data/part0/tmp/jobs/001/1160/tmp LD_LIBRARY_PATH=/.singularity.d/libs SINGULARITY_NAME=t_coffee:11.0.8--py37hea885bf_8 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/data/part0/tmp/jobs/001/1160/working GALAXY_SLOTS=1 LANG=C SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh GALAXY_MEMORY_MB=4096 SINGULARITY_BIND=/data/:/data/:ro,/srv/galaxy/server:/srv/galaxy/server:ro,/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee:ro,/data/part0/tmp/jobs/001/1160/working:/data/part0/tmp/jobs/001/1160/working,/data/part0/tmp/jobs/001/1160:/data/part0/tmp/jobs/001/1160,/cvmfs/:/cvmfs/:ro SHLVL=1 HOME=/srv/galaxy/ TMP=/data/part0/tmp/jobs/001/1160/tmp PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND SINGULARITY_CONTAINER=/srv/galaxy/containers/singularity/mulled/t_coffee:11.0.8--py37hea885bf_8 _=/usr/bin/env sh: can't create /tmp/filexQItwh: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 27194 27194 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-09
sh: can't create /tmp/fileHivuOD: Read-only file system *********************************************************************************************** ... Result: None Error message: None **************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/fileHivuOD: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 26298 26298 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** sh: can't create /tmp/filez1wsBf: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 26303 26303 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** **************************************************************************** Command line arguments: ['/usr/local/bin/t_coffee', '/data/part0/001/dataset_1434.dat', '-n_core', '1', '-run_name', 't_coffee_out', '-quiet'] Install folder: /usr/local/lib/t_coffee-11.0.8 **************************************************************************** [this line in 2 times] Result: None Error message: None ****************************************************************************** ------------------------------------------------------------------	1	2024-04-09
sh: can't create /tmp/fileQ3ph2E: Read-only file system ************************************************************************************************* ... * FULL TRACE BACK PID: 21478 21478 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** ------------------------- Extended error ------------------------- sh: can't create /tmp/fileQ3ph2E: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 21473 21473 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) *********************************************************************************************** sh: can't create /tmp/filehmyrog: Read-only file system *********************************************************************************************** * FULL TRACE BACK PID: 21478 21478 -- ERROR: COREDUMP: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) ************************************************************************************************* ------------------------------------------------------------------	1	2024-04-09
--ERROR: : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE] --ERROR: : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE] ... File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee/t_coffee_to_cigar.py", line 30, in main with open(sys.argv[1]) as fh: FileNotFoundError: [Errno 2] No such file or directory: 't_coffee_out.fasta_aln' ------------------------- Extended error ------------------------- --ERROR: : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE] --ERROR: : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE] COULD NOT Append anything to /t_coffee.tmp/tmp.slurm.usegalaxy.no.29614///.29614.slurm.usegalaxy.no.error4tcoffee --ERROR: : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE] [this line in 2 times] COULD NOT Append anything to /t_coffee.tmp/tmp.slurm.usegalaxy.no.29618///.29618.slurm.usegalaxy.no.error4tcoffee Traceback (most recent call last): File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee/t_coffee_to_cigar.py", line 47, in main() File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee/t_coffee_to_cigar.py", line 30, in main with open(sys.argv[1]) as fh: FileNotFoundError: [Errno 2] No such file or directory: 't_coffee_out.fasta_aln' ------------------------------------------------------------------	1	2022-10-28