The workflow completed with success, but the rocrate failed to build because it was trying to use the /tmp filesystem and ran out of space, threw an error then proceeded to delete all the results, thereby loosing 9 days compute work.
INFO [workflow ] completed success
ERROR Unhandled error, try again with --debug for more information:
can only concatenate str (not "bool") to str
ls: cannot access '*.merged.CDS.I5_*.tsv.gz': No such file or directory
ls: cannot access '*.merged.CDS.I5_*.tsv.gz': No such file or directory
export...
Traceback (most recent call last):
File "utils/edit-ro-crate.py", line 470, in <module>
main(args.target_directory, args.extended_config_yaml, args.ena_run_accession_id, args.metagoflow_version)
File "utils/edit-ro-crate.py", line 441, in main
crate.write_zip("".join([target_directory,".zip"]))
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/site-packages/rocrate/rocrate.py", line 440, in write_zip
self.write(tmp_dir)
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/site-packages/rocrate/rocrate.py", line 430, in write
writable_entity.write(base_path)
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/site-packages/rocrate/model/file.py", line 68, in write
shutil.copy(self.source, out_file_path)
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/shutil.py", line 418, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/shutil.py", line 275, in copyfile
_fastcopy_sendfile(fsrc, fdst)
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/shutil.py", line 166, in _fastcopy_sendfile
raise err from None
File "/usr/local/src/miniconda3/envs/metaGOflow/lib/python3.8/shutil.py", line 152, in _fastcopy_sendfile
sent = os.sendfile(outfd, infd, offset, blocksize)
OSError: [Errno 28] No space left on device: 'HWLTKDRXY.UDI210/results/DBH_AAAAOSDA_1_2_HWLTKDRXY.UDI235_clean.fastq.trimmed.fasta' -> '/tmp/rocrate_ilrd4kfh/results/DBH_AAAAOSDA_1_2_HWLTKDRXY.UDI235_clean.fastq
.trimmed.fasta'
(metaGOflow)
The rocrate building should not be trying to use the (very small, in my case 50G) root files system rather than partition on which the wf is launched (20TB).
Building the ro-crate should perhaps be separated from the workflow, or at the very least the wf needs to check that the rocrate build successful before deleting all the results.
The workflow completed with success, but the rocrate failed to build because it was trying to use the /tmp filesystem and ran out of space, threw an error then proceeded to delete all the results, thereby loosing 9 days compute work.
The rocrate building should not be trying to use the (very small, in my case 50G) root files system rather than partition on which the wf is launched (20TB). Building the ro-crate should perhaps be separated from the workflow, or at the very least the wf needs to check that the rocrate build successful before deleting all the results.