boas@RIVM-BBTLVV3:~$ df -h .
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdb        672G  642G  139M 100% /
boas@RIVM-BBTLVV3:~$ singularity exec --bind /home/boas/analysis/:/home/boas/analysis/ --bind /home/boas/checkm_out:/home/boas/checkm_out --bind /run:/run checkm-genome_1.1.3.sif checkm taxonomy_wf genus Streptococcus analysis/juno/test_assembly_out/de_novo_assembly_filtered/ checkm_out/ -t 1 -x .fasta
[2024-03-28 14:14:29] INFO: CheckM v1.1.3
[2024-03-28 14:14:29] INFO: checkm taxonomy_wf genus Streptococcus analysis/juno/test_assembly_out/de_novo_assembly_filtered/ checkm_out/ -t 1 -x .fasta
[2024-03-28 14:14:29] INFO: [CheckM - taxon_set] Generate taxonomic-specific marker set.
[2024-03-28 14:14:31] INFO: Marker set for Streptococcus contains 551 marker genes arranged in 259 sets.
[2024-03-28 14:14:31] INFO: Marker set inferred from 226 reference genomes.
[2024-03-28 14:14:31] INFO: Marker set for Streptococcaceae contains 524 marker genes arranged in 282 sets.
[2024-03-28 14:14:31] INFO: Marker set inferred from 240 reference genomes.
[2024-03-28 14:14:31] INFO: Marker set for Lactobacillales contains 335 marker genes arranged in 183 sets.
[2024-03-28 14:14:31] INFO: Marker set inferred from 490 reference genomes.
[2024-03-28 14:14:31] INFO: Marker set for Bacilli contains 250 marker genes arranged in 136 sets.
[2024-03-28 14:14:31] INFO: Marker set inferred from 821 reference genomes.
[2024-03-28 14:14:31] INFO: Marker set for Firmicutes contains 172 marker genes arranged in 99 sets.
[2024-03-28 14:14:31] INFO: Marker set inferred from 1349 reference genomes.
[2024-03-28 14:14:31] INFO: Marker set for Bacteria contains 104 marker genes arranged in 58 sets.
[2024-03-28 14:14:31] INFO: Marker set inferred from 5449 reference genomes.
[2024-03-28 14:14:31] INFO: Marker set written to: checkm_out/Streptococcus.ms
[2024-03-28 14:14:31] INFO: { Current stage: 0:00:02.629 || Total: 0:00:02.629 }
[2024-03-28 14:14:31] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2024-03-28 14:14:31] INFO: Identifying marker genes in 5 bins with 1 threads:
Fatal exception (source file p7_hmmfile.c, line 2138):
hmm write failed
system error: No space left on device
Aborted

Error: bad file format in HMM file /tmp/8188ddca-0eee-4e28-b05c-9e09f577a9bd

Error: File format problem in trying to open HMM file /tmp/8188ddca-0eee-4e28-b05c-9e09f577a9bd.
a /tmp/8188ddca-0eee-4e28-b05c-9e09f577a9bd.ssi file exists (an SSI index), but its SSI format is not recognized

Process Process-2:ssing 1 of 5 (20.00%) bins.
OSError: [Errno 28] No space left on device

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/lib/python3.10/site-packages/checkm/markerGeneFinder.py", line 122, in __processBin
    hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile)
  File "/opt/conda/lib/python3.10/site-packages/checkm/markerSets.py", line 336, in createHmmModelFile
    self.__createMarkerHMMs(binMarkerSets, hmmModelFile, bReportProgress=False)
  File "/opt/conda/lib/python3.10/site-packages/checkm/markerSets.py", line 464, in __createMarkerHMMs
    fout.close()
OSError: [Errno 28] No space left on device

[2024-03-28 14:14:53] INFO: Saving HMM info to file.
[2024-03-28 14:14:53] INFO: { Current stage: 0:00:21.170 || Total: 0:00:23.800 }
[2024-03-28 14:14:53] INFO: Parsing HMM hits to marker genes:
[Errno 2] No such file or directory: 'checkm_out/bins/MGAS5005/hmmer.analyze.txt'

[2024-03-28 14:14:53] INFO: Aligning marker genes with multiple hits in a single bin:
    Finished processing 1 of 1 (100.00%) bins.
[2024-03-28 14:14:53] INFO: { Current stage: 0:00:00.016 || Total: 0:00:23.816 }
[2024-03-28 14:14:53] INFO: Calculating genome statistics for 5 bins with 1 threads:
    Finished processing 5 of 5 (100.00%) bins.
[2024-03-28 14:14:53] INFO: { Current stage: 0:00:00.147 || Total: 0:00:23.964 }
[2024-03-28 14:14:53] INFO: [CheckM - qa] Tabulating genome statistics.
[2024-03-28 14:14:53] INFO: Calculating AAI between multi-copy marker genes.
[2024-03-28 14:14:53] INFO: Reading HMM info from file.
[2024-03-28 14:14:53] INFO: Parsing HMM hits to marker genes:
[Errno 2] No such file or directory: 'checkm_out/bins/MGAS5005/hmmer.analyze.txt'

---------------------------------------------------------------------------------------------------------------------------------------------------------
  Bin Id       Marker lineage    # genomes   # markers   # marker sets    0    1   2   3   4   5+   Completeness   Contamination   Strain heterogeneity
---------------------------------------------------------------------------------------------------------------------------------------------------------
  MGAS5005   Streptococcus (5)      226         551           259        551   0   0   0   0   0        0.00            0.00               0.00
---------------------------------------------------------------------------------------------------------------------------------------------------------
[2024-03-28 14:14:53] INFO: { Current stage: 0:00:00.010 || Total: 0:00:23.974 }
boas@RIVM-BBTLVV3:~$ echo $?
0