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hoelzer-lab / ribap

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
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Unable to find image 'nanozoo/python_ribap:3.7--33a36cd' locally #71

Open shlomobl opened 6 days ago

shlomobl commented 6 days ago

Hi again, I looked like it was working alright, but then I got the error below. ==> Unable to find image 'nanozoo/python_ribap:3.7--33a36cd' locally Any ideas? Thanks!

shlomo@shlomo-HP-Z840:/media/shlomo/DATADRIVE3/CoNS/CoNS_FINAL$ sudo nextflow run hoelzer-lab/ribap -r 1.1.1 --fasta './Pilon_scaffolds_200/*.fasta' --gcode 11 --reference aureus_RF122.gb --tree --core_perc 99 --output '/media/shlomo/DATADRIVE3/CoNS/CoNS_FINAL/RIBAP' --keepILPs -w /media/shlomo/DATADRIVE3/CoNS/CoNS_FINAL/RIBAP_work -profile local,docker
\
 N E X T F L O W   ~  version 24.10.1

Pulling hoelzer-lab/ribap ...
 downloaded from https://github.com/hoelzer-lab/ribap.git
Launching `https://github.com/hoelzer-lab/ribap` [maniac_pauling] DSL2 - revision: a61ffa369a [1.1.1]

Profile: local,docker

Current User: root
Nextflow-version: 24.10.1
Starting time: 18-11-2024 12:21 UTC
Workdir location (intermediate files):
  /media/shlomo/DATADRIVE3/CoNS/CoNS_FINAL/RIBAP_work
Output dir name:
  /media/shlomo/DATADRIVE3/CoNS/CoNS_FINAL/RIBAP

WARNING: ILPs will be stored which can take a lot of disk space!
executor >  local (463)
[1e/3a2445] process > RIBAP:rename (SSA8530)      [100%] 223 of 223 ✔
[c2/a6a664] process > RIBAP:prokka (223)          [100%] 223 of 223 ✔
[10/d6133a] process > RIBAP:strain_ids            [100%] 1 of 1 ✔
[e6/e251ef] process > RIBAP:roary (1)             [100%] 5 of 5 ✔
[c4/09b2dd] process > RIBAP:mmseqs2               [100%] 1 of 1 ✔
[c7/9e51c7] process > RIBAP:mmseqs2tsv            [100%] 1 of 1 ✔
[e2/df28ef] process > RIBAP:ilp_refinement (9)    [ 11%] 1 of 9
[-        ] process > RIBAP:combine_roary_ilp     -
[-        ] process > RIBAP:prepare_msa           -
[-        ] process > RIBAP:mafft                 -
[-        ] process > RIBAP:fasttree              -
[-        ] process > RIBAP:nw_display            -
[-        ] process > RIBAP:generate_html         -
[-        ] process > RIBAP:generate_upsetr_input -
[-        ] process > RIBAP:upsetr                -
[-        ] process > RIBAP:filter_alignment      -
[-        ] process > RIBAP:nexus_core            -
[-        ] process > RIBAP:iqtree                -
ERROR ~ Error executing process > 'RIBAP:ilp_refinement (7)'

Caused by:
  Process `RIBAP:ilp_refinement (7)` terminated with an error exit status (1)

Command executed:

  derive_ilp_solutions.py --tmlim 240 --max --indel mmseqs_compressed_chunk6.pkl --keep

Command exit status:
  1

Command output:
  (empty)

Command error:
  Unable to find image 'nanozoo/python_ribap:3.7--33a36cd' locally
  3.7--33a36cd: Pulling from nanozoo/python_ribap
  3f4ca61aafcd: Pulling fs layer
  69a5d9e1ecd6: Pulling fs layer
  7b4354700ca4: Pulling fs layer
  c7f57f419954: Pulling fs layer
  f427023642b5: Pulling fs layer
  ef4b6175897e: Pulling fs layer
  c7f57f419954: Waiting
  f427023642b5: Waiting
  ef4b6175897e: Waiting
  3f4ca61aafcd: Verifying Checksum
  3f4ca61aafcd: Download complete
executor >  local (463)
[1e/3a2445] process > RIBAP:rename (SSA8530)      [100%] 223 of 223 ✔
[c2/a6a664] process > RIBAP:prokka (223)          [100%] 223 of 223 ✔
[10/d6133a] process > RIBAP:strain_ids            [100%] 1 of 1 ✔
[e6/e251ef] process > RIBAP:roary (1)             [100%] 5 of 5 ✔
[c4/09b2dd] process > RIBAP:mmseqs2               [100%] 1 of 1 ✔
[c7/9e51c7] process > RIBAP:mmseqs2tsv            [100%] 1 of 1 ✔
[42/b59531] process > RIBAP:ilp_refinement (5)    [ 22%] 2 of 9, failed: 1
[-        ] process > RIBAP:combine_roary_ilp     -
[-        ] process > RIBAP:prepare_msa           -
[-        ] process > RIBAP:mafft                 -
[-        ] process > RIBAP:fasttree              -
[-        ] process > RIBAP:nw_display            -
[-        ] process > RIBAP:generate_html         -
[-        ] process > RIBAP:generate_upsetr_input -
[-        ] process > RIBAP:upsetr                -
[-        ] process > RIBAP:filter_alignment      -
[-        ] process > RIBAP:nexus_core            -
[-        ] process > RIBAP:iqtree                -
ERROR ~ Error executing process > 'RIBAP:ilp_refinement (7)'

Caused by:
  Process `RIBAP:ilp_refinement (7)` terminated with an error exit status (1)

Command executed:

  derive_ilp_solutions.py --tmlim 240 --max --indel mmseqs_compressed_chunk6.pkl --keep

Command exit status:
  1

Command output:
  (empty)

Command error:
  Unable to find image 'nanozoo/python_ribap:3.7--33a36cd' locally
  3.7--33a36cd: Pulling from nanozoo/python_ribap
  3f4ca61aafcd: Pulling fs layer
  69a5d9e1ecd6: Pulling fs layer
  7b4354700ca4: Pulling fs layer
  c7f57f419954: Pulling fs layer
  f427023642b5: Pulling fs layer
  ef4b6175897e: Pulling fs layer
  c7f57f419954: Waiting
  f427023642b5: Waiting
  ef4b6175897e: Waiting
  3f4ca61aafcd: Verifying Checksum
  3f4ca61aafcd: Download complete
  c7f57f419954: Verifying Checksum
  c7f57f419954: Download complete
  3f4ca61aafcd: Pull complete
  f427023642b5: Verifying Checksum
  f427023642b5: Download complete
  69a5d9e1ecd6: Verifying Checksum
  69a5d9e1ecd6: Download complete
  7b4354700ca4: Verifying Checksum
  7b4354700ca4: Download complete
  69a5d9e1ecd6: Pull complete
  7b4354700ca4: Pull complete
  c7f57f419954: Pull complete
  f427023642b5: Pull complete
  ef4b6175897e: Verifying Checksum
  ef4b6175897e: Download complete
  ef4b6175897e: Pull complete
  Digest: sha256:3ee539be385c3495d6c84d04cb7cd5ead19f77429988cfefa88ce40efd620b96
  Status: Image is up to date for nanozoo/python_ribap:3.7--33a36cd
  Traceback (most recent call last):
    File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/derive_ilp_solutions.py", line 151, in <module>
      main()
    File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/derive_ilp_solutions.py", line 76, in main
      pool_workload(pairwiseSpecies, similarities)
    File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/derive_ilp_solutions.py", line 113, in pool_workload
      ilpGen.generate_lp(problem, self_edge_cost=s, alpha=alpha, MATCHING_SIZE=matching_size, MAXIMAL_MATCHING=maximal, tolerance=fix_adj_tolerance, INDEL=indel)
    File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/ILPBuilder.py", line 350, in generate_lp
      self.broadcast_streams(outputStreams, "c"+str(constraintID)+": " + "%s - %s - b_%s <= 0\n" % (self.edge_var(currentGene, 'h', currentGene, 't'), self.edge_var(nextGene, 'h', nextGene, 't'), currentGene))
    File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/ILPBuilder.py", line 119, in broadcast_streams
      stream.write(message)
  OSError: [Errno 28] No space left on device

Work dir:
  /media/shlomo/DATADRIVE3/CoNS/CoNS_FINAL/RIBAP_work/fd/76e59f9224e2a4c2a9d79ec63bdba9

Container:
  nanozoo/python_ribap:3.7--33a36cd

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
shlomobl commented 6 days ago

I was warned :-D

Caused by: java.io.IOException: No space left on device

4 TB disk?!

Is it possible to assign a new working folder in the middle of a run, to continue? Also, is it possible to change the genomes in the analysis (add and remove) without running the whole thing again, if I do not keep ILPs? Last one: how can I delete ILPs? :-) The ILP file in the ILP folder (step 4) is not that big. I don't think this is the one.

hoelzer commented 4 days ago

Hey @shlomobl - yeah sorry.

As said, the disk space and runtime are getting crazy for >100 and/or larger genomes.

That's why we per default discard the intermediate ILP results, but you are right, you can then not -resume a calculation.

Is it possible to assign a new working folder in the middle of a run, to continue?

I don't think so

Also, is it possible to change the genomes in the analysis (add and remove) without running the whole thing again, if I do not keep ILPs?

As you feared, this is only possible when you keep the intermediate ILP results.

Last one: how can I delete ILPs? :-) The ILP file in the ILP folder (step 4) is not that big. I don't think this is the one.

Yes, the ILP files in the ILP output folder are not that big, but the ones in the work directories are. To free up your disk space you have to remove the work dir content (but then -resume will not work)

Sorry, I think for the moment RIBAP reaches its limits for a dataset like yours and you would need to somehow make your input smaller (pre-clustering based on ANI, POCP, ...)