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MattiaPandolfoVR / MetaPhage

GNU General Public License v3.0
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Issue with vcontact2 classification #67

Open MarwanMaj opened 9 months ago

MarwanMaj commented 9 months ago

Caused by: Process vcontact2 (megahit) terminated with an error exit status (1)

Command executed:

run vConTACT2

vcontact2_local -t 4 --blast-fp allVSall_Jan2022_app.csv --rel-mode 'Diamond' --proteins-fp viral_genomes_combined.csv --db 'None' --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/cluster_one-1.0.jar --output-dir ./

Command exit status: 1

Command output:

============================This is vConTACT2 0.9.19============================

----------------------------------Pre-Analysis----------------------------------

------------------------------Reference databases-------------------------------

-------------------------------Protein clustering-------------------------------

----------------------------------Loading data----------------------------------

------------------------Calculating Similarity Networks-------------------------

Command error: 25 .................... 0.08 1.33 1.00/0.90/1.00 1.00 1.00 0.11 0 26 .................... 0.07 1.32 1.00/0.92/1.00 1.00 1.00 0.11 0 27 .................... 0.11 1.33 1.00/0.93/1.00 1.00 1.00 0.11 0 28 .................... 0.16 1.32 1.00/0.85/1.00 1.00 1.00 0.11 0 29 .................... 0.14 1.32 1.00/0.84/1.00 1.00 1.00 0.11 0 30 .................... 0.05 1.32 1.00/0.95/1.00 1.00 1.00 0.11 0 31 .................... 0.00 1.34 1.00/1.00/1.00 1.00 1.00 0.11 0 32 .................... 0.00 1.31 1.00/1.00/1.00 1.00 1.00 0.11 0 [mcl] jury pruning marks: <43,90,98>, out of 100 [mcl] jury pruning synopsis: <61.6 or satisfactory> (cf -scheme, -do log) [mcl] output is in ./allVSall_Jan2022_app.csv_mcl20.clusters [mcl] 101605 clusters found [mcl] output is in ./allVSall_Jan2022_app.csv_mcl20.clusters

Please cite: Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000. ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf or http://micans.org/mcl/lit/svdthesis.pdf.gz) OR Stijn van Dongen, A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z or http://micans.org/mcl/lit/INS-R0010.ps.Z)

INFO:vcontact2: Building the cluster and profiles (this may take some time...) If it fails, try re-running using --blast-fp flag and specifiying merged.self-diamond.tab (or merged.self-blastp.tab) INFO:vcontact2: Saving intermediate files... INFO:vcontact2: Read 1981872 entries (dropped 117915 singletons) from ./vConTACT_profiles.csv Traceback (most recent call last): File "/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/vcontact2_local", line 761, in main(options) File "/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/vcontact2_local", line 596, in main args.mod_sig, args.mod_shared_min) File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 71, in init self.ntw = self.network(self.matrix, self.singletons, thres=sig, max_sig=max_sig, threads=self.threads) File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in network final_results = list(chain.from_iterable([r.get() for r in results])) File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in final_results = list(chain.from_iterable([r.get() for r in results])) File "/opt/software/conda_env/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value File "/opt/software/conda_env/lib/python3.7/multiprocessing/pool.py", line 431, in _handle_tasks put(task) File "/opt/software/conda_env/lib/python3.7/multiprocessing/connection.py", line 206, in send self._send_bytes(_ForkingPickler.dumps(obj)) File "/opt/software/conda_env/lib/python3.7/multiprocessing/connection.py", line 393, in _send_bytes header = struct.pack("!i", n) struct.error: 'i' format requires -2147483648 <= number <= 2147483647

Work dir: /srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/work/3b/80c6bf421b91e9658ef6c9633eb62e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out Sep.-21 11:15:16.961 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process vcontact2 (megahit) terminated with an error exit status (1) Sep.-21 11:15:17.034 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] summary status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: - port 2: (queue) OPEN ; channel: metadata port 3: (cntrl) - ; channel: $

[process] phylo_obj status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) OPEN ; channel: - port 2: (queue) OPEN ; channel: metadata port 3: (cntrl) - ; channel: $

[process] file_chopper status=ACTIVE port 0: (value) bound ; channel: - port 1: (value) bound ; channel: - port 2: (value) bound ; channel: - port 3: (cntrl) - ; channel: $

[process] taxonomy_table status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: - port 2: (value) bound ; channel: - port 3: (value) bound ; channel: - port 4: (value) bound ; channel: - port 5: (queue) OPEN ; channel: metadata port 6: (cntrl) - ; channel: $

[process] heatmap status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) OPEN ; channel: - port 2: (queue) OPEN ; channel: metadata port 3: (cntrl) - ; channel: $

[process] alpha_diversity status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: - port 2: (queue) OPEN ; channel: metadata port 3: (cntrl) - ; channel: $

[process] betadiversity status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: - port 2: (queue) OPEN ; channel: metadata port 3: (cntrl) - ; channel: $

[process] violin_plots status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: - port 2: (queue) OPEN ; channel: metadata port 3: (cntrl) - ; channel: $

[process] multiqc status=ACTIVE port 0: (value) bound ; channel: min_comp port 1: (value) OPEN ; channel: summary_table port 2: (value) OPEN ; channel: taxo_table port 3: (value) bound ; channel: fastp port 4: (value) bound ; channel: kraken2 port 5: (value) bound ; channel: krakenfiles port 6: (value) bound ; channel: metaquast port 7: (cntrl) - ; channel: $

Sep.-21 11:15:17.062 [Actor Thread 51] WARN nextflow.processor.TaskProcessor - Input tuple does not match input set cardinality declared by process taxonomy_table -- offending value: [] Sep.-21 11:15:17.074 [main] DEBUG nextflow.Session - Session await > all processes finished Sep.-21 11:15:17.074 [main] DEBUG nextflow.Session - Session await > all barriers passed Sep.-21 11:15:17.089 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (1) Sep.-21 11:15:17.128 [Actor Thread 54] WARN nextflow.processor.TaskProcessor - Input tuple does not match input set cardinality declared by process summary -- offending value: [] Sep.-21 11:15:17.134 [Actor Thread 34] WARN nextflow.processor.TaskProcessor - Input tuple does not match input set cardinality declared by process phylo_obj -- offending value: [] Sep.-21 11:15:17.159 [Actor Thread 42] WARN nextflow.processor.TaskProcessor - Input tuple does not match input set cardinality declared by process alpha_diversity -- offending value: [] Sep.-21 11:15:17.162 [Actor Thread 53] WARN nextflow.processor.TaskProcessor - Input tuple does not match input set cardinality declared by process violin_plots -- offending value: [] Sep.-21 11:15:17.273 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=7; ignoredCount=6; cachedCount=2754; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=1; succeedDuration=0ms; failedDuration=8h 6m 41s; cachedDuration=740d 14h 9m 28s;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=8; peakMemory=850 GB; ] Sep.-21 11:15:17.273 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Sep.-21 11:15:18.849 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: 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(megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"},"timeUsage":{"mean":4.06,"min":4.06,"q1":4.06,"q2":4.06,"q3":4.06,"max":4.06,"minLabel":"prodigal (megahit)","maxLabel":"prodigal (megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"},"vmem":{"mean":129359872,"min":129359872,"q1":129359872,"q2":129359872,"q3":129359872,"max":129359872,"minLabel":"prodigal (megahit)","maxLabel":"prodigal (megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"},"reads":{"mean":1112394836,"min":1112394836,"q1":1112394836,"q2":1112394836,"q3":1112394836,"max":1112394836,"minLabel":"prodigal (megahit)","maxLabel":"prodigal (megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"},"cpu":{"mean":99.7,"min":99.7,"q1":99.7,"q2":99.7,"q3":99.7,"max":99.7,"minLabel":"prodigal (megahit)","maxLabel":"prodigal (megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"},"time":{"mean":6861344,"min":6861344,"q1":6861344,"q2":6861344,"q3":6861344,"max":6861344,"minLabel":"prodigal (megahit)","maxLabel":"prodigal (megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"},"writes":{"mean":818432597,"min":818432597,"q1":818432597,"q2":818432597,"q3":818432597,"max":818432597,"minLabel":"prodigal (megahit)","maxLabel":"prodigal (megahit)","q1Label":"prodigal (megahit)","q2Label":"prodigal (megahit)","q3Label":"prodigal (megahit)"}},{"cpuUsage":{"mean":98.55,"min":98.55,"q1":98.55,"q2":98.55,"q3":98.55,"max":98.55,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"process":"diamond_vcontact2","mem":{"mean":6461841408,"min":6461841408,"q1":6461841408,"q2":6461841408,"q3":6461841408,"max":6461841408,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"memUsage":{"mean":0.93,"min":0.93,"q1":0.93,"q2":0.93,"q3":0.93,"max":0.93,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"timeUsage":{"mean":35.83,"min":35.83,"q1":35.83,"q2":35.83,"q3":35.83,"max":35.83,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"vmem":{"mean":7013941248,"min":7013941248,"q1":7013941248,"q2":7013941248,"q3":7013941248,"max":7013941248,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"reads":{"mean":20611520290,"min":20611520290,"q1":20611520290,"q2":20611520290,"q3":20611520290,"max":20611520290,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"cpu":{"mean":394.2,"min":394.2,"q1":394.2,"q2":394.2,"q3":394.2,"max":394.2,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"time":{"mean":29671262,"min":29671262,"q1":29671262,"q2":29671262,"q3":29671262,"max":29671262,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"},"writes":{"mean":21771625070,"min":21771625070,"q1":21771625070,"q2":21771625070,"q3":21771625070,"max":21771625070,"minLabel":"diamond_vcontact2 (megahit)","maxLabel":"diamond_vcontact2 (megahit)","q1Label":"diamond_vcontact2 (megahit)","q2Label":"diamond_vcontact2 (megahit)","q3Label":"diamond_vcontact2 (megahit)"}},{"cpuUsage":{"mean":4.74,"min":4.74,"q1":4.74,"q2":4.74,"q3":4.74,"max":4.74,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"process":"file_chopper","mem":{"mean":6270713856,"min":6270713856,"q1":6270713856,"q2":6270713856,"q3":6270713856,"max":6270713856,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"memUsage":{"mean":5.84,"min":5.84,"q1":5.84,"q2":5.84,"q3":5.84,"max":5.84,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"timeUsage":{"mean":28.33,"min":28.33,"q1":28.33,"q2":28.33,"q3":28.33,"max":28.33,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"vmem":{"mean":7387615232,"min":7387615232,"q1":7387615232,"q2":7387615232,"q3":7387615232,"max":7387615232,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"reads":{"mean":1944927816,"min":1944927816,"q1":1944927816,"q2":1944927816,"q3":1944927816,"max":1944927816,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"cpu":{"mean":37.9,"min":37.9,"q1":37.9,"q2":37.9,"q3":37.9,"max":37.9,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"time":{"mean":23457605,"min":23457605,"q1":23457605,"q2":23457605,"q3":23457605,"max":23457605,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"},"writes":{"mean":1734579337,"min":1734579337,"q1":1734579337,"q2":1734579337,"q3":1734579337,"max":1734579337,"minLabel":"file_chopper (megahit)","maxLabel":"file_chopper (megahit)","q1Label":"file_chopper (megahit)","q2Label":"file_chopper (megahit)","q3Label":"file_chopper (megahit)"}},{"cpuUsage":null,"process":"vcontact2","mem":null,"memUsage":null,"timeUsage":{"mean":8.82,"min":8.82,"q1":8.82,"q2":8.82,"q3":8.82,"max":8.82,"minLabel":"vcontact2 (megahit)","maxLabel":"vcontact2 (megahit)","q1Label":"vcontact2 (megahit)","q2Label":"vcontact2 (megahit)","q3Label":"vcontact2 (megahit)"},"vmem":null,"reads":null,"cpu":null,"time":{"mean":7300238,"min":7300238,"q1":7300238,"q2":7300238,"q3":7300238,"max":7300238,"minLabel":"vcontact2 (megahit)","maxLabel":"vcontact2 (megahit)","q1Label":"vcontact2 (megahit)","q2Label":"vcontact2 (megahit)","q3Label":"vcontact2 (megahit)"},"writes":null},{"cpuUsage":null,"process":"covtocounts2","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}] Sep.-21 11:15:20.029 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Sep.-21 11:15:20.138 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

MattiaPandolfoVR commented 9 months ago

Hi there Marwan, it seems that your problem is related to the low number of cores you are allocating to vcontact2. I always run this tool with a minimum of 24 cores (as you can see in conf/load/slurm.config) and I suggest you do as well. Cheers, Mattia

MarwanMaj commented 9 months ago

hi Mattia, I have tried to increase the number of cores to a minimum and i have also increased the memory as well, but it still does not seem to be working from my end.

I've included the report below.

Error executing process > 'vcontact2 (megahit)'

Caused by:
  Process `vcontact2 (megahit)` terminated with an error exit status (1)

Command executed:

  # run vConTACT2
  vcontact2_local     -t 24     --blast-fp allVSall_Jan2022_app.csv     --rel-mode 'Diamond'     --proteins-fp viral_genomes_combined.csv     --db 'None'     --pcs-mode MCL     --vcs-mode ClusterONE     --c1-bin /srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/cluster_one-1.0.jar     --output-dir ./

Command exit status:
  1

Command output:

  ============================This is vConTACT2 0.9.19============================

  ----------------------------------Pre-Analysis----------------------------------

  ------------------------------Reference databases-------------------------------

  -------------------------------Protein clustering-------------------------------

  ----------------------------------Loading data----------------------------------

  ------------------------Calculating Similarity Networks-------------------------

Command error:
   25  ....................   0.08  1.08 1.00/0.90/1.00 1.00 1.00 0.11   0
   26  ....................   0.07  1.06 1.00/0.92/1.00 1.00 1.00 0.11   0
   27  ....................   0.11  1.06 1.00/0.93/1.00 1.00 1.00 0.11   0
   28  ....................   0.16  1.05 1.00/0.85/1.00 1.00 1.00 0.11   0
   29  ....................   0.14  1.05 1.00/0.84/1.00 1.00 1.00 0.11   0
   30  ....................   0.05  1.06 1.00/0.95/1.00 1.00 1.00 0.11   0
   31  ....................   0.00  1.05 1.00/1.00/1.00 1.00 1.00 0.11   0
   32  ....................   0.00  1.06 1.00/1.00/1.00 1.00 1.00 0.11   0
  [mcl] jury pruning marks: <43,90,98>, out of 100
  [mcl] jury pruning synopsis: <61.6 or satisfactory> (cf -scheme, -do log)
  [mcl] output is in ./allVSall_Jan2022_app.csv_mcl20.clusters
  [mcl] 101605 clusters found
  [mcl] output is in ./allVSall_Jan2022_app.csv_mcl20.clusters

  Please cite:
      Stijn van Dongen, Graph Clustering by Flow Simulation.  PhD thesis,
      University of Utrecht, May 2000.
         (  http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
         or  http://micans.org/mcl/lit/svdthesis.pdf.gz)
  OR
      Stijn van Dongen, A cluster algorithm for graphs. Technical
      Report INS-R0010, National Research Institute for Mathematics
      and Computer Science in the Netherlands, Amsterdam, May 2000.
         (  http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
         or  http://micans.org/mcl/lit/INS-R0010.ps.Z)

  INFO:vcontact2: Building the cluster and profiles (this may take some time...)
  If it fails, try re-running using --blast-fp flag and specifiying merged.self-diamond.tab (or merged.self-blastp.tab)
  INFO:vcontact2: Saving intermediate files...
  INFO:vcontact2: Read 1981871 entries (dropped 117915 singletons) from ./vConTACT_profiles.csv
  Traceback (most recent call last):
    File "/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/vcontact2_local", line 761, in <module>
      main(options)
    File "/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/vcontact2_local", line 596, in main
      args.mod_sig, args.mod_shared_min)
    File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 71, in __init__
      self.ntw = self.network(self.matrix, self.singletons, thres=sig, max_sig=max_sig, threads=self.threads)
    File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in network
      final_results = list(chain.from_iterable([r.get() for r in results]))
    File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in <listcomp>
      final_results = list(chain.from_iterable([r.get() for r in results]))
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/pool.py", line 657, in get
      raise self._value
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/pool.py", line 431, in _handle_tasks
      put(task)
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/connection.py", line 206, in send
      self._send_bytes(_ForkingPickler.dumps(obj))
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/connection.py", line 393, in _send_bytes
      header = struct.pack("!i", n)
  struct.error: 'i' format requires -2147483648 <= number <= 2147483647

Work dir:
  /srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/work/57/a8f5ecbc1ced5b0f920ec2b80c7d81

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

WARN: Input tuple does not match input set cardinality declared by process `betadiversity` -- offending value: []
WARN: Input tuple does not match input set cardinality declared by process `heatmap` -- offending value: []
WARN: Input tuple does not match input set cardinality declared by process `violin_plots` -- offending value: []
WARN: Input tuple does not match input set cardinality declared by process `phylo_obj` -- offending value: []
WARN: Input tuple does not match input set cardinality declared by process `alpha_diversity` -- offending value: []

executor >  pbspro (7)
[99/13ff44] process > csv_validator (Checking met... [100%] 2 of 2, cached: 2 ✔
[5c/536370] process > db_manager (Downloading mis... [100%] 1 of 1, cached: 1 ✔
[c6/131299] process > fastp (MTG116)                 [100%] 250 of 250, cache...
[57/c23017] process > remove_phix (MTG116)           [100%] 250 of 250, cache...
[87/b2d2da] process > kraken2 (MTG116)               [100%] 250 of 250, cache...
[96/884d33] process > krona (MTG116)                 [100%] 250 of 250, cache...
[de/7ea18f] process > megahit (MTG116)               [100%] 250 of 250, cache...
[96/9d9b4e] process > metaquast (megahit-MTG116)     [100%] 250 of 250, cache...
[7e/888c90] process > vibrant (megahit-MTG116)       [100%] 250 of 250, cache...
[c0/48e03f] process > phigaro (megahit-MTG107)       [100%] 250 of 250, cache...
[b0/ef80e5] process > virsorter (megahit-MTG116)     [100%] 250 of 250, cache...
[51/ac76be] process > virfinder (megahit-MTG116)     [100%] 250 of 250, cache...
[3a/0fb918] process > cdhit (megahit)                [100%] 1 of 1, cached: 1 ✔
[0d/f26570] process > prodigal (megahit)             [100%] 1 of 1, cached: 1 ✔
[68/5a3c0c] process > bowtie2_derep (megahit)        [100%] 250 of 250, cache...
[73/11132b] process > covtocounts2 (megahit)         [100%] 1 of 1, cached: 1 ✔
[79/8c9ca6] process > diamond_vcontact2 (megahit)    [100%] 1 of 1, cached: 1 ✔
[57/a8f5ec] process > vcontact2 (megahit)            [100%] 1 of 1, failed: 1 ✘
[-        ] process > graphanalyzer                  -
[e3/128016] process > kraken_file (Creating the t... [100%] 2 of 2, cached: 2 ✔
[74/4ea1e7] process > miner_comparison (megahit)     [100%] 1 of 1, cached: 1 ✔
[-        ] process > summary                        -
[-        ] process > phylo_obj                      -
[c4/6499ec] process > file_chopper (megahit)         [100%] 1 of 1, cached: 1 ✔
[-        ] process > taxonomy_table                 -
[-        ] process > heatmap                        -
[-        ] process > alpha_diversity                -
[-        ] process > betadiversity                  -
[-        ] process > violin_plots                   -
[-        ] process > multiqc                        -
WARN: Input tuple does not match input set cardinality declared by process `taxonomy_table` -- offending value: []
Error executing process > 'vcontact2 (megahit)'

Caused by:
  Process `vcontact2 (megahit)` terminated with an error exit status (1)

Command executed:

  # run vConTACT2
  vcontact2_local     -t 24     --blast-fp allVSall_Jan2022_app.csv     --rel-mode 'Diamond'     --proteins-fp viral_genomes_combined.csv     --db 'None'     --pcs-mode MCL     --vcs-mode ClusterONE     --c1-bin /srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/cluster_one-1.0.jar     --output-dir ./

Command exit status:
  1

Command output:

  ============================This is vConTACT2 0.9.19============================

  ----------------------------------Pre-Analysis----------------------------------

  ------------------------------Reference databases-------------------------------

  -------------------------------Protein clustering-------------------------------

  ----------------------------------Loading data----------------------------------

  ------------------------Calculating Similarity Networks-------------------------

Command error:
   25  ....................   0.08  1.08 1.00/0.90/1.00 1.00 1.00 0.11   0
   26  ....................   0.07  1.06 1.00/0.92/1.00 1.00 1.00 0.11   0
   27  ....................   0.11  1.06 1.00/0.93/1.00 1.00 1.00 0.11   0
   28  ....................   0.16  1.05 1.00/0.85/1.00 1.00 1.00 0.11   0
   29  ....................   0.14  1.05 1.00/0.84/1.00 1.00 1.00 0.11   0
   30  ....................   0.05  1.06 1.00/0.95/1.00 1.00 1.00 0.11   0
   31  ....................   0.00  1.05 1.00/1.00/1.00 1.00 1.00 0.11   0
   32  ....................   0.00  1.06 1.00/1.00/1.00 1.00 1.00 0.11   0
  [mcl] jury pruning marks: <43,90,98>, out of 100
  [mcl] jury pruning synopsis: <61.6 or satisfactory> (cf -scheme, -do log)
  [mcl] output is in ./allVSall_Jan2022_app.csv_mcl20.clusters
  [mcl] 101605 clusters found
  [mcl] output is in ./allVSall_Jan2022_app.csv_mcl20.clusters

  Please cite:
      Stijn van Dongen, Graph Clustering by Flow Simulation.  PhD thesis,
      University of Utrecht, May 2000.
         (  http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
         or  http://micans.org/mcl/lit/svdthesis.pdf.gz)
  OR
      Stijn van Dongen, A cluster algorithm for graphs. Technical
      Report INS-R0010, National Research Institute for Mathematics
      and Computer Science in the Netherlands, Amsterdam, May 2000.
         (  http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
         or  http://micans.org/mcl/lit/INS-R0010.ps.Z)

  INFO:vcontact2: Building the cluster and profiles (this may take some time...)
  If it fails, try re-running using --blast-fp flag and specifiying merged.self-diamond.tab (or merged.self-blastp.tab)
  INFO:vcontact2: Saving intermediate files...
  INFO:vcontact2: Read 1981871 entries (dropped 117915 singletons) from ./vConTACT_profiles.csv
  Traceback (most recent call last):
    File "/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/vcontact2_local", line 761, in <module>
      main(options)
    File "/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/bin/vcontact2_local", line 596, in main
      args.mod_sig, args.mod_shared_min)
    File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 71, in __init__
      self.ntw = self.network(self.matrix, self.singletons, thres=sig, max_sig=max_sig, threads=self.threads)
    File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in network
      final_results = list(chain.from_iterable([r.get() for r in results]))
    File "/opt/software/conda_env/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in <listcomp>
      final_results = list(chain.from_iterable([r.get() for r in results]))
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/pool.py", line 657, in get
      raise self._value
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/pool.py", line 431, in _handle_tasks
      put(task)
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/connection.py", line 206, in send
      self._send_bytes(_ForkingPickler.dumps(obj))
    File "/opt/software/conda_env/lib/python3.7/multiprocessing/connection.py", line 393, in _send_bytes
      header = struct.pack("!i", n)
  struct.error: 'i' format requires -2147483648 <= number <= 2147483647

Work dir:
  /srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/work/57/a8f5ecbc1ced5b0f920ec2b80c7d81

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

/var/spool/pbs/mom_priv/jobs/4849406.kman.restech.unsw.edu.au.SC: line 20: -m: command not found

================================================================================
telatin commented 9 months ago

I cannot understand the very last line:

/var/spool/pbs/mom_priv/jobs/4849406.kman.restech.unsw.edu.au.SC: line 20: -m: command not found

It might have something to do with your system and the way jobs get scheduled.# You might find some insight in files in the job's directory (e.g. .command.sh, and its output/error files)

/srv/scratch/z3192995/Softwares/MetaPhage-0.3.3/work/57/a8f5ecbc1ced5b0f920ec2b80c7d81
MarwanMaj commented 9 months ago

Thanks I will have a look. There were more than 80000 vOTUs in my study Do you have any recommendation for resources to be allocated for the vcontact2 step. Diamond_vcontact2 ran successfully

tpall commented 6 months ago

I ran into similar issue.

There is also topic on Stackoverflow:

https://stackoverflow.com/questions/47776486/python-struct-error-i-format-requires-2147483648-number-2147483647

ESC[1;42mINFOESC[1;0m:vcontact2: Verifying clusterONE works...
ESC[1;42mINFOESC[1;0m:vcontact2: It appears that clusterONE is functional!
ESC[1;42mINFOESC[1;0m:vcontact2: Found Diamond: linux-centos7-x86_64/gcc-9.2.0/diamond-2.0.15-4yz2nljtstvjm62pi5if6uiipnxbu2mn/bin/diamond
ESC[1;42mINFOESC[1;0m:vcontact2: Found MCL: miniconda3/envs/vcontact2/bin/mcxload
ESC[1;42mINFOESC[1;0m:vcontact2: Identified 24 CPUs
ESC[1;42mINFOESC[1;0m:vcontact2: Using reference database: ProkaryoticViralRefSeq211-Merged
ESC[1;42mINFOESC[1;0m:vcontact2: Using existing directory results/vcontact2-MGV.
ESC[1;42mINFOESC[1;0m:vcontact2: Identified existing 'merged.faa' in output path: re-using...
ESC[1;42mINFOESC[1;0m:vcontact2: Creating Diamond database and running Diamond...
ESC[1;42mINFOESC[1;0m:vcontact2.protein_clusters: Creating Diamond database...
diamond v2.0.15.153 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 24
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: results/vcontact2-MGV/merged.faa
Opening the database file...  [0.107s]
Loading sequences...  [4.865s]
Masking sequences...  [3.027s]
Writing sequences...  [0.613s]
Hashing sequences...  [0.483s]
Loading sequences...  [4.321s]
Masking sequences...  [3.086s]
Writing sequences...  [0.788s]
Hashing sequences...  [0.66s]
Loading sequences...  [4.275s]
Masking sequences...  [3.471s]
Writing sequences...  [0.51s]
Hashing sequences...  [0.337s]
Loading sequences...  [0.034s]
Masking sequences...  [0.044s]
Writing sequences...  [0.004s]
Hashing sequences...  [0.003s]
Loading sequences...  [0s]
Writing trailer...  [0.098s]
Closing the input file...  [0s]
Closing the database file...  [0s]

Database sequences  13315164
  Database letters  3008790188
     Database hash  f5df620d1bac924959c48c6d10d7c8ae
        Total time  26.736000s

...

ESC[1;42mINFOESC[1;0m:vcontact2: Read 13052909 entries (dropped 46280 singletons) from results/vcontact2-MGV/vConTACT_profiles.csv

============================This is vConTACT2 0.11.3============================

----------------------------------Pre-Analysis----------------------------------

------------------------------Reference databases-------------------------------

-------------------------------Protein clustering-------------------------------

----------------------------------Loading data----------------------------------

--------------------------------Adding Taxonomy---------------------------------

------------------------Calculating Similarity Networks-------------------------
Traceback (most recent call last):
  File "miniconda3/envs/vcontact2/bin/vcontact2", line 834, in <module>
    main(options)
  File "miniconda3/envs/vcontact2/bin/vcontact2", line 669, in main
    args.mod_sig, args.mod_shared_min)
  File "miniconda3/envs/vcontact2/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 71, in __init__
    self.ntw = self.network(self.matrix, self.singletons, thres=sig, max_sig=max_sig, threads=self.threads)
  File "miniconda3/envs/vcontact2/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in network
    final_results = list(chain.from_iterable([r.get() for r in results]))
  File "miniconda3/envs/vcontact2/lib/python3.7/site-packages/vcontact2/pcprofiles.py", line 150, in <listcomp>
    final_results = list(chain.from_iterable([r.get() for r in results]))
  File "miniconda3/envs/vcontact2/lib/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
  File "miniconda3/envs/vcontact2/lib/python3.7/multiprocessing/pool.py", line 431, in _handle_tasks
    put(task)
  File "miniconda3/envs/vcontact2/lib/python3.7/multiprocessing/connection.py", line 206, in send
    self._send_bytes(_ForkingPickler.dumps(obj))
  File "miniconda3/envs/vcontact2/lib/python3.7/multiprocessing/connection.py", line 393, in _send_bytes
    header = struct.pack("!i", n)
struct.error: 'i' format requires -2147483648 <= number <= 2147483647