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)
οΏ½[1;42mINFOοΏ½[1;0m: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)
οΏ½[1;42mINFOοΏ½[1;0m:vcontact2: Saving intermediate files...
οΏ½[1;42mINFOοΏ½[1;0m: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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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