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Process ALIGNER:chainMerge (chainmerge) terminated with an error exit status (1) -- Execution is retried (1) #3

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zhoudreames opened this issue May 19, 2022 · 19 comments
Closed

Process ALIGNER:chainMerge (chainmerge) terminated with an error exit status (1) -- Execution is retried (1) #3

zhoudreames opened this issue May 19, 2022 · 19 comments

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@zhoudreames
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I got the error information when runing the n-Lo,this log showing in blow:

WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config
Launching https://github.com/evotools/nf-LO [pedantic_ptolemy] DSL2 - revision: 312fb56 [main]

======================================
__ _ ____
/ | | | / __
_ __ | | ______ | | | | | |
| '_ | | || | | | | | |
| | | | | | || || |
|| ||| |____/

  Nextflow LiftOver v 1.6.0

======================================
source : chrY.oldVersin.fa
target : DRC.chrY.fa
aligner : minimap2
distance : medium
custom align : -cx asm5 -l 10000
custom chain : false
source chunk : 20000000
source overlap : 0
target chunk : 10000000
target overlap : 100000
output folder : ./liftover_Minimap2
liftover name : liftover
annot : false
annot type : false
liftover meth. : liftover
igenomes_base : s3://ngi-igenomes/igenomes/
igenomes_ignore : false
no_maf : false
skip netsynt : true
max cpu : 143
max mem : 26 GB
max rt : 240.h
Using CrossMap
executor > local (5)
[13/61a6e5] process > PREPROC:src2bit (src2Bit) [100%] 1 of 1 ✔
executor > local (10)
[13/61a6e5] process > PREPROC:src2bit (src2Bit) [100%] 1 of 1 ✔
[cb/e667b4] process > PREPROC:tgt2bit (tgt2Bit) [100%] 1 of 1 ✔
[3e/c206c5] process > PREPROC:splitsrc (splitsrc) [100%] 1 of 1 ✔
[83/de485d] process > PREPROC:splittgt (splittgt) [100%] 1 of 1 ✔
[73/c5a594] process > PREPROC:pairs (mkpairs) [100%] 1 of 1 ✔
[58/cefc2c] process > ALIGNER:minimap2 (minimap2.medium.src.tgt) [100%] 1 of 1 ✔
[26/7d4da4] process > ALIGNER:axtChain (axtchain_m) [100%] 1 of 1 ✔
[33/4e27ca] process > ALIGNER:chainMerge (chainmerge) [100%] 3 of 3, failed: 3, retries: 2 ✔
[- ] process > ALIGNER:chainNet -
[- ] process > ALIGNER:chainsubset -
[- ] process > ALIGNER:chain2maf -
[- ] process > ALIGNER:name_maf_seq -
[- ] process > ALIGNER:mafstats -
[c7/cb6d2d] NOTE: Process ALIGNER:chainMerge (chainmerge) terminated with an error exit status (1) -- Execution is retried (1)
[8d/9085f1] NOTE: Process ALIGNER:chainMerge (chainmerge) terminated with an error exit status (1) -- Execution is retried (2)
[33/4e27ca] NOTE: Process ALIGNER:chainMerge (chainmerge) terminated with an error exit status (1) -- Error is ignored
@RenzoTale88
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@zhoudreames thank you for using nf-LO! I probably need a bit more information on how you run the workflow. Do you mind sharing the .nextflow.log file, so that I can have a bit more insight into it? Also, what type of configuration are you using?

Best
Andrea

@KristinaGagalova
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KristinaGagalova commented Jun 6, 2022 •
edited
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Hi
I am having the same issue with running the pipeline on local files. I am using the conda environment.
This is the error about chainMerger

NOTE: Process `ALIGNER:chainMerge (chainmerge)` terminated with an error exit status (1) -- Execution is retried (1)
Jun.-06 17:05:40.824 [Task submitter] INFO  nextflow.Session - [aa/ada0cd] Re-submitted process > ALIGNER:chainMerge (chainmerge)
Jun.-06 17:05:41.546 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: ALIGNER:chainMerge (chainmerge); status: COMPLETED; exit: 1; error: -; workDir: /my/work/dir
Jun.-06 17:05:41.547 [Task monitor] INFO  nextflow.processor.TaskProcessor - [aa/ada0cd] NOTE: Process `ALIGNER:chainMerge (chainmerge)` terminated with an error exit status (1) -- Execution is retried (2)
Jun.-06 17:05:41.554 [Task submitter] INFO  nextflow.Session - [a3/b6cb05] Re-submitted process > ALIGNER:chainMerge (chainmerge)
Jun.-06 17:05:42.229 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: ALIGNER:chainMerge (chainmerge); status: COMPLETED; exit: 1; error: -; workDir: /my/work/dir

Probably an error about mafstats installation?

@RenzoTale88
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Hi @KristinaGagalova
Thank you for using nf-LO.
The chainMerge process doesn't need access to mafStats, so that shouldn't be the problem.
Could you please share some more details into it?
By instance, do you mind sharing the following:

  1. The command line used, as well as the size of the genomes processed
  2. The content of .command.err and rom the folder where the process is being run (should be in the path starting as work/a3/b6cb05).
    This can probably help me find the solution to your problem.

Best
Andrea

@KristinaGagalova
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Thank you for the fast reply @RenzoTale88

Here some more details:

  1. I used the same identical command as the example on your tutorial - https://github.com/evotools/nf-LO#example (obviously switching with my local genomes). The genome size is of a few Mbp so I don't think there is any memory issue with that.
  2. This is the error I have from that directory
mv: cannot stat 'run/000.chain': No such file or directory

so its probably chainMerge that doesn't produce the output.
I hope this helps

Thank you in advance
Kristina

@RenzoTale88
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@KristinaGagalova Thanks, this suggests me that some step before that probably failed for one reason or another.
Could you please share with me both:

  1. The content of the .command.sh file
  2. The list of files in the current folder
  3. Whether the input files for the .command.sh file contain anything.

In this way we can try to trace back where the issue originated.
Thanks!
Andrea

@KristinaGagalova
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  1. .command.sh file
#!/bin/bash -ue
chainMergeSort src16.tgt19.chain | chainSplit run stdin -lump=1 
mv run/000.chain ./rawchain.chain
  1. List of file in work/a3/b6cb
.command.begin  .command.err  .command.log  .command.out  .command.run  .command.sh  .command.trace  .exitcode  run  src16.tgt19.chain
  1. This is the content of src16.tgt19.chain
##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
##gapPenalties=axtChain O=400 E=30

@RenzoTale88
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Ok for whatever reason the chain file is effectively empty. The issue lies upstream from this. We can trace back the issue by looking at the folder in which src16.tgt19.chain is. You can trace it back by ls -al work/a3/b6cb*/src16.tgt19.chain. This should be a link to the file, specified after the -> symbols. You can then enter that folder and check what went wrong there in the .command.err file.

@KristinaGagalova
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I don't get the same error on the test set so its probbaly something related to runs on local files

nextflow run evotools/nf-LO -profile test,conda

@RenzoTale88
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Yeah I suspect that too. You can trace back each process, and see what went wrong and in which stage. To do so, I recommend you open the .nextflow.log file and check the content of the folders in the order they have been executed. This way you should be able to trace back the issue, and I can provide better assistance with configuring the workflow to work.

@KristinaGagalova
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That's weird, if I check the output in the directory with the symlink there is no error (.exitcode is 0)
This this is the sh command in that directory (if needed)

#!/bin/bash -ue
axtChain -minScore=5000 -linearGap=medium -verbose=0 -psl src16.tgt19.psl source.2bit target.2bit stdout | chainAntiRepeat source.2bit target.2bit stdin stdout > src16.tgt19.chain

This is my .nexflow.log

Jun.-07 11:38:44.776 [main] INFO  nextflow.Nextflow - Using CrossMap
Jun.-07 11:38:45.303 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: chainNet, axtchain_far, lastz_custom, make_report, axtchain_custom, liftover, pairs, lastz_far, make2bitS, crossmap, make2bit, make2bitT, chainNet_old, name_maf_seq, dataset_target, axtchain_near, splitsrc, chain2maf, chainMerge, lastz_near, lastz_medium, features_stats, makeSizeS, makeSizeT, groupsrc, lastz_primates, tgt2bit, grouptgt, splittgt, lastz_general, dataset_genome, axtChain, makeooc, dataset_source, netSynt, mafstats, axtchain_medium, chainsubset, lifter, lastz, dataset, src2bit
Jun.-07 11:38:45.347 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name PREPROC:src2bit
Jun.-07 11:38:45.350 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.350 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.353 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun.-07 11:38:45.356 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=125.7 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
Jun.-07 11:38:45.420 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:small` matches label `small` for process with name PREPROC:tgt2bit
Jun.-07 11:38:45.421 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.422 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.425 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:small` matches label `small` for process with name PREPROC:splitsrc
Jun.-07 11:38:45.425 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.425 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name PREPROC:groupsrc
Jun.-07 11:38:45.428 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.428 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:small` matches label `small` for process with name PREPROC:splittgt
Jun.-07 11:38:45.431 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.431 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name PREPROC:grouptgt
Jun.-07 11:38:45.434 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.434 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:small` matches label `small` for process with name PREPROC:pairs
Jun.-07 11:38:45.437 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.437 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:lastz
Jun.-07 11:38:45.483 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.483 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:small` matches label `small` for process with name ALIGNER:axtChain
Jun.-07 11:38:45.491 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.491 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:chainMerge
Jun.-07 11:38:45.501 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.501 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.503 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:chainNet
Jun.-07 11:38:45.503 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.503 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:netSynt
Jun.-07 11:38:45.506 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.506 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.508 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:chainsubset
Jun.-07 11:38:45.509 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.509 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:chain2maf
Jun.-07 11:38:45.511 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.511 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:name_maf_seq
Jun.-07 11:38:45.514 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.514 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.519 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name ALIGNER:mafstats
Jun.-07 11:38:45.520 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.520 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name LIFTOVER:lifter
Jun.-07 11:38:45.529 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.529 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.531 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medium` matches label `medium` for process with name LIFTOVER:features_stats
Jun.-07 11:38:45.532 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.532 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.533 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:small` matches label `small` for process with name make_report
Jun.-07 11:38:45.534 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:make_report` matches process make_report
Jun.-07 11:38:45.534 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun.-07 11:38:45.534 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun.-07 11:38:45.535 [main] DEBUG nextflow.Session - Ignite dataflow network (20)
Jun.-07 11:38:45.536 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:src2bit
Jun.-07 11:38:45.536 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:tgt2bit
Jun.-07 11:38:45.536 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:splitsrc
Jun.-07 11:38:45.536 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:groupsrc
Jun.-07 11:38:45.537 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:splittgt
Jun.-07 11:38:45.537 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:grouptgt
Jun.-07 11:38:45.537 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROC:pairs
Jun.-07 11:38:45.538 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:lastz
Jun.-07 11:38:45.538 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:axtChain
Jun.-07 11:38:45.539 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:chainMerge
Jun.-07 11:38:45.542 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:chainNet
Jun.-07 11:38:45.543 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:netSynt
Jun.-07 11:38:45.544 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:chainsubset
Jun.-07 11:38:45.545 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:chain2maf
Jun.-07 11:38:45.545 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:name_maf_seq
Jun.-07 11:38:45.546 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ALIGNER:mafstats
Jun.-07 11:38:45.553 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > LIFTOVER:lifter
Jun.-07 11:38:45.554 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > LIFTOVER:features_stats
Jun.-07 11:38:45.554 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > make_report
Jun.-07 11:38:45.554 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Jun.-07 11:38:45.554 [main] DEBUG nextflow.Session - Session await
Jun.-07 11:38:45.646 [Actor Thread 15] INFO  nextflow.conda.CondaCache - Creating Conda env: /home/kgagalova/.nextflow/assets/evotools/nf-LO/assets/environment.yml [cache /home/kgagalova/Genome_annotation/cenpk/liftover/test_run2/work/conda/nf-LO-ff58c531b37003213c976724f043244e]
Jun.-07 11:38:58.286 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
Jun.-07 11:38:58.299 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active:
[process] PREPROC:src2bit
  status=ACTIVE
  port 0: (value) bound ; channel: source
  port 1: (cntrl) -     ; channel: $

[process] PREPROC:tgt2bit
  status=ACTIVE
  port 0: (value) bound ; channel: target
  port 1: (cntrl) -     ; channel: $

[process] PREPROC:splitsrc
  status=ACTIVE
  port 0: (value) bound ; channel: source
  port 1: (cntrl) -     ; channel: $

[process] PREPROC:groupsrc
  status=ACTIVE
  port 0: (value) OPEN  ; channel: src_fld
  port 1: (cntrl) -     ; channel: $

[process] PREPROC:splittgt
  status=ACTIVE
  port 0: (value) bound ; channel: target
  port 1: (cntrl) -     ; channel: $

[process] PREPROC:grouptgt
  status=ACTIVE
  port 0: (value) OPEN  ; channel: tgt_fld
  port 1: (cntrl) -     ; channel: $

[process] PREPROC:pairs
  status=ACTIVE
  port 0: (value) OPEN  ; channel: sources
  port 1: (value) OPEN  ; channel: targets
  port 2: (cntrl) -     ; channel: $

[process] ALIGNER:lastz
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: tgtlift
  port 2: (value) OPEN  ; channel: srclift
  port 3: (cntrl) -     ; channel: $

[process] ALIGNER:axtChain
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: twoBitS
  port 2: (value) OPEN  ; channel: twoBitT
  port 3: (cntrl) -     ; channel: $

[process] ALIGNER:chainMerge
  status=ACTIVE
  port 0: (value) OPEN  ; channel: chains
  port 1: (cntrl) -     ; channel: $

[process] ALIGNER:chainNet
  status=ACTIVE
  port 0: (value) OPEN  ; channel: rawchain
  port 1: (value) OPEN  ; channel: twoBitS
  port 2: (value) OPEN  ; channel: twoBitT
  port 3: (value) OPEN  ; channel: twoBitsizeS
  port 4: (value) OPEN  ; channel: twoBitsizeT
  port 5: (cntrl) -     ; channel: $

[process] ALIGNER:netSynt
  status=ACTIVE
  port 0: (value) OPEN  ; channel: netfile
  port 1: (cntrl) -     ; channel: $

[process] ALIGNER:chainsubset
  status=ACTIVE
  port 0: (value) OPEN  ; channel: netfile
  port 1: (value) OPEN  ; channel: rawchain
  port 2: (cntrl) -     ; channel: $

[process] ALIGNER:chain2maf
  status=ACTIVE
  port 0: (value) OPEN  ; channel: chain
  port 1: (value) OPEN  ; channel: twoBitS
  port 2: (value) OPEN  ; channel: twoBitT
  port 3: (value) OPEN  ; channel: twoBitsizeS
  port 4: (value) OPEN  ; channel: twoBitsizeT
  port 5: (cntrl) -     ; channel: $

[process] ALIGNER:name_maf_seq
  status=ACTIVE
  port 0: (value) OPEN  ; channel: maf
  port 1: (cntrl) -     ; channel: $

[process] ALIGNER:mafstats
  status=ACTIVE
  port 0: (value) OPEN  ; channel: final_maf
  port 1: (value) bound ; channel: sourceName
  port 2: (value) bound ; channel: targetName
  port 3: (cntrl) -     ; channel: $

[process] LIFTOVER:lifter
  status=ACTIVE
  port 0: (value) OPEN  ; channel: chain
  port 1: (queue) OPEN  ; channel: annotation
  port 2: (value) bound ; channel: tgt_ch
  port 3: (cntrl) -     ; channel: $

[process] LIFTOVER:features_stats
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: all_feature
  port 1: (queue) OPEN  ; channel: lifted_features
  port 2: (cntrl) -     ; channel: $

[process] make_report
  status=ACTIVE
  port 0: (value) OPEN  ; channel: mafstats
  port 1: (value) OPEN  ; channel: mafcov
  port 2: (value) OPEN  ; channel: mafidn
  port 3: (queue) OPEN  ; channel: feat
  port 4: (cntrl) -     ; channel: $

Jun.-07 11:38:58.301 [main] DEBUG nextflow.Session - Session await > all process finished
Jun.-07 11:38:58.302 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun.-07 11:38:58.312 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Jun.-07 11:38:58.312 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Jun.-07 11:38:58.314 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Jun.-07 11:38:58.317 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  []
Jun.-07 11:38:58.744 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Jun.-07 11:38:58.832 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jun.-07 11:38:58.845 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

@RenzoTale88
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Is the file src16.tgt19.psl empty by any mean? I would proceed by looking at the single output, and if they're empty, trace backward by going to the linked folder as we've done for the previous file (i.e. ls -al work/*/*/src16.tgt19.psl, go the linked folder, check the input/output/err file).

@KristinaGagalova
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Ok, I found the error. the src16.tgt19.psl was indeed empty and tracing back I fount this error:

Got 17 lifts in source.lift
Lifting stdin
Got 20 lifts in target.lift
Lifting stdin
FAILURE: 
/mydir/liftover/test_run2/work/31/db7c6e2b8910ee8b7d1f3ecd95433a/CLUST_src/src16.fa contains more than one sequence
consider using the "multiple" action (see "lastz --help=files")
stdin is empty
stdin is empty

I am not familiar with chainfiles or coordinates liftover but is there possible that I need to change the overlap or src sizes to different values? Is there any rule you follow based on the genome size?
Thank you in advance

@RenzoTale88
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I see! That is a situation I haven't considered (working on larger genomes I never came across this type of situation).
You can probably try to reduce the chunking size. This will increase the number of fragments to process, but it might fix the issue you are finding.
You can probably try using the parameters for the test profile:

    tgtSize = 2000000
    tgtOvlp=100000
    srcSize = 1000000

And reducing progressively while you perform the reduction.

On my side, I'll work on a possible fix for this tomorrow. Thanks for spotting this!

Andrea

@RenzoTale88
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@KristinaGagalova @zhoudreames thank you both for your patience. This turned out to be a possible relevant issue, and thanks to this it is probably now fixed. I've uploaded a new version of the workflow, that should sort the problem out. If you are running the previous version of the workflow, I would suggest you to drop the previous version and then repeat the analyses:

nextflow drop evotools/nf-LO
nextflow run evotools/nf-LO ...

Or alternatively to run everything using the -latest flag:

nextflow run -latest evotools/nf-LO ...

Please, do let me know if you come across further issues, and thank you again for using nf-LO!

Andrea

@zhoudreames
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thanks for your help, I resolved it.

@zhoudreames
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tell me to close this problem if you solved it, thanks~

@RenzoTale88
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@zhoudreames thanks, I'll wait for @KristinaGagalova to confirm or rise more points on this. If it works for her I'll close it. Thanks again!

@KristinaGagalova
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@RenzoTale88 looks good now! Thank you for the fast fix

@RenzoTale88
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@KristinaGagalova glad to have fixed this :)

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@RenzoTale88 @KristinaGagalova @zhoudreames