Closed zhoudreames closed 2 years ago
@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
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?
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:
.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
Thank you for the fast reply @RenzoTale88
Here some more details:
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
@KristinaGagalova Thanks, this suggests me that some step before that probably failed for one reason or another. Could you please share with me both:
.command.sh
file contain anything.In this way we can try to trace back where the issue originated. Thanks! Andrea
.command.sh file
#!/bin/bash -ue
chainMergeSort src16.tgt19.chain | chainSplit run stdin -lump=1
mv run/000.chain ./rawchain.chain
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
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
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.
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
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.
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
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).
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
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
@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
thanks for your help, I resolved it.
tell me to close this problem if you solved it, thanks~
@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!
@RenzoTale88 looks good now! Thank you for the fast fix
@KristinaGagalova glad to have fixed this :)
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: 312fb56810 [main]======================================
_ | |_ __ | | | | | | | ' | | |___| | | | | | | | | | | | | |_| |_| | || ||| |________/
====================================== 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: ProcessALIGNER:chainMerge (chainmerge)
terminated with an error exit status (1) -- Execution is retried (2) [33/4e27ca] NOTE: ProcessALIGNER:chainMerge (chainmerge)
terminated with an error exit status (1) -- Error is ignored