Closed AgustoLuz closed 7 months ago
Hi @AgustoLuz
Thanks for reporting it. Is it definitely not a resource problem - it was theoretically possible, but I thought it will never happen on practice. I will investigate and fix.
UPD: the problem definitely sits in the
steps_implementations.lastz_step.create_lastz_jobs
and upstream in the steps_implementations.partition.do_partition_for_genome
Hi @AgustoLuz pls try the updated version (2.0.8).
I continue getting the same error
/nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py /nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/chicken_turkey/target.2bit:chr1:175000000-197608386 BULK_5:/nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/chicken_turkey/query.2bit:chr24:chr24_NW_011100164v1_random:chr24_NW_011100165v1_random:chr24_NW_011100166v1_random:chr24_NW_011100167v1_random:chr24_NW_011100168v1_random:chr24_NW_011100169v1_random:chr24_NW_011100170v1_random:chr24_NW_011100171v1_random:chr24_NW_011100172v1_random:chr24_NW_011100173v1_random:chr24_NW_011100174v1_random:chr24_NW_011100175v1_random:chr24_NW_011100176v1_random:chr24_NW_011100177v1_random:chr24_NW_011100178v1_random:chr24_NW_011100179v1_random:chr24_NW_011100180v1_random:chr24_NW_011100181v1_random:chr24_NW_011100182v1_random:chr24_NW_011100183v1_random:chr24_NW_011100184v1_random:chr24_NW_011100185v1_random:chr24_NW_011100186v1_random:chr24_NW_011100187v1_random:chr24_NW_011100188v1_random:chr24_NW_011100189v1_random:chr24_NW_011100190v1_random:chr24_NW_011100191v1_random:chr24_NW_011100192v1_random:chr24_NW_011100193v1_random:chr24_NW_011100194v1_random:chr24_NW_011100195v1_random:chr24_NW_011100196v1_random:chr24_NW_011100197v1_random:chr24_NW_011100198v1_random:chr24_NW_011100199v1_random:chr24_NW_011100200v1_random:chr24_NW_011100201v1_random:chr24_NW_011100202v1_random:chr24_NW_011100203v1_random:chr24_NW_011100204v1_random:chr24_NW_011100205v1_random:chr24_NW_011100206v1_random:chr24_NW_011100207v1_random:chr24_NW_011100208v1_random:chr24_NW_011100209v1_random:chr24_NW_011100210v1_random:chr24_NW_011100211v1_random:chr24_NW_011100212v1_random:chr24_NW_011100213v1_random:chr24_NW_011100214v1_random:chr24_NW_011100215v1_random:chr24_NW_011100216v1_random:chr24_NW_011100217v1_random:chr24_NW_011100218v1_random:chr24_NW_011100219v1_random:chr24_NW_011100220v1_random:chr24_NW_011100221v1_random:chr24_NW_011100222v1_random:chr24_NW_011100223v1_random:chr24_NW_011100224v1_random:chr24_NW_011100225v1_random:chr24_NW_011100226v1_random:chr24_NW_011100227v1_random:chr24_NW_011100228v1_random:chr24_NW_011100229v1_random:chr25:chr25_NW_011100230v1_random:chr25_NW_011100231v1_random:chr25_NW_011100232v1_random:chr25_NW_011100233v1_random:chr25_NW_011100234v1_random:chr25_NW_011100235v1_random:chr25_NW_011100236v1_random:chr25_NW_011100237v1_random:chr25_NW_011100238v1_random:chr25_NW_011100239v1_random:chr25_NW_011100240v1_random:chr25_NW_011100241v1_random:chr25_NW_011100242v1_random:chr25_NW_011100243v1_random:chr25_NW_011100244v1_random:chr25_NW_011100245v1_random:chr25_NW_011100246v1_random:chr25_NW_011100247v1_random:chr25_NW_011100248v1_random:chr25_NW_011100249v1_random:chr25_NW_011100250v1_random:chr25_NW_011100251v1_random:chr25_NW_011100252v1_random:chr25_NW_011100253v1_random:chr25_NW_011100254v1_random:chr25_NW_011100255v1_random:chr25_NW_011100256v1_random:chr25_NW_011100257v1_random:chr25_NW_011100258v1_random:chr25_NW_011100259v1_random:chr25_NW_011100260v1_random:chr25_NW_011100261v1_random:chr25_NW_011100262v1_random:chr25_NW_011100263v1_random:chr25_NW_011100264v1_random:chr25_NW_011100265v1_random:chr25_NW_011100266v1_random:chr25_NW_011100267v1_random:chr25_NW_011100268v1_random:chr25_NW_011100269v1_random:chr25_NW_011100270v1_random:chr25_NW_011100271v1_random:chr25_NW_011100272v1_random:chr25_NW_011100273v1_random:chr25_NW_011100274v1_random:chr25_NW_011100275v1_random:chr25_NW_011100276v1_random:chr25_NW_011100277v1_random:chr25_NW_011100278v1_random:chr25_NW_011100279v1_random:chr25_NW_011100280v1_random:chr25_NW_011100281v1_random:chr25_NW_011100282v1_random:chr25_NW_011100283v1_random:chr25_NW_011100284v1_random:chr25_NW_011100285v1_random:chr25_NW_011100286v1_random:chr25_NW_011100287v1_random:chr25_NW_011100288v1_random:chr25_NW_011100289v1_random:chr25_NW_011100290v1_random:chr25_NW_011100291v1_random:chr25_NW_011100292v1_random:chr25_NW_011100293v1_random:chr25_NW_011100294v1_random:chr25_NW_011100295v1_random:chr25_NW_011100296v1_random:chr25_NW_011100297v1_random:chr25_NW_011100298v1_random:chr25_NW_011100299v1_random:chr25_NW_011100300v1_random:chr25_NW_011100301v1_random:chr26:chr26_NW_011100302v1_random:chr26_NW_011100303v1_random:chr26_NW_011100304v1_random:chr26_NW_011100305v1_random:chr26_NW_011100306v1_random:chr26_NW_011100307v1_random:chr26_NW_011100308v1_random:chr26_NW_011100309v1_random:chr26_NW_011100310v1_random:chr26_NW_011100311v1_random:chr26_NW_011100312v1_random:chr26_NW_011100313v1_random:chr26_NW_011100314v1_random:chr26_NW_011100315v1_random:chr26_NW_011100316v1_random:chr26_NW_011100317v1_random:chr26_NW_011100318v1_random:chr26_NW_011100319v1_random:chr26_NW_011100320v1_random:chr26_NW_011100321v1_random:chr26_NW_011100322v1_random:chr26_NW_011100323v1_random:chr26_NW_011100324v1_random:chr26_NW_011100325v1_random:chr26_NW_011100326v1_random:chr26_NW_011100327v1_random:chr26_NW_011100328v1_random:chr26_NW_011100329v1_random:chr26_NW_011100330v1_random:chr26_NW_011100331v1_random:chr26_NW_011100332v1_random:chr26_NW_011100333v1_random:chr26_NW_011100334v1_random:chr26_NW_011100335v1_random:chr26_NW_011100336v1_random:chr26_NW_011100337v1_random:chr26_NW_011100338v1_random:chr26_NW_011100339v1_random:chr26_NW_011100340v1_random:chr26_NW_011100341v1_random:chr26_NW_011100342v1_random:chr26_NW_011100343v1_random:chr26_NW_011100344v1_random:chr26_NW_011100345v1_random:chr26_NW_011100346v1_random:chr26_NW_011100347v1_random:chr26_NW_011100348v1_random:chr26_NW_011100349v1_random:chr26_NW_011100350v1_random:chr26_NW_011100351v1_random:chr26_NW_011100352v1_random:chr26_NW_011100353v1_random:chr26_NW_011100354v1_random:chr26_NW_011100355v1_random:chr26_NW_011100356v1_random:chr26_NW_011100357v1_random:chr26_NW_011100358v1_random:chr26_NW_011100359v1_random:chr26_NW_011100360v1_random:chr26_NW_011100361v1_random:chr26_NW_011100362v1_random:chr26_NW_011100363v1_random:chr26_NW_011100364v1_random:chr26_NW_011100365v1_random:chr26_NW_011100366v1_random:chr26_NW_011100367v1_random:chr26_NW_011100368v1_random:chr26_NW_011100369v1_random:chr26_NW_011100370v1_random:chr26_NW_011100371v1_random:chr26_NW_011100372v1_random:chr26_NW_011100373v1_random:chr26_NW_011100374v1_random:chr26_NW_011100375v1_random:chr26_NW_011100376v1_random:chr26_NW_011100377v1_random:chr26_NW_011100378v1_random:chr26_NW_011100379v1_random:chr26_NW_011100380v1_random:chr26_NW_011100381v1_random:chr26_NW_011100382v1_random:chr26_NW_011100383v1_random:chr26_NW_011100384v1_random:chr26_NW_011100385v1_random:chr26_NW_011100386v1_random:chr26_NW_011100387v1_random:chr26_NW_011100388v1_random:chr26_NW_011100389v1_random:chr26_NW_011100390v1_random:chr26_NW_011100391v1_random:chr26_NW_011100392v1_random:chr26_NW_011100393v1_random:chr26_NW_011100394v1_random:chr26_NW_011100395v1_random:chr26_NW_011100396v1_random:chr26_NW_011100397v1_random:chr26_NW_011100398v1_random:chr26_NW_011100399v1_random:chr26_NW_011100400v1_random:chr26_NW_011100401v1_random:chr26_NW_011100402v1_random:chr26_NW_011100403v1_random:chr26_NW_011100404v1_random:chr26_NW_011100405v1_random:chr26_NW_011100406v1_random:chr26_NW_011100407v1_random:chr26_NW_011100408v1_random:chr26_NW_011100409v1_random:chr26_NW_011100410v1_random:chr26_NW_011100411v1_random:chr26_NW_011100412v1_random:chr26_NW_011100413v1_random:chr26_NW_011100414v1_random:chr26_NW_011100415v1_random:chr26_NW_011100416v1_random:chr26_NW_011100417v1_random:chr26_NW_011100418v1_random:chr26_NW_011100419v1_random:chr26_NW_011100420v1_random:chr26_NW_011100421v1_random:chr26_NW_011100422v1_random:chr26_NW_011100423v1_random:chr26_NW_011100424v1_random:chr26_NW_011100425v1_random:chr26_NW_011100426v1_random:chr26_NW_011100427v1_random:chr26_NW_011100428v1_random:chr26_NW_011100429v1_random:chr26_NW_011100430v1_random:chr26_NW_011100431v1_random:chr26_NW_011100432v1_random:chr26_NW_011100433v1_random:chr26_NW_011100434v1_random:chr26_NW_011100435v1_random:chr26_NW_011100436v1_random:chr26_NW_011100437v1_random:chr26_NW_011100438v1_random:chr26_NW_011100439v1_random:chr26_NW_011100440v1_random:chr26_NW_011100441v1_random:chr26_NW_011100442v1_random:chr26_NW_011100443v1_random:chr26_NW_011100444v1_random:chr26_NW_011100445v1_random:chr26_NW_011100446v1_random:chr26_NW_011100447v1_random:chr26_NW_011100448v1_random:chr26_NW_011100449v1_random:chr26_NW_011100450v1_random:chr26_NW_011100451v1_random:chr26_NW_011100452v1_random:chr26_NW_011100453v1_random:chr26_NW_011100454v1_random:chr26_NW_011100455v1_random:chr26_NW_011100456v1_random:chr26_NW_011100457v1_random:chr26_NW_011100458v1_random:chr26_NW_011100459v1_random:chr26_NW_011100460v1_random:chr26_NW_011100461v1_random:chr26_NW_011100462v1_random:chr26_NW_011100463v1_random:chr27:chr27_NW_011100464v1_random:chr27_NW_011100465v1_random:chr27_NW_011100466v1_random:chr27_NW_011100467v1_random:chr27_NW_011100468v1_random:chr27_NW_011100469v1_random:chr27_NW_011100470v1_random:chr27_NW_011100471v1_random:chr27_NW_011100472v1_random:chr27_NW_011100473v1_random:chr27_NW_011100474v1_random:chr27_NW_011100475v1_random:chr27_NW_011100476v1_random:chr27_NW_011100477v1_random:chr27_NW_011100478v1_random:chr27_NW_011100479v1_random:chr27_NW_011100480v1_random:chr27_NW_011100481v1_random:chr27_NW_011100482v1_random:chr27_NW_011100483v1_random:chr27_NW_011100484v1_random:chr27_NW_011100485v1_random:chr27_NW_011100486v1_random:chr27_NW_011100487v1_random:chr27_NW_011100488v1_random:chr27_NW_011100489v1_random:chr27_NW_011100490v1_random:chr27_NW_011100491v1_random:chr27_NW_011100492v1_random:chr28:chr28_NW_011100493v1_random:chr28_NW_011100494v1_random:chr28_NW_011100495v1_random:chr28_NW_011100496v1_random:chr28_NW_011100497v1_random:chr28_NW_011100498v1_random:chr28_NW_011100499v1_random:chr28_NW_011100500v1_random:chr28_NW_011100501v1_random:chr28_NW_011100502v1_random:chr28_NW_011100503v1_random:chr28_NW_011100504v1_random:chr28_NW_011100505v1_random:chr28_NW_011100506v1_random:chr28_NW_011100507v1_random:chr28_NW_011100508v1_random:chr28_NW_011100509v1_random:chr28_NW_011100510v1_random:chr28_NW_011100511v1_random:chr28_NW_011100512v1_random:chr28_NW_011100513v1_random:chr28_NW_011100514v1_random:chr28_NW_011100515v1_random:chr28_NW_011100516v1_random:ch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/nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/chicken_turkey/pipeline_parameters.json /nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/chicken_turkey/temp_lastz_psl_output/bucket_ref__chr1_in_175000000_197608386/chr1_BULK_5__56.psl /nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/standalone_scripts/run_lastz.py --output_format psl --axt_to_psl /home/aluzuriaganeira/nas5/software/miniconda3/envs/env_toga/bin/axtToPsl
Command exit status: 1
Command output: (empty)
Command error: .command.sh: line 2: /nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py: Argument list too long
Work dir: /nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/chicken_turkey/temp_lastz_run/work/6d/8977db60ff81d4fa973a229ab1d882
I have attached the error line, is there another, possible way to chain genomes for TOGA??
Hi @AgustoLuz
thank you for providing the exact command, it really helps. Interesting, but must not happen, I will continue fixing it.
About the ways to do it:
@AgustoLuz
I just checked - I accidentally misplaced a condition that should limit the number of arguments for this command. The new version was pushed to master a few seconds ago, I labelled it with v2.0.8 again
https://github.com/hillerlab/make_lastz_chains/commit/3ccd514d66cb0ad3c3223a44ff6cf9d6300b673a
thank you
Hi I am trying to chain the chicken and turkey genomes but I am getting this error :
/nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/chicken_turkey/temp_lastz_run/work/33/98c1845c4ef249c5f4bae4eb8e5517/.command.sh: line 2: /nas5/aluzuriaganeira/birds/TOGA/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py: Argument list too long
Any ideas on how to fix it, I am running it in a cluster with 50 cpus and 80GB of memory so I don't think is a problem of resources.