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hillerlab / make_lastz_chains

Portable solution to generate genome alignment chains using lastz
MIT License
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Argument list too long - lastz #35

Closed AgustoLuz closed 7 months ago

AgustoLuz commented 10 months ago

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.

kirilenkobm commented 10 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

kirilenkobm commented 10 months ago

Hi @AgustoLuz pls try the updated version (2.0.8).

AgustoLuz commented 10 months ago

I continue getting the same error

AgustoLuz commented 10 months ago

/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_rando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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

AgustoLuz commented 10 months ago

I have attached the error line, is there another, possible way to chain genomes for TOGA??

kirilenkobm commented 10 months ago

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:

kirilenkobm commented 10 months ago

@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

AgustoLuz commented 10 months ago

thank you