chain_run issue

[lhauff]

Hi all,

I've been running into this issue when attempting the chain_run step. Any suggestions?

`# Make Lastz Chains #
Version 2.0.6
Commit: 9f16d8b
Branch: main

• found run_lastz.py at /cache/home/lrh85/make_lastz_chains/standalone_scripts/run_lastz.py
• found run_lastz_intermediate_layer.py at /cache/home/lrh85/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py
• found chain_gap_filler.py at /cache/home/lrh85/make_lastz_chains/standalone_scripts/chain_gap_filler.py
• found faToTwoBit at /home/lrh85/.conda/envs/toga/bin/faToTwoBit
• found twoBitToFa at /home/lrh85/.conda/envs/toga/bin/twoBitToFa
• found pslSortAcc at /cache/home/lrh85/make_lastz_chains/HL_kent_binaries/pslSortAcc
• found axtChain at /home/lrh85/.conda/envs/toga/bin/axtChain
• found axtToPsl at /home/lrh85/.conda/envs/toga/bin/axtToPsl
• found chainAntiRepeat at /home/lrh85/.conda/envs/toga/bin/chainAntiRepeat
• found chainMergeSort at /home/lrh85/.conda/envs/toga/bin/chainMergeSort
• found chainCleaner at /cache/home/lrh85/make_lastz_chains/HL_kent_binaries/chainCleaner
• found chainSort at /home/lrh85/.conda/envs/toga/bin/chainSort
• found chainScore at /cache/home/lrh85/make_lastz_chains/HL_kent_binaries/chainScore
• found lastz at /home/lrh85/lastz-distrib/bin/lastz
• found chainFilter at /cache/home/lrh85/make_lastz_chains/HL_kent_binaries/chainFilter
  found chainNet in $PATH
  All necessary executables found.

Trying to continue from step: chain_run

Making chains for 2bit/hg38.2bit and 2bit/bamboo.2bit files, saving results to /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman
Pipeline started at 2025-12-23 11:02:17.457983

• Setting up genome sequences for target
  genomeID: hg38
  input sequence file: 2bit/hg38.2bit
  is 2bit: True
  planned genome dir location: /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/target.2bit
  Created symlink from /scratch/lrh85/nanopore/2bit/hg38.2bit to /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/target.2bit
  For hg38 (target) sequence file: /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/target.2bit; chrom sizes saved to: /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/target.chrom.sizes
• Setting up genome sequences for query
  genomeID: bamboo_lemur
  input sequence file: 2bit/bamboo.2bit
  is 2bit: True
  planned genome dir location: /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/query.2bit
  Created symlink from /scratch/lrh85/nanopore/2bit/bamboo.2bit to /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/query.2bit
  For bamboo_lemur (query) sequence file: /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/query.2bit; chrom sizes saved to: /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/query.chrom.sizes

Build Chains Step

Sorting PSL files, saving the results to /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_chain_run/sorted_psl
/cache/home/lrh85/make_lastz_chains/HL_kent_binaries/pslSortAcc nohead /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_chain_run/sorted_psl /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_kent /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_3.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_68.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_6.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_10.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_71.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_11.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_20.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_69.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_73.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_17.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_35.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_29.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_24.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_21.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_2.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_19.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_4.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_28.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_61.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_64.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_65.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_13.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_44.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_25.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_47.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_62.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_40.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_60.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_16.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_27.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_39.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_49.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_45.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_23.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_57.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_74.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_37.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_50.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_54.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_14.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_31.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_70.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_38.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_48.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_1.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_72.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_58.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_59.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_12.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_75.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_53.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_18.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_26.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_9.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_0.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_15.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_5.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_56.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_46.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_52.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_7.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_8.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_51.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_66.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_41.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_55.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_36.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_30.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_43.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_42.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_63.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_67.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_33.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_32.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_22.psl.gz /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_concat_lastz_output/concat_34.psl.gz
An error occurred while executing chain_run: The sort command failed with exit code 255.Error message: Couldn't open /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_kent/tmp495.psl , Too many open files

Traceback (most recent call last):
File "/cache/home/lrh85/make_lastz_chains/modules/step_manager.py", line 70, in execute_steps
step_result = step_to_function[step](params, project_paths, step_executables)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cache/home/lrh85/make_lastz_chains/modules/pipeline_steps.py", line 64, in chain_run_step
do_chain_run(params, project_paths, executables)
File "/cache/home/lrh85/make_lastz_chains/steps_implementations/chain_run_step.py", line 88, in do_chain_run
psl_bundle(project_paths.cat_out_dirname, project_paths, executables, params)
File "/cache/home/lrh85/make_lastz_chains/steps_implementations/chain_run_step.py", line 33, in psl_bundle
raise PipelineSubprocessError(
modules.error_classes.PipelineSubprocessError: The sort command failed with exit code 255.Error message: Couldn't open /scratch/lrh85/nanopore/results/chains/bamboo_chainhuman/temp_kent/tmp495.psl , Too many open files`