gzip: stdin: No data available

[eeaunin]

Hello. Below is a log from an FCS-GX run that crashed with the message gzip: stdin: No data available. What has happened here, and how to prevent this problem?

=============================================================================== 
Source:      /mft-volume 
Destination: /app/db/gxdb 
Resuming failed transfer in /app/db/gxdb... 
Space check: Available:1.14TiB; Existing:0B; Incoming:464.34GiB; Delta:464.34GiB

Requires transfer: 59B all.meta.jsonl 
Copying /mft-volume/all.meta.jsonl to /app/db/gxdb/all.meta.jsonl.part... 

Requires transfer: 187B all.README.txt 
Copying /mft-volume/all.README.txt to /app/db/gxdb/all.README.txt.part... 

Requires transfer: 6.09MiB all.taxa.tsv 
Copying /mft-volume/all.taxa.tsv to /app/db/gxdb/all.taxa.tsv.part... 

Requires transfer: 7.86MiB all.blast_div.tsv.gz 
Copying /mft-volume/all.blast_div.tsv.gz to /app/db/gxdb/all.blast_div.tsv.gz.part... 

Requires transfer: 8.48MiB all.assemblies.tsv 
Copying /mft-volume/all.assemblies.tsv to /app/db/gxdb/all.assemblies.tsv.part... 

Requires transfer: 21.51MiB all.seq_info.tsv.gz 
Copying /mft-volume/all.seq_info.tsv.gz to /app/db/gxdb/all.seq_info.tsv.gz.part... 

Requires transfer: 165.14GiB all.gxs 
Copying /mft-volume/all.gxs to /app/db/gxdb/all.gxs.part... 

Requires transfer: 299.16GiB all.gxi 
Copying /mft-volume/all.gxi to /app/db/gxdb/all.gxi.part... 
Done. 
-----------------------------------------------------------------------------

tax-id    : 476027
fasta     : /sample-volume/assembly.fasta
size      : 2495.09 MiB
split-fa  : True
####### Starting process ['zcat', '-f', '/app/db/gxdb/gx_mapper_2955715/all.blast_div.tsv.gz']
####### Starting process ['grep', '-E', '^476027\t']
####### Cleaning up process ['zcat', '-f', '/app/db/gxdb/gx_mapper_2955715/all.blast_div.tsv.gz']
####### Cleaning up process ['grep', '-E', '^476027\t']
BLAST-div : sponges
gx-div    : anml:basal metazoans
w/same-tax: True
bin-dir   : /app/bin
gx-db     : /app/db/gxdb/gx_mapper_2955715/all.gxi
gx-ver    : Nov 27 2023 11:05:36; git:v0.5.0+branch--HEAD
output    : /output-volume//assembly.476027.taxonomy.rpt

-----------------------------------------------------------------------------

####### args: Namespace(fasta='/sample-volume/assembly.fasta', tax_id=476027, species=None, split_fasta=True, div='anml:basal metazoans', gx_db='/app/db/gxdb/gx_mapper_2955715/all.gxi', mask_transposons=None, bin_dir='/app/bin', allow_same_species=True, ignore_same_kingdom=False, out_basename='/output-volume//assembly.476027', out_dir='/output-volume/', action_report=True, save_hits=False, generate_logfile=False, debug=True, phone_home_label=None, gc_acc=None, gc_genomes_root_dir=None, production_build_name=None, gzip_c='gzip -c', out_taxonomy_rpt='/output-volume//assembly.476027.taxonomy.rpt') 

####### Starting process ['cat', '/sample-volume/assembly.fasta']
####### Starting process ['gzip', '-cdf']
####### Starting process ['/app/bin/gx', 'split-fasta']
####### Starting process ['pv', '-Wbratpe', '--interval=0.5', '--size=2616292917']
####### Starting process ['cat', '/sample-volume/assembly.fasta']
####### Starting process ['gzip', '-cdf']
####### Starting process ['/busybox/time', '-v', 'nice', '-n19', '/app/bin/gx', 'align', '--gx-db=/app/db/gxdb/gx_mapper_2955715/all.gxi', '--repeats-basis-fa=/dev/fd/5']
####### Starting process ['/app/bin/gx', 'taxify', '--gx-db=/app/db/gxdb/gx_mapper_2955715/all.gxi', '--output=/output-volume//assembly.476027.taxonomy.rpt.tmp', '--asserted-div=anml:basal metazoans', '--db-exclude-locs=/app/bin/db_exclude.locs.tsv']
Using GX_PREFETCH=0
Collecting masking statistics...
Collected masking stats:  2.58323 Gbp; 30.8123s; 83.8376 Mbp/s. Baseline: 3.34072


gzip: stdin: No data available
####### Cleaning up process ['cat', '/sample-volume/assembly.fasta']
Error: Process failed with retcode -13: ['cat', '/sample-volume/assembly.fasta'])
####### Cleaning up process ['gzip', '-cdf']
Error: Process failed with retcode 1: ['gzip', '-cdf'])
####### Cleaning up process ['/app/bin/gx', 'split-fasta']
####### Cleaning up process ['pv', '-Wbratpe', '--interval=0.5', '--size=2616292917']
####### Cleaning up process ['/busybox/time', '-v', 'nice', '-n19', '/app/bin/gx', 'align', '--gx-db=/app/db/gxdb/gx_mapper_2955715/all.gxi', '--repeats-basis-fa=/dev/fd/5']
####### Cleaning up process ['/app/bin/gx', 'taxify', '--gx-db=/app/db/gxdb/gx_mapper_2955715/all.gxi', '--output=/output-volume//assembly.476027.taxonomy.rpt.tmp', '--asserted-div=anml:basal metazoans', '--db-exclude-locs=/app/bin/db_exclude.locs.tsv']
####### Cleaning up process ['cat', '/sample-volume/assembly.fasta']
####### Cleaning up process ['gzip', '-cdf']

-----------------------------------------------------------------------------

Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_rs4oazym/runfiles/cgr_fcs/apps/fcs_genome/public/run_gx/run_gx.py", line 1037, in <module>
    main()
  File "/tmp/Bazel.runfiles_rs4oazym/runfiles/cgr_fcs/apps/fcs_genome/public/run_gx/run_gx.py", line 1012, in main
    run_gx_pipeline(args)
  File "/tmp/Bazel.runfiles_rs4oazym/runfiles/cgr_fcs/apps/fcs_genome/public/run_gx/run_gx.py", line 678, in run_gx_pipeline
    run(p_zcat_fasta, p_save_hits, p_main)
  File "/tmp/Bazel.runfiles_rs4oazym/runfiles/cgr_fcs/apps/fcs_genome/public/run_gx/run_gx.py", line 278, in __exit__
    self.wait()
  File "/tmp/Bazel.runfiles_rs4oazym/runfiles/cgr_fcs/apps/fcs_genome/public/run_gx/run_gx.py", line 268, in wait
    assert num_errors == 0, "Had errors."

These are the software versions used for this run: OS: Ubuntu 22.04.4 LTS Singularity: v3.11.4 FCS image: 0.5.0 Python: 3.8.12 Platform: LSF