error haplotag rule

[eedhaene]

Hi,

While running the pipeline on the test data, I keep getting an error concerning the haplotag rule (all previous jobs excited successfully):

(pore-c-snakemake) [vsc42297@gligar05 Pore-C-Snakemake]$ snakemake --use-conda --cluster "qsub -l walltime=10:00:00,nodes=1:ppn=4,mem=8gb" --jobs 4 test --config=output_dir=results.test
Building DAG of jobs...
Updating job 14 (create_contact_fofn).
Updating job 1 (summarise_contacts).
Using shell: /usr/bin/bash
Provided cluster nodes: 4
Job counts:
	count	jobs
	1	assign_fragments
	1	create_alignment_table
	1	create_contact_fofn
	1	create_hic
	1	create_mcool_file
	1	haplotag
	1	index_pairs
	1	merge_contact_files
	1	summarise_contacts
	1	test
	1	to_contacts
	1	to_cooler
	1	to_mnd
	1	to_salsa_bed
	1	to_sorted_pairs
	1	to_unsorted_pairs
	16

[Wed Jul 14 12:29:17 2021]
rule haplotag:
    input: results.test/mapping/NlaIII_run01_batch1_GRCh38.coord_sort.bam, results.test/mapping/NlaIII_run01_batch1_GRCh38.coord_sort.bam.bai, results.test/refgenome/GRCh38.rg.fa
    output: results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt
    log: results.test/logs/results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt.log
    jobid: 23
    benchmark: results.test/benchmarks/results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt.bench.txt
    wildcards: enzyme=NlaIII, run_id=run01, batch_id=batch1, refgenome_id=GRCh38, phase_set_id=unphased

Submitted job 23 with external jobid '11039634'.
[Wed Jul 14 12:33:27 2021]
Error in rule haplotag:
    jobid: 23
    output: results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt
    log: results.test/logs/results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt.log (check log file(s) for error message)
    conda-env: /kyukon/data/gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/.snakemake/conda/6c79fdc2
    cluster_jobid: 11039634

Error executing rule haplotag on cluster (jobid: 23, external: 11039634, jobscript: /kyukon/data/gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/.snakemake/tmp.0s4fysdp/snakejob.haplotag.23.sh). For error details see the cluster log and the log files of the involved rule(s).
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /kyukon/data/gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/.snakemake/log/2021-07-14T122916.668658.snakemake.log`

The cluster error log points to an issue on line 54 of mapping.smk (line specifying the wrapper):

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	haplotag
	1

[Wed Jul 14 12:33:17 2021]
rule haplotag:
    input: results.test/mapping/NlaIII_run01_batch1_GRCh38.coord_sort.bam, results.test/mapping/NlaIII_run01_batch1_GRCh38.coord_sort.bam.bai, results.test/refgenome/GRCh38.rg.fa
    output: results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt
    log: results.test/logs/results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt.log
    jobid: 0
    benchmark: results.test/benchmarks/results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt.bench.txt
    wildcards: enzyme=NlaIII, run_id=run01, batch_id=batch1, refgenome_id=GRCh38, phase_set_id=unphased

Activating conda environment: /vscmnt/gent_kyukon_data/_kyukon_data_gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/.snakemake/conda/d8db8bef
[Wed Jul 14 12:33:20 2021]
Error in rule haplotag:
    jobid: 0
    output: results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt
    log: results.test/logs/results.test/mapping/NlaIII_run01_batch1_GRCh38_unphased.haplotagged.txt.log (check log file(s) for error message)
    conda-env: /vscmnt/gent_kyukon_data/_kyukon_data_gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/.snakemake/conda/d8db8bef

RuleException:
NoSuchProcess in line 54 of /kyukon/data/gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/rules/mapping.smk:
psutil.NoSuchProcess no process found with pid 237532
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2114, in run_wrapper
  File "/kyukon/data/gent/vo/000/gvo00082/vsc42297/porec/analysis/Pore-C-Snakemake/rules/mapping.smk", line 54, in __rule_haplotag
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/contextlib.py", line 113, in __enter__
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/site-packages/psutil/__init__.py", line 326, in __init__
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/site-packages/psutil/__init__.py", line 367, in _init
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 529, in _callback
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/concurrent/futures/thread.py", line 57, in run
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 515, in cached_or_run
  File "/data/gent/vo/000/gvo00082/vsc42297/.conda/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2199, in run_wrapper
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

I haven't been able to find out how I could resolve this issue and would appreciate any input.

Thanks in advance!