STAR alignment parameter changing

[Dylan-LElab]

Thank you very much for the tool, which is very convenient to run. May I know if there are any methods to change the STAR alignment parameters?

[y9c]

Hi Dylan,

Thank you for reaching out. Unfortunately, in the current version, changing the STAR alignment parameters is not straightforward and requires running the code from scratch. Could you please let me know which specific STAR parameters you would like to modify? I can look into implementing a patch in the current version to accommodate these changes.

[Dylan-LElab]

Thank you very much for your response. I would like to modify the alignment parameters by changing the --alignIntronMax setting to 1.

[y9c]

Yes. It is possible to do so. I have push a new test version for your application. To use this, you can add the following chunk into your data.yaml file.

star_params:
  alignEndsType: Local
  scoreDelOpen: -1
  scoreDelBase: -1
  scoreInsOpen: -2
  scoreInsBase: -2
  outFilterMatchNmin: 15
  outFilterMatchNminOverLread: 0.8
  outFilterMismatchNmax: 10
  outFilterMismatchNoverLmax: 0.2
  outFilterIntronMotifs: RemoveNoncanonicalUnannotated
  alignSJDBoverhangMin: 1
  alignIntronMax: 1
  alignSJoverhangMin: 5
  chimSegmentMin: 20
  chimOutType: WithinBAM HardClip
  chimJunctionOverhangMin: 15
  chimScoreJunctionNonGTAG: 0
  outFilterMultimapNmax: 10
  outFilterMultimapScoreRange: 0
  outSAMmultNmax: -1
  outMultimapperOrder: Random
  outSAMattributes: NH HI AS nM NM MD jM jI MC ch

and run the code by:

apptainer run docker://y9ch/bidseq:test

[Dylan-LElab]

Thank you so much for the update! I have tried the following code : 'apptainer run docker://y9ch/bidseq:test' and it raised a WorkflowError. I find genome.tsv.gz and readsStats.html file are not generated. It was stopped due to the error and I re-run 'apptainer run docker://y9ch/bidseq:test' at the same dir without changing anything to check which jobs are not run properly. The newest BIDSEQ_LOG file shows: (By the way, data.yaml can be run successfully without adding STAR parameter using 'apptainer run docker://y9ch/bidseq'. )

job count

---

adjust_sites 1
all 1
count_bases_combined 1
post_filter_sites 1
pre_filter_sites 1
report_reads_stat 1
total 6
localrule report_reads_stat:
input: (all input files)
output: report_reads/readsStats.html
jobid: 1
reason: Missing output files: report_reads/readsStats.html
resources: tmpdir=/tmp
localrule count_bases_combined:
input: (all input files)
jobid: 90
reason: Missing output files: .tmp/pileup_bases/genome.tsv
wildcards: reftype=genome
threads: 4
resources: tmpdir=/tmp

localrule adjust_sites:
input: .tmp/pileup_bases/genome.tsv
output: call_sites/genome.tsv.gz
jobid: 89
reason: Missing output files: call_sites/genome.tsv.gz; Input files updated by another job: .tmp/pileup_bases/genome.tsv
wildcards: reftype=genome
resources: tmpdir=/tmp
/// MultiQC 🔍 v1.24.1
multiqc_yc | Multiqc (Chang Y forked) - Updating config

Finished job 89.
2 of 6 steps (33%) done
Removing temporary output .tmp/pileup_bases/genome.tsv.
Select jobs to execute...
Execute 1 jobs...

localrule pre_filter_sites:
input: call_sites/genome.tsv.gz
output: .tmp/prefilter_sites/genome.tsv.gz
jobid: 110
reason: Missing output files: .tmp/prefilter_sites/genome.tsv.gz; Input files updated by another job: call_sites/genome.tsv.gz
wildcards: reftype=genome
resources: tmpdir=/tmp

localrule post_filter_sites:
input: .tmp/prefilter_sites/genome.tsv.gz
output: filter_sites/genome.tsv.gz
jobid: 109
reason: Missing output files: filter_sites/genome.tsv.gz; Input files updated by another job: .tmp/prefilter_sites/genome.tsv.gz
wildcards: reftype=genome
resources: tmpdir=/tmp

Waiting at most 5 seconds for missing files.
MissingOutputException in rule report_reads_stat in file /pipeline/Snakefile, line 629:
Job 1 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
report_reads/readsStats.html (missing locally, parent dir contents: deduping, joining, mapping, trimming)
[Wed Sep 11 12:47:26 2024]
Finished job 109.
4 of 6 steps (67%) done
Removing temporary output .tmp/prefilter_sites/genome.tsv.gz.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-09-11T124717.613405.snakemake.log
WorkflowError:
At least one job did not complete successfully.