Error in rule make_annot

[Antidington]

Hi all,

When running the CELLECT-LDSC pipeline's annotation generation step, the process fails with an IndexError indicating list index out of range when trying to access the score column from BED file.

Traceback (most recent call last):
  File "/hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/03_CELLECT_LDSC/.snakemake/scripts/tmp9vh1pxx6.make_annot_from_geneset_all_chr_snake.py", line 301, in <mod
ule>
    make_annot_file_per_chromosome(chromosome, dict_of_beds, out_dir, out_prefix, annot_per_geneset, bimfile, all_genes)
  File "/hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/03_CELLECT_LDSC/.snakemake/scripts/tmp9vh1pxx6.make_annot_from_geneset_all_chr_snake.py", line 180, in make
_annot_file_per_chromosome
    annotation_value = [x.fields[7] for x in annotbed] # returns list of strings. Extract the 'score' column. This is column 7 in the 0-based column indexing. *OBS*:
x.fields[7] is a string.
  File "/hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/03_CELLECT_LDSC/.snakemake/scripts/tmp9vh1pxx6.make_annot_from_geneset_all_chr_snake.py", line 180, in <lis
tcomp>
    annotation_value = [x.fields[7] for x in annotbed] # returns list of strings. Extract the 'score' column. This is column 7 in the 0-based column indexing. *OBS*:
x.fields[7] is a string.
IndexError: list index out of range
[Mon Nov 25 23:54:51 2024]
Error in rule make_annot:
    jobid: 63
    input: /hwmaster/wenjichen/HumanAS/output/snRNA-seq/CELLECT/02_generate_celltype_specificty_input/cellex_raw_output/HumanAS_S_CELLEX_filtered_esmu.csv, /hwmaster/
wenjichen/HumanAS/src/snRNA-seq/CELLECCT/00_software/CELLECT/data/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.bim, /hwmaster/wenjichen/HumanAS/output/snRNA-seq/CELLEC
T/03_CELLECT_LDSC/CELLECT-LDSC/precomputation/bed/overlap_segments_100kb.15.bed
    output: /hwmaster/wenjichen/HumanAS/output/snRNA-seq/CELLECT/03_CELLECT_LDSC/CELLECT-LDSC/precomputation/HumanAS_S/HumanAS_S.COMBINED_ANNOT.15.annot.gz, /hwmaster
/wenjichen/HumanAS/output/snRNA-seq/CELLECT/03_CELLECT_LDSC/CELLECT-LDSC/out/annots/HumanAS_S/HumanAS_S.COMBINED_ANNOT.15.annot.gz
    log: /hwmaster/wenjichen/HumanAS/output/snRNA-seq/CELLECT/03_CELLECT_LDSC/CELLECT-LDSC/logs/log.make_annot_snake.HumanAS_S.15.txt (check log file(s) for error det
ails)
    conda-env: /hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/03_CELLECT_LDSC/.snakemake/conda/10a3e58014d28334b5c27517a7cf66b6_

RuleException:
CalledProcessError in file /hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/00_software/CELLECT/cellect-ldsc.snakefile, line 259:
Command 'source /pmaster/wenjichen/miniconda3/bin/activate '/hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/03_CELLECT_LDSC/.snakemake/conda/10a3e58014d28334b5c275
17a7cf66b6_'; set -euo pipefail;  /pmaster/wenjichen/miniconda3/envs/CELLECT_snakemake/bin/python3.8 /hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/03_CELLECT_LDS
C/.snakemake/scripts/tmp9vh1pxx6.make_annot_from_geneset_all_chr_snake.py' returned non-zero exit status 1.
  File "/hwmaster/wenjichen/HumanAS/src/snRNA-seq/CELLECCT/00_software/CELLECT/cellect-ldsc.snakefile", line 259, in __rule_make_annot
  File "/pmaster/wenjichen/miniconda3/envs/CELLECT_snakemake/lib/python3.8/concurrent/futures/thread.py", line 57, in run

Would you like me to help investigate any specific aspect of this error or provide guidance on potential solutions?

Thanks,
Jichen