filter_fasta did not run

[lydiayliu]

In my config https://github.com/uclahs-cds/project-MissingPeptides-Method/blob/lyl-test-ccle/src/call-noncanonical/CCLE/meta-call-NonCanonicalPeptide_parse_call_filter.config

I am confident to have included

        entrypoint = 'parser'
        filter_fasta = true
        split_fasta = false
        encode_fasta = true
        decoy_fasta = true

and

        filterFasta {

            variant_peptides {
                skip_lines = 1
                tx_id_col = 1
                quant_col = 2
                quant_cutoff = 0.001
            }
            noncoding_peptides {
                skip_lines = 1
                tx_id_col = 1
                quant_col = 2
                quant_cutoff = 0.001
            }

        }

But I don't believe filter_fasta was ever run?

executor >  local (2)
[3d/35326d] process > parse_VEP (1)        [  0%] 0 of 1
[9b/6e5f12] process > parse_STARFusion (1) [100%] 1 of 1 ✔
[-        ] process > parse_FusionCatcher  -
[-        ] process > parse_Arriba         -
[-        ] process > parse_REDItools      -
[-        ] process > parse_CIRCexplorer   -
[-        ] process > parse_rMATS          -
[-        ] process > call_variant         -
[-        ] process > summarize_fasta_pre  -
[-        ] process > encode_fasta         -
[-        ] process > decoy_fasta          -
[ 2022-05-07 10:54:41 ] moPepGen parseSTARFusion started
[ 2022-05-07 10:57:47 ] Reference indices loaded.
[ 2022-05-07 10:57:47 ] STAR-Fusion output ACH-000506.txt loaded.
[ 2022-05-07 10:57:47 ] Variants sorted.
[ 2022-05-07 10:57:47 ] Variant info written to disk.
[ 2022-05-07 10:57:50 ] rss=166 MiB, vms=2.192 GiB, wallclock=0:01:31.190000, system=0:00:07.280000, cpu_usage=51.6%

[lydiayliu]

I also did a run without call_variant https://github.com/uclahs-cds/project-MissingPeptides-Method/blob/lyl-test-ccle/src/call-noncanonical/CCLE/meta-call-NonCanonicalPeptide_fasta.config

        entrypoint = 'fasta'
        filter_fasta = true
        split_fasta = true
        encode_fasta = true
        decoy_fasta = true

        filterFasta {

            variant_peptides {
                skip_lines = 1
                tx_id_col = 1
                quant_col = 2
                quant_cutoff = 0.001
            }
            noncoding_peptides {
                skip_lines = 1
                tx_id_col = 1
                quant_col = 2
                quant_cutoff = 0.001
            }

        }

Also didn't show up?

executor >  local (10)
[c1/a0166e] process > resolve_filename_conflict (2) [100%] 2 of 2 ✔
[0d/13a5ff] process > summarize_fasta_pre (1)       [100%] 1 of 1 ✔
[7a/7a9112] process > split_fasta (1)               [100%] 1 of 1 ✔
[52/7be7c4] process > encode_fasta (3)              [100%] 3 of 3 ✔
[78/d848f1] process > decoy_fasta (3)               [100%] 3 of 3 ✔
[ 2022-05-12 21:03:29 ] moPepGen decoyFasta started
[ 2022-05-12 21:03:58 ] Input database FASTA file loaded.
[ 2022-05-12 21:05:01 ] Decoy sequences created.
[ 2022-05-12 21:05:01 ] Number of decoy sequences created: 3218174
[ 2022-05-12 21:05:01 ] Number of decoy sequences overlap with either target or decoy: 0
[ 2022-05-12 21:05:15 ] Decoy database written.
[ 2022-05-12 21:05:20 ] rss=115.2 MiB, vms=2.124 GiB, wallclock=0:01:43.320000, system=0:00:10.030000, cpu_usage=98.4%

Command to run

indir=/hot/project/algorithm/moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/2022-05-06/pipeline-meta-call-NonCanonicalPeptide-0.0.1/
outdir=/hot/project/algorithm/moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/
cd ${outdir}

sbatch --partition F2 --exclusive -J CCLE-test-fasta --mail-type ALL --mail-user YiyangLiu@mednet.ucla.edu -o ${outdir}/log/CCLE-test-fasta.log -e ${outdir}/log/CCLE-test-fasta.err --wrap "nextflow run /hot/users/yiyangliu/project-MissingPeptides-Method/pipelines/pipeline-meta-call-NonCanonicalPeptide/main.nf -c /hot/users/yiyangliu/project-MissingPeptides-Method/src/call-noncanonical/CCLE/meta-call-NonCanonicalPeptide_fasta.config --input_csv ${outdir}/gvf_csvs/CCLE-test.csv --variant_fasta_csv ${outdir}/variant_fasta_csvs/CCLE-test.csv --exprs_table_csv ${outdir}/exprs_table_csvs/CCLE.csv --output_dir ${outdir}/2022-05-09/ --meta_work_dir ${outdir}/work"

[lydiayliu]

nvm issue was due to exprs_table_csv being empty!