Details
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Bug
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Status: Resolved
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Major
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Resolution: Fixed
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Capacitor 1.2 (API 1.17)
Description
I tried to run the capacitor with a bam file and this error has been reported:
[ERROR] You cannot specify the read descriptor when using BAM input files.
Here is the command and output:
flux-capacitor --threads 4 -i ../bams/CF_10_CGATGT_L005_R1_001.bam -o CF_10_gencode.gtf -r -a /project/devel/rna_pipeline/data/annotations/hg/gencode_v12.gtf
Flux-Capacitor v1.2.1-SNAPSHOT (Flux Library: 1.18-SNAPSHOT)
[PRE-CHECK] I am checking availability of the required lpsolve JNI libs.
[PRE-CHECK] * successfully loaded lpsolve JNI (version 5.5,release 0,build 14)
Scanning annotation file Checking GTF ********** OK (00:00:19)
scanning [WARN] skipped line chr1 HAVANA gene 11869 14412 . + . transcript_id "ENSG00000223972.4"; havana_gene "OTTHUMG00000000961.2"; level "2"; transcript_name "DDX11L1"; gene_name "DDX11L1"; transcript_status "KNOWN"; gene_id "ENSG00000223972.4"; gene_type "pseudogene"; transcript_type "pseudogene"; gene_status "KNOWN";
OK (00:01:12)
[WARN] Skipped 724375 lines.
[INFO] 45013 loci, 183086 transcripts, 1188378 exons.
OK (00:01:12)
Scanning mapping file OK (00:02:44)
[WARN] Skipped 148178 lines.
[INFO] 21330986 reads, 63678600 mappings: R-factor 2.9852629
[INFO] 62707765 entire, 970835 split mappings (0.1524586%)
[ERROR] You cannot specify the read descriptor when using BAM input files.