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  1. Barna Package
  2. BARNA-261

Capacitor complains about read descriptor for bam files

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      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.

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            emilio Emilio Palumbo
            aesteve Anna Esteve
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              Updated:
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