.log show successful completion, but there is no file

[algaebrown]

Hi!

I run this command

        CIRIquant -t 4 \
            -1 {input.read1} \
            -2 {input.read2} \
            --config {input.yaml} \
            --library-type {params.library_type} \
            -o {params.outdir} \
            -p {params.name} \
            -t 12 \
            --RNaseR {input.rnase_treated_gtf}

the log showed:

[Sun 2022-06-05 20:56:22] [INFO ] De novo alignment for circular RNAs ..
67704673 reads; of these:
  67704673 (100.00%) were paired; of these:
    47403061 (70.01%) aligned concordantly 0 times
    1982294 (2.93%) aligned concordantly exactly 1 time
    18319318 (27.06%) aligned concordantly >1 times
    ----
    47403061 pairs aligned concordantly 0 times; of these:
      4257 (0.01%) aligned discordantly 1 time
    ----
    47398804 pairs aligned 0 times concordantly or discordantly; of these:
      94797608 mates make up the pairs; of these:
        87639670 (92.45%) aligned 0 times
        1025015 (1.08%) aligned exactly 1 time
        6132923 (6.47%) aligned >1 times
35.28% overall alignment rate
[bam_sort_core] merging from 96 files and 12 in-memory blocks...
[Sun 2022-06-05 22:08:21] [INFO ] Detecting reads containing Back-splicing signals
[Sun 2022-06-05 22:17:12] [INFO ] Detecting FSJ reads from genome alignment file
[Sun 2022-06-05 22:31:51] [INFO ] Merge bsj and fsj results
[Sun 2022-06-05 22:31:58] [INFO ] RNase R treatment coefficient correction
[Sun 2022-06-05 22:31:58] [INFO ] Fitting Model
[Sun 2022-06-05 22:32:27] [INFO ] Generate prior distribution ..
[Sun 2022-06-05 22:32:33] [INFO ] Loading annotation gtf ..
[Sun 2022-06-05 22:32:46] [INFO ] Output circRNA expression values
[Sun 2022-06-05 22:34:35] [WARNING] chrom of contig "GL000009.2" not in annotation gtf, please check
[Sun 2022-06-05 22:34:35] [WARNING] chrom of contig "GL000219.1" not in annotation gtf, please check
[Sun 2022-06-05 22:34:35] [WARNING] chrom of contig "KI270742.1" not in annotation gtf, please check
[Sun 2022-06-05 22:34:35] [WARNING] chrom of contig "KI270744.1" not in annotation gtf, please check
[Sun 2022-06-05 22:34:44] [INFO ] circRNA Expression profile: APO-50-A.APO-50-R.gtf
[Sun 2022-06-05 22:34:44] [INFO ] Finished!

but the output file does not exist APO-50-A.APO-50-R.gtf in the filesystem. the .bam file exists though

[Kevinzjy]

Could you show me the output of tree params.outdir ?

[algaebrown]

| |____APO-50-A.APO-50-R_genes.list
| |____APO-50-A.APO-50-R_out.gtf
| |____APO-50-A.APO-50-R_cov.gtf
|____APO-50-A.APO-50-R.log
| |____APO-50-A.APO-50-R.sorted.bam
| |____APO-50-A.APO-50-R.sorted.bam.bai
|____APO-50-A.APO-50-R.bed
| |____APO-50-A.APO-50-R_index.4.ht2
| |____APO-50-A.APO-50-R_index.3.ht2
| |____APO-50-A.APO-50-R_index.2.ht2
| |____APO-50-A.APO-50-R_index.5.ht2
| |____APO-50-A.APO-50-R_denovo.sorted.bam.bai
| |____APO-50-A.APO-50-R.ciri
| |____APO-50-A.APO-50-R_index.fa
| |____APO-50-A.APO-50-R_index.8.ht2
| |____APO-50-A.APO-50-R_index.6.ht2
| |____APO-50-A.APO-50-R_index.1.ht2
| |____APO-50-A.APO-50-R_denovo.sorted.bam
| |____APO-50-A.APO-50-R_index.7.ht2

[Kevinzjy]

| |____APO-50-A.APO-50-R_genes.list
| |____APO-50-A.APO-50-R_out.gtf
| |____APO-50-A.APO-50-R_cov.gtf
|____APO-50-A.APO-50-R.log
| |____APO-50-A.APO-50-R.sorted.bam
| |____APO-50-A.APO-50-R.sorted.bam.bai
|____APO-50-A.APO-50-R.bed
| |____APO-50-A.APO-50-R_index.4.ht2
| |____APO-50-A.APO-50-R_index.3.ht2
| |____APO-50-A.APO-50-R_index.2.ht2
| |____APO-50-A.APO-50-R_index.5.ht2
| |____APO-50-A.APO-50-R_denovo.sorted.bam.bai
| |____APO-50-A.APO-50-R.ciri
| |____APO-50-A.APO-50-R_index.fa
| |____APO-50-A.APO-50-R_index.8.ht2
| |____APO-50-A.APO-50-R_index.6.ht2
| |____APO-50-A.APO-50-R_index.1.ht2
| |____APO-50-A.APO-50-R_denovo.sorted.bam
| |____APO-50-A.APO-50-R_index.7.ht2

This result seems to be truncated?