unable to exit the program and no output (*.corset-reads) was generated

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Ting-Hsuan Chen

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Apr 1, 2022, 2:59:22 AM4/1/22

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Hi,

I used the following steps to generate the bam files for Corset:
1. de novo assembly using Trinity
2. Select a subset of transcripts that are likely to contain CDS by EvidentialGene
3. Mapping sequencing reads to the transcript subset mentioned above using bowtie2 (with -k 100)
Then I tried to generate the equivalence class information of a bam file using Corset.
I used this code "corset -r true-stop $BAM" but it seemed to get stuck after reading the bam file.

The terminal showed something like:
1843.2 million alignments read
1843.4 million alignments read
1843.6 million alignments read
Done reading 041_BCP7656.species_ok.bam

It just held there without exiting the program or generating any output file.
Could you please advise me where could be the problem from and how to solve it?
I was using Corset v1.09.

Much appreciated,

Ting

Nadia Davidson

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Jul 4, 2022, 2:53:12 AM7/4/22

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Dear Ting,

Sorry for the slow reply. You have a lot of alignments to process for the .bam file, so I suspect corset was still processing this. You could try running version 1.07 of corset which behaves slightly differently in it memory usage at this stage and may be faster.

Cheers,

Nadia.

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