pseudoaln.bin and tmp.x.bam output files.

[amv33576]

Hello,

I am running kallisto 0.46.2 in a conda environment (Linux).

I used the command:
kallisto quant -i transcript.index -t 4 -b 2 --genomebam --gtf features.gtf --chromosomes chrm_size.txt -o sample sample_R1.fq.gz sample_R2.fq.gz &> out.log

The output directory has the following files:
abundance.h5 run_info.json tmp.10.bam tmp.13.bam tmp.16.bam tmp.19.bam tmp.21.bam tmp.24.bam tmp.27.bam tmp.3.bam tmp.4.bam tmp.7.bam
abundance.tsv tmp.0.bam tmp.11.bam tmp.14.bam tmp.17.bam tmp.2.bam tmp.22.bam tmp.25.bam tmp.28.bam tmp.30.bam tmp.5.bam tmp.8.bam
pseudoaln.bin tmp.1.bam tmp.12.bam tmp.15.bam tmp.18.bam tmp.20.bam tmp.23.bam tmp.26.bam tmp.29.bam tmp.31.bam tmp.6.bam tmp.9.bam

Any suggestions on how to get pseudoalignments.bam and pseudoalignments.bam.bai?

UPDATE: I rolled back to version 0.46.1 and now works

Thanks,

Anyi

[tizilys]

Thanks, I had the same problem!

[njbowen]

Same here, any resolution?

[nehmea]

Probably the kallisto process was killed by the system before finishing due to low memory.