getting 'Segmentation fault' while writing pseudoalignments to BAM format in kallisto version 0.50.1

[saurabhinfocusp]

I was running following commands in v0.50.1, but I am unable to generate pseudoalignments bam file (getting Segmentation fault** ) as it was generating in v0.48

Kallisto quant   -i kallisto_index/Zm-B73-REFERENCE-NAM-5.0.idx   -o output_directory-no-jump --no-jump -t 20 --pseudobam ./../sra_data_download/PRJNA1201562/SRR31818013_1.fastq.gz ./../sra_data_download/PRJNA1201562/SRR31818013_2.fastq.gz 

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 687
[index] number of k-mers: 820,598,382
[quant] running in paired-end mode
[quant] will process pair 1: ./../sra_data_download/PRJNA1201562/SRR31818013_1.fastq.gz
                             ./../sra_data_download/PRJNA1201562/SRR31818013_2.fastq.gz
[progress] 24M reads processed (90.6% mapped)              done
[quant] processed 25,108,718 reads, 22,755,468 reads pseudoaligned
[quant] estimated average fragment length: 322.4
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 463 rounds
**[  bam] writing pseudoalignments to BAM format .. Segmentation fault**

Provide me best possible solution for same

[Yenaled]

Pseudobam files are not supported in versions 50+

[SouthernCD]

When running kallisto 0.51.1, even without pseudobam, I got 'Segmentation fault'.

kallisto quant -i Sbicolor_730_v5.1.transcript_primaryTranscriptOnly.fa.kallisto_index -o output_dir -b 100 --bias -t 8 SRR13367649_1.trim.fq.pe.20.fastq SRR13367649_2.trim.fq.pe.20.fastq

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 32,160
[index] number of k-mers: 58,225,694
[quant] running in paired-end mode
[quant] will process pair 1: SRR13367649_1.trim.fq.pe.20.fastq
                             SRR13367649_2.trim.fq.pe.20.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] learning parameters for sequence specific bias
[quant] processed 5 reads, 4 reads pseudoaligned
[quant] estimated average fragment length: 208
[   em] quantifying the abundances ...Segmentation fault

[Yenaled]

bias is not supported either (and even in older versions of kallisto, we don’t really recommend bias)