kallisto genomebam won't write bam files

Question

[sstewar2]

Hi, and yes I am new to this stuff...

Using kallisto to align RNAseq data downloaded as SRA files. Kallisto quant and pseudobam work fine. Cannot get genomebam to work at all. Wont write the bam files; segmentation fault: 11. I cannot get the kallisto test files to work with genomebam either (same error segmentation fault: 11 when trying to write the bam files) , but again pseudobam works fine.

For the test files I did this

kallisto quant -i transcripts.idx -o gbam --genomebam --gtf transcripts.gtf.gz --chromosome chrom.txt r1.fastq r2.fastq

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 10
[index] number of k-mers: 21,351
[index] number of equivalence classes: 11
Warning: 27 transcripts were defined in GTF file, but not in the index
[quant] running in paired-end mode
[quant] will process pair 1: r1.fastq
                             r2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 9,737 reads, 9,618 reads pseudoaligned
[quant] estimated average fragment length: 500.661
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds
[  bam] writing pseudoalignments to BAM format .. Segmentation fault: 11

And when I do pseudobam I get this:

kallisto quant -i transcripts.idx -o pbam --pseudobam r1.fastq r2.fastq

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 10
[index] number of k-mers: 21,351
[index] number of equivalence classes: 11
[quant] running in paired-end mode
[quant] will process pair 1: r1.fastq
                             r2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 9,737 reads, 9,618 reads pseudoaligned
[quant] estimated average fragment length: 500.661
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds
[  bam] writing pseudoalignments to BAM format .. done

And there's a bam file where it should be with the pseudoalignments.

Suggestions? Could it be an issue with my mac and memory etc?

Why does pseudobam work but not genomebam??

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[sstewar2]

Model Name: MacBook Pro Model Identifier: MacBookPro11,3 Processor Name: Intel Core i7 Processor Speed: 2.5 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 157.0.0.0.0 SMC Version (system): 2.19f12

Hardware UUID: DFC008AA-C2E1-5BC7-8DA9-EEEBF301F259

Available: 31.98 GB (31,975,972,864 bytes) Capacity: 500.07 GB (500,068,036,608 bytes) Mount Point: / File System: APFS Writable: Yes Ignore Ownership: No BSD Name: disk1s5 Volume UUID: 7403075B-9E86-452E-AE0B-5B4A59E362DE Physical Drive: Device Name: APPLE SSD SM0512F Media Name: AppleAPFSMedia Medium Type: SSD Protocol: PCI Internal: Yes Partition Map Type: Unknown S.M.A.R.T. Status: Verified

[Kevin Blighe]

Have you checked that the RAM is not filling up when you do this? Kallisto will also sort the BAM, which can use up a lot of RAM.

Answer 1

[Kevin Blighe]

With --genomebam, you are using up all RAM / memory. That is the simple problem. I can infer this from the error message:

[  bam] writing pseudoalignments to BAM format .. Segmentation fault: 11

What are your system's specifications?

Kevin