Kallisto M1 Macbook Pro · Biostar

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Kallisto M1 Macbook Pro

Trying to run kallisto on new M1 Pro Macbook; 10 core CPU; four paired-end reads in my sample alignment; taking very long time. Is this expected? Am I doing something wrong?

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m1 rnaseq kallisto mac

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updated 4.5 years ago by GenoMax

• written 4.5 years ago by ryancaugustin •

taking very long time

Quantify long time. Can you also provide your command line? Sounds like you are using the -t option already. If the job is running then you need to patient and wait.

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written 4.5 years ago by GenoMax

kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o 21_0566 -t 10 21-0566_S1_L001_R1_001.fastq.gz 21-0566_S1_L001_R2_001.fastq.gz 21-0566_S1_L002_R1_001.fastq.gz 21-0566_S1_L002_R2_001.fastq.gz 21-0566_S1_L003_R1_001.fastq.gz 21-0566_S1_L003_R2_001.fastq.gz 21-0566_S1_L004_R1_001.fastq.gz 21-0566_S1_L004_R2_001.fastq.gz

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written 4.5 years ago by ryancaugustin •

I let it run for 75 minutes before I stopped it

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written 4.5 years ago by ryancaugustin •

Update, ran for 12 hours and still didn't finish

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written 4.5 years ago by ryancaugustin •

Strange. Is this a NovaSeq dataset with billions of reads?

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written 4.5 years ago by GenoMax

Gave up on my first sample (eight fastq files; four pairs) and tried the next sample -- finished within 1 minute! Looked through some of the fastQC reports from the first sample, nothing glaringly stood out. So not sure what's happening with that sample, especially since kallisto seems to be running on it....just not able to finish...Thanks for your input!

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written 4.5 years ago by ryancaugustin •

Files for first sample are likely not corrupt since you ran FastQC on them. Can you try just one pair and see if that completes?

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written 4.5 years ago by GenoMax

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