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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 by GenoMax 16K • | written by ryancaugustin 0

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 by GenoMax 16K 
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 by ryancaugustin 0

I let it run for 75 minutes before I stopped it

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written by ryancaugustin 0

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

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written by ryancaugustin 0

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

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written by GenoMax 16K

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 by ryancaugustin 0

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 by GenoMax 16K

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