cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
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13 months ago
Yingying • 0

Hi all, I'm attempting to use cellranger-arc mkfastq to convert BCL files to FASTQ files, but encountered with errors and would like help from you.

Command I ran is:

cellranger-arc mkfastq --id=ATAC1_fastq \
> --run=/mnt/c/Users/helen/Desktop/Analysis/Raw_bcl_files/ATAC1/230120_NB551308_0209_AH5W5LBGXN \
> --csv=/mnt/c/Users/helen/Desktop/Analysis/230120_NB551308_0209_AH5W5LBGXN.csv \
> --localcores=4

Error messsage is:

Running preflight checks (please wait)...
Checking run folder...
Checking RunInfo.xml...
Checking system environment...
Emitting run information...
Checking read specification...
Checking samplesheet specs...
2023-02-03 11:03:25 [runtime] (ready)           ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET
2023-02-03 11:03:25 [runtime] (run:local)       ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET.fork0.chnk0.main
2023-02-03 11:03:25 [runtime] (chunks_complete) ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET
2023-02-03 11:03:25 [runtime] (ready)           ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET
2023-02-03 11:03:25 [runtime] (run:local)       ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET.fork0.split
2023-02-03 11:03:25 [runtime] (split_complete)  ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET
2023-02-03 11:03:25 [runtime] (run:local)       ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET.fork0.chnk0.main
2023-02-03 11:03:26 [runtime] (failed)          ID.ATAC1_fastq.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET

**[error] bcl2fastq was killed with signal -11.**

Sequencing data were generated by NextSeq-550. And I'm running cellranger-arc-2.0.2 in WLS Ubuntu 20.04 LTS. Illumina bcl2fastq v2.20.0.422 was installed.

Does anyone know what this error means? Is it because of short of memory since it was only using 28GB RAM.

Help please! Thank you!

bcl2fastq cellranger-arc mkfastq cellranger • 1.6k views
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You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about uploading it directly to get help.

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Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.

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Hello Yingying! I have the same problem, did you have an answer?

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Hi, it seems like my bcl2fastq from Illumina wasn't installed correctly. You may try running bcl2fastq directly to check if it is working. Unfortunately, I couldn't get it installed in my Ubuntu. But if you are using other Linux distributions, you can ask Illumina for support!

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Thanks for your help! I sent a message to Illumina support. The bcl2fastq is working. I don't know why it is not running using the cellranger mkfastq package. The Illumina support sent me a message yesterday but the solution isn't working.

If I will have a solution I will send it to you.

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I have the issue, did you find a solution please

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