Command failed with exit code 255

MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets

MIT License

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Command failed with exit code 255 #77

Closed Arknights2 closed 3 months ago

Arknights2 commented 3 months ago

Dear Professor

I encountered such an error when using dnbctools to process the offline data

scATAC data were analyzed, and the script followed the github prompts strictly

dnbc4tools atac run \

--fastq1 Sample1_1.fq.gz,Sample2_1.fq.gz \

--fastq2 Sample1_2.fq.gz,Sample2_2.fq.gz \

--genomeDir /human_hg38 \

--name DIPSEQT1 --threads 20

There are no problems in the other several samples for the time being. I sincerely ask how you can solve this error

lishuangshuang0616 commented 3 months ago

Please capture the full error message. I need it for reference.

Arknights2 commented 3 months ago

Sorry for not showing more information about this error

I added this part of the main information in the link

Log file:

2024-06-04 12:49:23, 475-data-ERROR-Command failed with exit code 255

2024-06-04 12:49:23, 476-data-ERROR -

alignment.report.tsv:

Didn't reach the end of sequence file, which might be corrupted!

error.txt

Terminates in the process of generating the 01.data file

lishuangshuang0616 commented 3 months ago

Chromap reported an error when aligning. Can you take a screenshot of the 01.data directory? I might suggest you rerun the command analysis.

Arknights2 commented 3 months ago

Thank you for your reply

I have repeated the calculation three times with the same error

I didn't have this problem when I was dealing with other files, only this sample had a problem, which made me very confused

lishuangshuang0616 commented 3 months ago

This is the first time I have seen this error. I want to see the information in the alignment.report.tsv file.

--fastq1 Sample1_1.fq.gz,Sample2_1.fq.gz \
--fastq2 Sample1_2.fq.gz,Sample2_2.fq.gz \

Is the datas one sample? sample1?sample2?

Arknights2 commented 3 months ago

Thank you for your reply

I have just re-checked the files and the data are samples from the same person

For privacy purposes, I have hidden the path of some files

The alignment.report.tsv file is shown to you as a screenshot

Most of the content is repetitive, such as: "Loaded sequence batch successfully in 0.41s, number of sequences: 500000." and "Mapped 500000 read pairs in 3.99s."

lishuangshuang0616 commented 3 months ago

https://github.com/haowenz/chromap/issues/134 refer to this, check the integrity of the input fastq files.

Arknights2 commented 3 months ago

Thank you for your help, I will go to test as soon as possible！

Arknights2 commented 3 months ago

Thank you very much for your help! I have found the problem and it was indeed due to incomplete fastq files.