Error code: SAW-A10400，get signal: 15

[Morriyaty]

Hi,

When I run DNBC4tools via singularity, I got an error like this:

The chemistry(darkreaction) automatically determined in cDNA : darkreaction
The chemistry(darkreaction) automatically determined in oligoR1 : darkreaction
The chemistry(darkreaction) automatically determined in oligoR2 : darkreaction
2023-05-26 23:12:18,992 - data - INFO - Promgram start...
2023-05-26 23:12:18,992 - data - INFO - Promgram start...
2023-05-26 23:12:18,993 - data - INFO - /opt/conda/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/soft/parseFq /data/01/user152/workspace/ScRNA-seq/test/E150009377/01.data/oligo_para
2023-05-26 23:12:18,993 - data - INFO - /opt/conda/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/soft/scStar --outSAMattributes singleCell --outSAMtype BAM Unsorted --genomeDir /data/01/user152/workspace/ScRNA-seq/input_prepare/GS/star --outFileNamePrefix /data/01/user152/workspace/ScRNA-seq/test/E150009377/01.data/ --stParaFile /data/01/user152/workspace/ScRNA-seq/test/E150009377/01.data/cDNA_para --outSAMmode NoQS --runThreadN 20 --limitOutSJcollapsed 10000000 --limitIObufferSize 350000000
2023-5-26  23:12:19 ..... started STAR run
May 26 23:12:19 ..... loading genome
May 26 23:12:40 ..... started mapping
Error code: SAW-A10400
get signal: 15
Terminated

My raw data of one sample is like this:

tree 08-lung_cDNA 08-lung_oligo
08-lung_cDNA
├── E150009377_L01_54_1.fq.gz
├── E150009377_L01_54_2.fq.gz
├── E150009377_L01_54.base.png
├── E150009377_L01_54.qual.png
├── E150009377_L01_62_1.fq.gz
├── E150009377_L01_62_2.fq.gz
├── E150009377_L01_62.base.png
├── E150009377_L01_62.qual.png
├── E150009377_L01_70_1.fq.gz
├── E150009377_L01_70_2.fq.gz
├── E150009377_L01_70.base.png
└── E150009377_L01_70.qual.png
08-lung_oligo
├── 08-lung_oligo_1.fq.gz
├── 08-lung_oligo_2.fq.gz
├── 08-肺_oligo.base.png
└── 08-肺_oligo.qual.png

Is there something wrong in command line? How can I handle this?

/data/00/software/singularity/singularity_built/bin/singularity exec -B /data /data/cold00/user152/SIF/DNBC4tools DNBC4tools run --cDNAfastq1 /data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_cDNA/E150009377_L01_54_1.fq.gz,/data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_cDNA/E150009377_L01_62_1.fq.gz,/data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_cDNA/E150009377_L01_70_1.fq.gz --cDNAfastq2 /data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_cDNA/E150009377_L01_54_2.fq.gz,/data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_cDNA/E150009377_L01_62_2.fq.gz,/data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_cDNA/E150009377_L01_70_2.fq.gz --genomeDir /data/01/user152/workspace/ScRNA-seq/input_prepare/GS/star --gtf /data/01/user152/workspace/ScRNA-seq/input_prepare/GS209-2.final.filter.gtf --name E150009377 --thread 20 --oligofastq1 /data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_oligo/08-lung_oligo_1.fq.gz --oligofastq2 /data/01/user152/workspace/ScRNA-seq/my_data/20230526/08-lung_oligo/08-lung_oligo_2.fq.gz

Bests, Yinjia

[lishuangshuang0616]

The error code SAW-A10400 indicates a memory shortage issue during the analysis process. The step of mapping needs to ensure memory.

[Morriyaty]

Thanks, I have fixed it.

[Morriyaty]

你好，

我遇到了一个warning： Warning! Found a transcript whose gene_id is not equal to that of gene, skip...

这是注释文件的问题吗，需要进行更正么。

期待你的回答，谢谢

[lishuangshuang0616]

Warning! Found a transcript whose gene_id is not equal to that of gene, skip... 很抱歉没有看到，这个问题的原因是gtf文件中基因的名称和他的转录本transcript的gene名称不一致，可以检查一下你的注释文件。

[Bathroomboss]

Hi ! Do i need re-bulid the index under this circumstance? Best, Yu Liang