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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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how would you convert the output of dnbc2tools to count matrix #78

Closed sherry1000001 closed 3 months ago

sherry1000001 commented 3 months ago

i got the output dir below:

微信图片_20240606153309

which software or codes can be used to generate count matrix ?

lishuangshuang0616 commented 3 months ago

You haven't finished the analysis. Check if it is still analyzing. If it is interrupted, check if there is any error message. Or send me the files in the log directory.

sherry1000001 commented 3 months ago

i think it was interrupted without any errors or warnings, because i got the output in my shell

Chemistry(darkreaction) determined in oligoR1 : darkreaction Chemistry(darkreaction) determined in oligoR2 : nodarkreaction Chemistry(darkreaction) determined in cDNAR1 : darkreaction 2024-06-06 06:13:58 Conduct quality control for cDNA library barcoding, perform alignment. 2024-06-06 06:13:58 Perform quality control for oligo library barcodes. Chemistry(darkreaction) determined in oligoR1 : darkreaction Chemistry(darkreaction) determined in oligoR2 : nodarkreaction Chemistry(darkreaction) determined in cDNAR1 : darkreaction 2024-06-06 06:39:09 Conduct quality control for cDNA library barcoding, perform alignment. 2024-06-06 06:39:09 Perform quality control for oligo library barcodes.

the log directory contains two files:"_bt_log" and "20240606.txt" "_bt_log" is a null file and "20240606.txt" is copied as below

/miniconda3/envs/dnbc4tools/bin/dnbc4tools rna data --cDNAfastq1 /RawData/P13-cDNA/E200018737_L01_P13-cDNA_1.fq.gz --cDNAfastq2 /RawData/P13-cDNA/E200018737_L01_P13-cDNA_2.fq.gz --oligofastq1 /RawData/P13-oligo/E200018737_L01_P13-oligo_1.fq.gz --oligofastq2 /RawData/P13-oligo/E200018737_L01_P13-oligo_2.fq.gz --threads 10 --name P13 --chemistry auto --darkreaction auto --genomeDir /reference --gtf /reference/genes.filter.gtf --chrMT chrM 2024-06-06 06:14:00,621 - INFO - cDNAR1 fastq includes 2024-06-06 06:14:00,622 - INFO - 2024-06-06 06:14:00,622 - INFO - /RawData/P13-cDNA/E200018737_L01_P13-cDNA_1.fq.gz 2024-06-06 06:14:00,622 - INFO - 2024-06-06 06:14:00,641 - INFO - cDNAR2 fastq includes 2024-06-06 06:14:00,641 - INFO - 2024-06-06 06:14:00,641 - INFO - /RawData/P13-cDNA/E200018737_L01_P13-cDNA_2.fq.gz 2024-06-06 06:14:00,641 - INFO - 2024-06-06 06:14:00,664 - INFO - cDNA fastq config file /miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/config/cellbarcode/scRNA_beads_darkReaction.json 2024-06-06 06:14:00,664 - INFO - 2024-06-06 06:14:00,693 - INFO - olgioR1 fastq includes 2024-06-06 06:14:00,693 - INFO - 2024-06-06 06:14:00,693 - INFO - ['/RawData/P13-oligo/E200018737_L01_P13-oligo_1.fq.gz'] 2024-06-06 06:14:00,693 - INFO - 2024-06-06 06:14:00,693 - INFO - olgioR2 fastq includes 2024-06-06 06:14:00,693 - INFO - 2024-06-06 06:14:00,693 - INFO - ['/RawData/P13-oligo/E200018737_L01_P13-oligo_2.fq.gz'] 2024-06-06 06:14:00,693 - INFO - 2024-06-06 06:14:00,693 - INFO - oligo fastq config file /miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/config/cellbarcode/scRNA_oligo_R2_noDarkReaction.json 2024-06-06 06:14:00,693 - INFO - 2024-06-06 06:14:00,737 - data - INFO - Executing command: /miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/scStar --outSAMattributes singleCell --outSAMtype BAM Unsorted --genomeDir /reference --outFileNamePrefix ../01.data/ --stParaFile /P13/01.data/cDNA_para --outSAMmode NoQS --runThreadN 10 --limitOutSJcollapsed 10000000 --limitIObufferSize 350000000 2024-06-06 06:14:00,737 - data - INFO - Executing command: /miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/parseFq /P13/01.data/oligo_para 2024-06-06 06:22:32,540 - data - INFO - mapped_dnbs: 2316986

and i checked the other samples' outputs dir, the '01.data' dir contains only 2 files cDNAin1 and cDNBin2 Please help me figure it out thx!!

lishuangshuang0616 commented 3 months ago

It looks like there is definitely an error. But there should also be an error message. Are you delivering the cluster or running it directly with sh? If it is delivering, is there no error recorded in the .e file?

sherry1000001 commented 3 months ago

nope, the output .sh.e* file is null.

微信图片_20240606175756

Have you run into this issue before, or did u update this repository. I wrote a loop to run 6 samples but none of them gave an error. source activate dnbc4tools for i in 'P13' 'P14' 'P15' 'M10' 'M18' 'M11' do dnbc4tools rna run \ --cDNAfastq1 ~/aging/RawData/${i}-cDNA/*_1.fq.gz \ --cDNAfastq2 ~/aging/RawData/${i}-cDNA/*_2.fq.gz \ --oligofastq1 ~/aging/RawData/${i}-oligo/*_1.fq.gz \ --oligofastq2 ~/aging/RawData/${i}-oligo/*_2.fq.gz \ --genomeDir ~/reference \ --name ${i} --outdir ~/aging/ --threads 10 done

lishuangshuang0616 commented 3 months ago

Didn't see any error message, which is strange. Please try to run a single sample and I will take a look at the information of single sample analysis.

sherry1000001 commented 3 months ago

These tasks were finished by 'qsub' one by one instead of a loop function. So what is the difference between the each circle and one tasks each time? By the way, thank u for your answering^-^

lishuangshuang0616 commented 3 months ago

There is no difference. I just want to see the exact error message when running a single sample. Because I saw that you submitted several samples, but there was not much output in the .o file. I am not sure if it is because of waiting or other reasons. If you run a single sample completely and let its log output be complete, you may be able to see the error message.