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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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dnbc4rna run报错- data - ERROR Command failed with exit code -6 #54

Closed ZiggeyQi closed 5 months ago

ZiggeyQi commented 5 months ago

技术团队的老师您好，不好意思打扰到您，我想用dnbc4tools rna multi运行多个样品时报错如下： Traceback (most recent call last): File "/home/liunyw/miniforge3/envs/DNBC4tools/bin/dnbc4tools", line 8, in sys.exit(main()) File "/home/liunyw/miniforge3/envs/DNBC4tools/lib/python3.8/site-packages/dnbc4tools/dnbc4tools.py", line 58, in main args.func(args) File "/home/liunyw/miniforge3/envs/DNBC4tools/lib/python3.8/site-packages/dnbc4tools/rna/multi.py", line 86, in multi Multi_list(args).run() File "/home/liunyw/miniforge3/envs/DNBC4tools/lib/python3.8/site-packages/dnbc4tools/rna/multi.py", line 33, in run cDNAr1 = get_abspath(lst[1].split(';')[0]) IndexError: list index out of range 但是我发现在我设定的output文件中已经成功生成了单个样品dnbc4tools rna run的代码，查看后也觉得没有问题，所以我就直接运行了output文件中生成的samplename.sh文件，生成代码如下： /home/liunyw/miniforge3/envs/DNBC4tools/bin/dnbc4rna run --name H1 --cDNAfastq1 /home/liunyw/qhs_data/0.rawdata/H1/6788-1-231129/cDNA-6788-1-231129/DP8480003117TL_L01_38_1.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-1-231129/cDNA-6788-1-231129/DP8480003122TL_L01_38_1.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-2-231129/cDNA-6788-2-231129/DP8480003117TL_L01_39_1.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-2-231129/cDNA-6788-2-231129/DP8480003122TL_L01_39_1.fq.gz --cDNAfastq2 /home/liunyw/qhs_data/0.rawdata/H1/6788-1-231129/cDNA-6788-1-231129/DP8480003117TL_L01_38_2.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-1-231129/cDNA-6788-1-231129/DP8480003122TL_L01_38_2.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-2-231129/cDNA-6788-2-231129/DP8480003117TL_L01_39_2.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-2-231129/cDNA-6788-2-231129/DP8480003122TL_L01_39_2.fq.gz --oligofastq1 /home/liunyw/qhs_data/0.rawdata/H1/6788-1-231129/oligo-6788-1-231129/DP8480003322TL_L01_62_1.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-2-231129/oligo-6788-2-231129/DP8480003322TL_L01_63_1.fq.gz --oligofastq2 /home/liunyw/qhs_data/0.rawdata/H1/6788-1-231129/oligo-6788-1-231129/DP8480003322TL_L01_62_2.fq.gz,/home/liunyw/qhs_data/0.rawdata/H1/6788-2-231129/oligo-6788-2-231129/DP8480003322TL_L01_63_2.fq.gz --genomeDir /home/liunyw/qhs_data/genome/mm10_hsv --threads 60 在运行samplename.sh脚本后，发现报错如下： The chemistry(darkreaction) automatically determined in cDNA : darkreaction The chemistry(darkreaction) automatically determined in oligoR1 : darkreaction The chemistry(darkreaction) automatically determined in oligoR2 : darkreaction 2024-01-13 19:32:53 Processing cDNA library barcodes and aligning. 2024-01-13 19:32:53 Processing oligo library barcodes. 2024-01-13 22:38:45 Annotating BAM files. 2024-01-13 22:39:33,942 - data - ERROR Command failed with exit code -6 2024-01-13 22:39:33,942 - data - ERROR 2024-01-13 22:39:32.796 W process: stoi terminate called after throwing an instance of 'std::runtime_error' what(): Failed makeOverlapDetector! Please check annotation file format. 2024-01-13 22:39:34,040 - data - ERROR Command failed with exit code 1 2024-01-13 22:39:34,041 - data - ERROR [E::hts_open_format] Failed to open file "/home/liunyw/qhs_data/matrix/output/H1/01.data/final.bam" : No such file or directory samtools sort: can't open "/home/liunyw/qhs_data/matrix/output/H1/01.data/final.bam": No such file or directory

Error: Cannot find input file or dir /home/liunyw/qhs_data/matrix/output/H1/01.data/final_sorted.bam

Error: Cannot find input file or dir /home/liunyw/qhs_data/matrix/output/H1/02.count/filter_feature.h5ad

2024-01-13 22:40:01 Summarizing results and generating a report.

Error: Cannot find input file or dir /home/liunyw/qhs_data/matrix/output/H1/02.count/cutoff.csv

Analysis Finished Elapsed Time: 3 hours 7 minutes 37 seconds 最终只生成了01.data和04.report文件夹，但是04.report文件夹里是空的，01.data文件夹内容如下： drwxrwxr-x. 2 liunyw liunyw 4.0K Jan 13 22:39 . drwxrwxr-x. 5 liunyw liunyw 65 Jan 13 22:40 .. -rw-rw-r--. 1 liunyw liunyw 55M Jan 13 22:38 cDNA_barcode_counts_raw.txt -rw-rw-r--. 1 liunyw liunyw 392 Jan 13 19:32 cDNAin1 -rw-rw-r--. 1 liunyw liunyw 392 Jan 13 19:32 cDNAin2 -rw-rw-r--. 1 liunyw liunyw 509 Jan 13 19:32 cDNA_para -rw-rw-r--. 1 liunyw liunyw 391 Jan 13 22:38 cDNA_sequencing_report.csv -rw-rw-r--. 1 liunyw liunyw 39M Jan 13 20:26 Index_barcode_counts_raw.txt -rw-rw-r--. 1 liunyw liunyw 12G Jan 13 20:26 Index_reads.fq.gz -rw-rw-r--. 1 liunyw liunyw 378 Jan 13 20:26 Index_sequencing_report.csv -rw-rw-r--. 1 liunyw liunyw 2.0K Jan 13 22:38 Log.final.out -rw-rw-r--. 1 liunyw liunyw 11K Jan 13 22:38 Log.out -rw-rw-r--. 1 liunyw liunyw 22K Jan 13 22:38 Log.progress.out -rw-rw-r--. 1 liunyw liunyw 773 Jan 13 19:32 oligo_para -rw-rw-r--. 1 liunyw liunyw 45M Jan 13 22:38 SJ.out.tab 在star比对过程中是有align.bam文件的，因为是晚上跑的不知道中途发生了什么，早上来就发现上面的报错，bam文件也不见了，于是我就去检查了star比对的log文件，也没有发现明显的问题。还需要说明一下的是，比对使用的是mouse和病毒基因组合在一起的fa文件，病毒的gtf文件也是我自己修改过的，在运行了tools mkgtf和rna mkref这两个代码后能在输出的geneinfo和transcriptsinfo文件中看到病毒的基因信息，但是我害怕我修改的gtf文件有问题，所以我就把star比对的log文件和病毒修改后的gtf文件都上传了，mouse的genome和gtf文件就是按quickstar里的链接下载的，辛苦老师您帮忙看看我这个报错是哪里的问题，该如何解决，谢谢 log和gtf文件 GCF_000859985.2_ViralProj15217_genomic_edited_gtf.txt Log.final.txt Log.progress.txt Log.txt