Error: unspliced. bus has no BUS records

[gabriellayi]

Hi guys,

I'm trying to pre-process my fastq file to get loom files. I'm working on mouse models, so I followed kallisto to build index for ref, I split the index into 8 parts (-n 8). When I ran pre-processing, I put all the index files on the command but seems it's not working, could you please help me with the issue?

Thank you in advance!

Yi

[ryansohny]

Hi, I have the same issue. Have you resolved this problem?

Thank you

[DiyaVaka]

I have the same issue. Can you please let me know how you were able to resolve it

kb count --tmp TMP --keep-tmp -i /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.k_idx -g /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.t2g -o cDNA_3_velocity --workflow lamanno -c1 /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.cdna_t2c.txt -c2 /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.intron_t2c.txt -t 10 -x 10XV3 --overwrite --h5ad $(find . -name "*.fastq.gz" | sort) [2021-12-29 15:47:41,850] INFO Using index /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.k_idx to generate BUS file to cDNA_3_velocity from [2021-12-29 15:47:41,850] INFO ./cDNA_3_S3_L002_R1_001.fastq.gz [2021-12-29 15:47:41,850] INFO ./cDNA_3_S3_L002_R2_001.fastq.gz [2021-12-29 15:47:41,850] INFO ./cDNA_3_S3_L003_R1_001.fastq.gz [2021-12-29 15:47:41,850] INFO ./cDNA_3_S3_L003_R2_001.fastq.gz [2021-12-29 17:06:05,600] INFO Sorting BUS file cDNA_3_velocity/output.bus to TMP/output.s.bus [2021-12-29 17:17:00,950] INFO Whitelist not provided [2021-12-29 17:17:00,951] INFO Copying pre-packaged 10XV3 whitelist to cDNA_3_velocity [2021-12-29 17:17:02,170] INFO Inspecting BUS file TMP/output.s.bus [2021-12-29 17:20:25,067] INFO Correcting BUS records in TMP/output.s.bus to TMP/output.s.c.bus with whitelist cDNA_3_velocity/10xv3_whitelist.txt [2021-12-29 17:22:40,811] INFO Sorting BUS file TMP/output.s.c.bus to cDNA_3_velocity/output.unfiltered.bus [2021-12-29 17:27:18,350] INFO Capturing records from BUS file cDNA_3_velocity/output.unfiltered.bus to TMP/spliced.bus with capture list /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.intron_t2c.txt [2021-12-29 17:30:05,125] INFO Sorting BUS file TMP/spliced.bus to cDNA_3_velocity/spliced.unfiltered.bus [2021-12-29 17:34:23,802] INFO Inspecting BUS file cDNA_3_velocity/spliced.unfiltered.bus [2021-12-29 17:37:21,885] INFO Generating count matrix cDNA_3_velocity/counts_unfiltered/spliced from BUS file cDNA_3_velocity/spliced.unfiltered.bus [2021-12-29 17:42:50,252] INFO Capturing records from BUS file cDNA_3_velocity/output.unfiltered.bus to TMP/unspliced.bus with capture list /home/projects/data/genomes/GRCm38.100/kb/GRCm38.100.cdna_t2c.txt [2021-12-29 17:43:35,386] ERROR An exception occurred Traceback (most recent call last): File "/usr/local/bin/miniconda3/envs/kallisto/lib/python3.9/site-packages/kb_python/main.py", line 837, in main COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir) File "/usr/local/bin/miniconda3/envs/kallisto/lib/python3.9/site-packages/kb_python/main.py", line 197, in parse_count count_velocity( File "/usr/local/bin/miniconda3/envs/kallisto/lib/python3.9/site-packages/kb_python/count.py", line 1567, in count_velocity capture_result = bustools_capture( File "/usr/local/bin/miniconda3/envs/kallisto/lib/python3.9/site-packages/kb_python/validate.py", line 124, in inner validate(arg) File "/usr/local/bin/miniconda3/envs/kallisto/lib/python3.9/site-packages/kb_python/validate.py", line 85, in validate VALIDATORSext File "/usr/local/bin/miniconda3/envs/kallisto/lib/python3.9/site-packages/kb_python/validate.py", line 40, in validate_bus raise FileVerificationFailed('{} has no BUS records'.format(path)) kb_python.validate.FileVerificationFailed: TMP/unspliced.bus has no BUS records