Lioscro
commented
3 years ago That error usually occurs when the process is out of usable memory. How much memory do you have on your machine?
Closed XYZuo closed 3 years ago
Lioscro
commented
3 years ago That error usually occurs when the process is out of usable memory. How much memory do you have on your machine?
rameshbalan
commented
3 years ago I get the same error too! I tried with the default, 64G and 120G memory.
Command:
kb count -i index.idx -g t2g.txt -x 10xv3 --workflow lamanno --overwrite --loom -c1 cdna_t2c.txt -c2 intron_t2c.txt reads/sample_S1_L001_R1_001.fastq.gz reads/sample_S1_L001_R2_001.fastq.gz -t 24 -m 64G
[2021-03-13 20:56:06,381] INFO Using index index.idx to generate BUS file to . from
[2021-03-13 20:56:06,381] INFO reads/sample_S1_L001_R1_001.fastq.gz
[2021-03-13 20:56:06,381] INFO reads/sample_S1_L001_R2_001.fastq.gz
[2021-03-13 21:16:10,398] ERROR
[index] k-mer length: 31
[index] number of targets: 0
[index] number of k-mers: 0
[index] number of equivalence classes: 0
[quant] will process sample 1: reads/sample_S1_L001_R1_001.fastq.gz
reads/sample_S1_L001_R2_001.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 419,679,501 reads, 0 reads pseudoaligned[~warn] no reads pseudoaligned.
[2021-03-13 21:16:10,399] ERROR An exception occurred
Traceback (most recent call last):
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/main.py", line 837, in main
COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir)
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/main.py", line 218, in parse_count
temp_dir=temp_dir
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/count.py", line 1510, in count_velocity
fastqs, index_paths[0], technology, out_dir, threads=threads
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/validate.py", line 112, in inner
results = func(*args, **kwargs)
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/count.py", line 149, in kallisto_bus
run_executable(command)
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/dry/__init__.py", line 24, in inner
return func(*args, **kwargs)
File "/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/utils.py", line 233, in run_executable
raise sp.CalledProcessError(p.returncode, ' '.join(command))
subprocess.CalledProcessError: Command '/home/user/miniconda3/envs/scRNA/lib/python3.6/site-packages/kb_python/bins/linux/kallisto/kallisto bus -i index.idx -o . -x 10xv3 -t 24 reads/sample_S1_L001_R1_001.fastq.gz reads/sample_S1_L001_R2_001.fastq.gz' returned non-zero exit status 1.Solutions Tried (Unsuccessfully):
I think it maybe an issue with bustools and not the way the wrappers invoke the program
Lioscro
commented
3 years ago Hi, @rameshbalan,
This is a different error than the one posted by @ZxyChopcat.
Your error is due to kallisto failing to pseudoalign any reads. I notice that there are zero targets, kmers, and equivalence classes.
This is most likely due to your index file. Please open a new issue if you are still having this problem. We can help you out there.
XYZuo
commented
3 years ago Thanks a lot for your reply!
I solved this issue by building the index again.
kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa -c1 cdna_t2c.txt -c2 intron_t2c.txt --workflow lamanno \ Homo_sapiens.GRCh38.dna.toplevel.fa.gz \ Homo_sapiens.GRCh38.97.gtf.gz
Maybe there were some problem when I build the index.
Hi, I ran kb count on my data which is 10Xv3.I had a similar error with issue 19(https://github.com/pachterlab/kallistobustools/issues/19) I'm sure my data should be 10XV3.Even if I changed the parameter '-x' to 10XV2 or 10XV1,the error still exists. My code: `kb count -i index.idx -g t2g.txt -x 10xv3 -o P01_SCC \
My example file:
`(zxy-kb) [zuoxinyi@es_node1 kb]$ zcat /lab_file_oridata/ITP/P01_SCC/Rawdata/P01_SCC_1.fq.gz | head @A00199:369:HGHWVDSXX:4:1101:1154:1016 1:N:0:ACTTCATA+TCTTTCCC NGGATAATCAACGTGTCCACGCGTGTACTAATCTATGATCTCACAGAGAGACAGTTTTGTTATAACTCTAAATTCTTGATGTTACACTATAACTCTACAGCCCGGGAACAGTGGCTCATGCCTGTAAACCCAGCAGTTTTGTGAGGCCAT +
FFFFFFFFFFFFFFFFFFFFFFFFFFFF::,F:F:,F,:::,,,,,,,,,,,,F:,:::F,,,,,:,:,,FF,FF:FF:FFF,:::,,,FFF,FF:FFFF:,:FF::FFF:::F::,FFF,FFFFF,FFF::FFF:FFF,F:,,:FFF,
@A00199:369:HGHWVDSXX:4:1101:1913:1016 1:N:0:ACTTCATA+TCTTTCCC NACAGGTTCGGAGTAGAGATGCTTTTCGTAAATATTGAGATCAGACTCTCTCTCTTGAAAAAAAAAAATTTTATTAAAATCAGTAGATTAGTCTCAGGAAGAACGTACAAATAATTTACAAAATTTAAACAACACAACAATCAGCTCACC +
FFFFFFFFFFFFFFFFFFFFFFFFFFF,F,,:FF,::,,:,,,,,F,:,:,:,FF,F,FF:,FFF:,F,:,::FF:FF,:F,F,:,,,,:,,,F:FF,,:,F::,,FF,F,FF,,:,,:,FF,,,FF:FF,,,:F::FF:FF,FF,:,F
@A00199:369:HGHWVDSXX:4:1101:2474:1016 1:N:0:ACTTCATA+TCTTTCCC NATGCTAGTAATCAAGTATTCAGAAGGCGGCGCCGGCACTTAAAACACACACATTTTTTTCACAGGGGCTAGGCGGAGGTGATTTGGGGCACACCCCGAGGAGGGCCCCGCGCCAAGAATACGGTGTTGGGGGGCGTGGTGGTGGAGCGT (zxy-kb) [zuoxinyi@es_node1 kb]$ zcat /lab_file_oridata/ITP/P01_SCC/Rawdata/P01_SCC_2.fq.gz | head @A00199:369:HGHWVDSXX:4:1101:1154:1016 2:N:0:ACTTCATA+TCTTTCCC CGAAATAAAGTGTGGAGGCCAGGCGTGGTGGCTCACGGTTGTGATCCCAGGTAGCTGGGATTACAGGCGTGCACCACTACCACCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTC + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00199:369:HGHWVDSXX:4:1101:1913:1016 2:N:0:ACTTCATA+TCTTTCCC TATAGCTGTTTGTGATGATGCCAGTATTTGGCGCTGGGATCGACTTCGATAAAATACTTTTGCCTAATCAAAATTAGAGTGTGTTTGTTGTCTGTGTAAAATAGAATTAATGTATCTTGCTAGTAAGGGCACGTAGAGCATTTAGAGTTG + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00199:369:HGHWVDSXX:4:1101:2474:1016 2:N:0:ACTTCATA+TCTTTCCC TGGGTGCCCGGCACCGCGCCCGAGCCCACTCCATTCAGATCATGAAGGTGGAGGAGATCGCGGCCAGCAAGTGCCGCCGGCCGGCTGTCAAGCAGTTCCACGACTCCAAGATCAAGTTCCCGCTGCCCCACCGGGTCCTGCGCCGTCAGC `
Could someone please help with this? Thanks!