Closed santhanakrishnanb closed 1 month ago
That looks like a FASTQ formatting error. Can you share the results of head -n 20 trimmed_CP045063.1.fastq
?
LOCUS CP045063 4930420 bp DNA circular BCT 12-NOV-2019 DEFINITION Salmonella enterica subsp. enterica serovar Muenchen strain LG26 chromosome, complete genome. ACCESSION CP045063 VERSION CP045063.1 DBLINK BioProject: PRJNA576706 BioSample: SAMN13002973 KEYWORDS . SOURCE Salmonella enterica subsp. enterica serovar Muenchen ORGANISM Salmonella enterica subsp. enterica serovar Muenchen Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella. REFERENCE 1 (bases 1 to 4930420) AUTHORS Tran,T.D., McGarvey,J.A., Huynh,S. and Parker,C.T. TITLE Genome sequence of Salmonella Muenchen str. LG26 JOURNAL Unpublished REFERENCE 2 (bases 1 to 4930420) AUTHORS Tran,T.D., McGarvey,J.A., Huynh,S. and Parker,C.T. TITLE Direct Submission JOURNAL Submitted (09-OCT-2019) Foodborne Toxin Detection and Prevention
Okay, yeah, this is not at all a FASTQ file. It looks like maybe you saved a request for a FASTQ file instead of the file itself?
yeah, this is not at all a FASTQ file. It looks like maybe you saved a request for a FASTQ file instead of the file itself?
The above output is the header to it. Attached is the complete file. I have tried with other fastq files downloaded from NCBI, but with similar results.
That isn't a FASTQ either. These seem to be raw NCBI data pages. Check out the wiki to see some examples of what FASTQ files look like: https://en.wikipedia.org/wiki/FASTQ_format
1. What were you trying to do? 2. What did you want to happen?
I was trying to map a new fastq file to a graph generated using a few genome sequences.
Step 1: vg construct -r Ref_genes.fasta > output.vg was succesful.
Step 2: vg index -x output.xg -g output.gcsa output.vg was succesful.
Step 3: vg map -x output.xg -g output.gcsa -f CP019206.1.fastq > mapped_reads.gam is where it got stuck.
3. What actually happened?
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt
, please copy-paste the contents of that file here:sb3700@cvm-Lambda-Vector: vg map -x output.xg -g output.gcsa -f trimmed_CP045063.1.fastq > mapped_reads.gam
terminate called after throwing an instance of 'std::runtime_error' what(): Found unexpected delimiter in fastq/fasta input ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.56.0 "Collalto" Stack trace (most recent call last) in thread 2077364:
14 Object "", at 0xffffffffffffffff, in
13 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7f719a52684f, in __clone3
12 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7f719a494ac2, in start_thread
11 Object "/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0", at 0x7f719abdbc0d, in
10 Object "/home/sb3700/Adam_Data/pggb/vg/bin/vg", at 0x56289717fb29, in unsigned long vg::io::unpaired_for_each_parallel(std::function<bool (vg::Alignment&)>, std::function<void (vg::Alignment&)>, unsigned long) [clone ._omp_fn.0]
9 Object "/home/sb3700/Adam_Data/pggb/vg/bin/vg", at 0x5628967de82c, in vg::get_next_alignment_from_fastq(gzFile_s, char, unsigned long, vg::Alignment&) [clone .cold]
8 Object "/usr/lib/x86_64-linux-gnu/libgcc_s.so.1", at 0x7f719abb52dc, in _Unwind_Resume
7 Object "/usr/lib/x86_64-linux-gnu/libgcc_s.so.1", at 0x7f719abb4883, in
6 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7f719a8ad958, in __gxx_personality_v0
5 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7f719a8ad1e8, in
4 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7f719a8ae20b, in
3 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7f719a8a2b9d, in
2 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7f719a4287f2, in abort
1 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7f719a442475, in raise
0 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7f719a4969fc, in pthread_kill@@GLIBC_2.34
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report!