3d-dna
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aidenlab
tail: +: invalid number of bytes with run-asm-pipeline.sh in haploid mode
Hello ! I hope for some solutions for my questions. My Bash version is: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu), and my 3d-dna version is version 180114. When running run-asm-pipeline.sh in haploid mode, I got a wrong FINAL fasta with full of N's. And when I set -s finalize to rerun run-asm-pipeline.sh, I got a run.log with content like this: /home/line/local/app/3d-dna/run-asm-pipeline.sh -r 2 -s finalize /mnt/5E100E34100E1425/CYM/01_Genome/output/02_polish/next_polish/02_rundir/genome.nextpolish.fasta /mnt/5E100E34100E1425/CYM/01_Genome/output/04_hic/juicer/aligned/merged_nodups.txt version: 180922 -r|--rounds flag was triggered, will run 2 round(s) of misjoin correction. -s|--stage flag was triggered, fast-forwarding to "finalize" pipeline section. ############### Finilizing output: ... -s flag was triggered, treating all contigs/scaffolds shorter than 15000 as unattempted. ... -l flag was triggered. Output will appear with headers of the form genome.nextpolish_hic_scaffold_#. ... -g flag was triggered, making gap size between scaffolded draft sequences to be equal to 500. Analyzing the merged assembly ...trimming N overhangs ...adding gaps tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes tail: +: invalid number of bytes
How can I solve it?
And my first run with run-asm-pipeline.sh get the error.log with many like these: nohup: ignoring input :| Warning: no explicit bundle size was listed. Will use the same one as listed for false positive size threshold: this is the most typical scenario. :| Warning: No input for label1 was provided. Default for label1 is ":::fragment_" :| Warning: No input for label2 was provided. Default for label2 is ":::debris" :| Warning: No input for label1 was provided. Default for label1 is ":::fragment_" :| Warning: No input for label2 was provided. Default for label2 is ":::debris" :| Warning: No input for label1 was provided. Default for label1 is ":::fragment_" :| Warning: No input for label2 was provided. Default for label2 is ":::debris" ... Is this the problems?
I check my the lengthes in mismatch_narrow.at.step.0.bed, with awk '{print $3-$2}' mismatch_narrow.at.step.0.bed | sort -k1,1nr | head, my results are: 143000 126000 113000 101000 98000 92000 89000 87000 81000 81000
If there anyone can help me? For I have sent questions in 3d-dna groups, but I have not approved.
try to check the assembly file, may be there are same comtigs with wrong length
