lcoombe
commented
5 years ago Hi @ewafula ,
Could you please enclose copy-and-paste blocks in triple back ticks? Using that formatting will make your pasted commands much easier to read. (https://help.github.com/articles/basic-writing-and-formatting-syntax/#quoting-code)
It looks like the error you are getting in tigmint-cut is very similar to what a user saw in a previous issue reported in the ARCS repo: https://github.com/bcgsc/arcs/issues/48
Try using a newer version of bedtools - I use v2.27.1 and don't get any errors.
Hope that helps! Lauren
tigmint-make fails after running for a day. I am not sure exactly how to deal with the error.
########################### run log #####################
[main] CMD: bwa mem -t50 -pC merged.fa barcoded.fq.gz [main] Real time: 19582.030 sec; CPU: 744783.844 sec [bam_sort_core] merging from 400 files and 50 in-memory blocks... /usr/local/bin/tigmint-molecule -a0.65 -n5 -q0 -d50000 -s2000 merged.barcoded.sortbx.bam | sort -k1,1 -k2,2n -k3,3n >merged.barcoded.as0.65.nm5.molecule.size2000.bed samtools faidx merged.fa /usr/local/bin/tigmint-cut -p50 -w1000 -n20 -t0 -o merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa merged.fa merged.barcoded.as0.65.nm5.molecule.size2000.bed Started at: 2019-03-04 01:32:53.356125 Reading contig lengths... Finding breakpoints... Cutting assembly at breakpoints...
Tool: bedtools getfasta (aka fastaFromBed) Version: v2.21.0 Summary: Extract DNA sequences into a fasta file based on feature coordinates.
Usage: bedtools getfasta [OPTIONS] -fi -bed <bed/gff/vcf> -fo
Options: -fi Input FASTA file -bed BED/GFF/VCF file of ranges to extract from -fi -fo Output file (can be FASTA or TAB-delimited) -name Use the name field for the FASTA header -split given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons) -tab Write output in TAB delimited format.
Default is FASTA format.
By default, strand information is ignored.
DONE! Ended at: 2019-03-04 01:55:48.834468 bwa index merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.00 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.00 sec [main] Version: 0.7.10-r789 [main] CMD: bwa index merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa [main] Real time: 0.247 sec; CPU: 0.004 sec bwa mem -t50 -pC merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa barcoded.fq.gz | samtools view -@50 -h -F4 -o merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.sortn.bam [M::main_mem] read 3610110 sequences (500000235 bp)... bash: line 1: 2396 Segmentation fault bwa mem -t50 -pC merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa barcoded.fq.gz 2397 Done | samtools view -@50 -h -F4 -o merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.sortn.bam /usr/local/bin/tigmint-make:215: recipe for target 'merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.sortn.bam' failed make: [merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.sortn.bam] Error 139 make: Deleting file 'merged.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.sortn.bam' [ekw10@debruijn tigmint]$