laxeye / yamb Goto Github PK

Hello there!
I had this issue while trying your tool:

Argument "LENGTH" isn't numeric in integer multiplication (*) at cut-contigs.pl line 47.

I think this can be fixed easily, there:

Hope that helps

when I run "yamb.sh -c idba/contig.fa -f 1.fastq -r 2.fastq -o output -t 80 -m 1000 -l 500"
I got this error:
Argument "LENGTH" isn't numeric in integer multiplication (*) at /uufs/chpc.utah.edu/common/home/schmidt-group2/software/YAMB/cut-contigs.pl line 47.
Illegal division by zero at /uufs/chpc.utah.edu/common/home/schmidt-group2/software/YAMB/cut-contigs.pl line 51.
19:51:03 Mapping reads with Bowtie2
Warning: Empty fasta file: 'output/cut.contigs.fna'
Warning: All fasta inputs were empty
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 -q output/cut.contigs.fna output/idx
Could not locate a Bowtie index corresponding to basename "output/idx"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /uufs/chpc.utah.edu/sys/installdir/bowtie/2.2.9/bowtie2-align-s --wrapper basic-0 -p 80 -q -x output/idx -S output/mapping.sam -1 1.fastq -2 2.fastq
(ERR): bowtie2-align exited with value 1
Converting SAM to BAM, sorting and indexing.
[main_samview] fail to read the header from "output/mapping.sam".
samtools sort: failed to read header from "-"
samtools index: "output/mapping.bam" is in a format that cannot be usefully indexed
19:51:03 Indexing fasta.
[faidx] Could not build fai index output/cut.contigs.fna.fai
19:51:03 Coverage calculation.
awk: fatal: cannot open file `output/cut.contigs.fna.fai' for reading (No such file or directory)
ERROR: fail to open index BAM file 'output/mapping.bam'
19:51:03 Tetramer occurence estimation.
19:51:03 Datafile generation.
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.delim -> read.table
Execution halted
which: no esl-sfetch in (/uufs/chpc.utah.edu/sys/installdir/bowtie/2.2.9:/uufs/chpc.utah.edu/sys/installdir/samtools/1.10/bin:/uufs/chpc.utah.edu/sys/installdir/R/3.6.1i/bin:/uufs/chpc.utah.edu/sys/installdir/pandoc/2.7.1/bin:/uufs/chpc.utah.edu/sys/installdir/jdk/1.8.0_112/bin:/uufs/chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2018.1.163/linux/bin/intel64:/uufs/chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/bin:/uufs/chpc.utah.edu/sys/pkg/perl/5.18.1/bin:/uufs/chpc.utah.edu/common/home/schmidt-group2/software/easel:/uufs/chpc.utah.edu/common/home/schmidt-group2/software/YAMB:/uufs/chpc.utah.edu/common/home/u0676503/anaconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/uufs/chpc.utah.edu/sys/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/uufs/notchpeak.peaks/sys/installdir/slurm/std/bin:/opt/dell/srvadmin/bin:/uufs/chpc.utah.edu/common/home/u0676503/bin)
tee: output/log.txt: No such file or directory
19:51:05 Error: Unable to locate esl-sfetch, no fasta files may be produced
19:51:05 Binning complete! Check output/ for results!