I am trying to run a PE library through bowtie2 and then into svDetect for Circos.
Bowtie2 run with
module load Bowtie2/18.104.22.168-foss-2016b bowtie2 -x w82 -1 SRR2163311_1.fastq.gz -2 SRR2163311_2.fastq.gz --un-conc unPEK.sam --al-conc alPEK.sam --met-file metPEK.txt -S samPEK.sam
My output provides me with alPEK.1.sam, alPEK.2.sam, samPEK.sam as well as in .txt.
Trying svDETECT with .conf file as (have tried using a comma to list both on the alPEK.sams)
general input_format = sam sv_type = all mates_orientation=FR read1_length=90 read2_length=90 mates_file=alPEK.sam cmap_file=gm20.len output_dir=results tmp_dir=tmp num_threads=14 general detection split_mate_file=1 window_size=750 step_length=150 /detection filtering split_link_file=0 strand_filtering=1
Output with error
# Linking procedure ... -- file=/scratch/sxd/workDir/svDETbase/alPEK.sam -- input format=sam -- type=all -- read1length=90, read2length=90 -- window size=750, step length=150 /usr/local/apps/eb/SVDetect/0.7-foss-2016b-Perl-5.24.1/bin/SVDetect: can't open /scratch/sxd/workDir/svDETbase/alPEK.sam:No such file or directory
Is it possible to input both .1.sam & .2.sam? I did try view/merge via samtools but unsuccessful. Is the bowtie2 output salvageable for svDetect or should I start over with BWA?