I have run
sprint main -1 G1_forward_paired.fq -2 G1_reverse_paired.fq Triticum_aestivum.IWGSC.dna.toplevel.fa G1_ES bwa samtools
I have faced the following errors during command execution. the following command create the desired output folder named as G1_ES (according to manual we are just supposed to write a Folder and it will automatically create the sub-folders in it) and sub directories in it but during the execution of commands error reads that these sub folder's File seems inaccessible.
[main] CMD: bwa samse -n4 Triticum_aestivum.IWGSC.dna.toplevel.fa G1_ES//tmp//genome/read2.sai G1_ES//tmp
[main] CMD: bwa samse -n4 Triticum_aestivum.IWGSC.dna.toplevel.fa G1_ES//tmp//genome/read2.sai G1_ES//tmp/cut_read2.fastq [main] Real time: 3829.614 sec; CPU: 3796.364 sec [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Afterwards I got this error
[E::hts_open_format] Failed to open file G1_ES//tmp//genome/name_read1_sorted.bam samtools merge: fail to open "G1_ES//tmp//genome/name_read1_sorted.bam": No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome/all.bam samtools view: failed to open "G1_ES//tmp//genome/all.bam" for reading: No such file or directory cp: cannot stat 'G1_ES//tmp//genome/./all.sam': No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome/all.bam samtools view: failed to open "G1_ES//tmp//genome/all.bam" for reading: No such file or directory
and then
[E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskAG/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskAG/all.bam" for reading: No such file or directory cp: cannot stat 'G1_ES//tmp//genome_mskAG/./all.sam': No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskAG/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskAG/all.bam" for reading: No such file or directory
and then
[E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskTC/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskTC/all.bam" for reading: No such file or directory cp: cannot stat 'G1_ES//tmp//genome_mskTC/./all.sam': No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskTC/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskTC/all.bam" for reading: No such file or directory Traceback (most recent call last):
