Question: Error in RNA editing tool sprint
0
gravatar for hirahameed222
8 months ago by
hirahameed2220 wrote:

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):

ADD COMMENTlink modified 7 months ago by cchmczhang0 • written 8 months ago by hirahameed2220
0
gravatar for cchmczhang
7 months ago by
cchmczhang0
cchmczhang0 wrote:

Please use SAMTOOLS==1.2, and you can download it from https://github.com/jumphone/SPRINT/tree/master/samtools_and_bwa

If you have any further question, please send email to fzhang15_at_fudan.edu.cn.

Best,

Feng

ADD COMMENTlink written 7 months ago by cchmczhang0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2198 users visited in the last hour