Comments (7)
- Please directly download and use the executable binary file "sprint": https://github.com/jumphone/SPRINT/tree/master/bin
- Please use βchmodβ to change the permission: "chmod 777 sprint"
Best,
Feng
from sprint.
Thank you soooo much Sir. Its working perfect.
Please tell me after running sprint prepare commands how many files will be generated?
Actually I obtained 35 files and i am confused which one should be used for further processing in sprint main
command
from sprint.
- You can download executable binary file "samtools" from : https://github.com/jumphone/SPRINT/tree/master/samtools_and_bwa
- After finishing "sprint prepare", you can directly use "sprint main" without considering about those generated files. (the input .fasta file of "sprint main" is still the original fasta (e.g. hg19.fa, mm9.fa, etc.))
from sprint.
By running following command getting these errors. My all files generated by sprint prepare, refernce genome, sam and bam tools are present in Downloads folder.
./sprint main -1 R1.fq -2 R2.fq buffalo_reference_genome.fa /home/iqra/Downloads ./samtools-1.2/samtools ./bwa-0.7.12/bwa
preprocessing...
mapping...
[main] unrecognized command 'aln'
[main] unrecognized command 'aln'
[main] unrecognized command 'samse'
[main] unrecognized command 'samse'
[main] unrecognized command 'view'
[main] unrecognized command 'view'
[main] unrecognized command 'sort'
[main] unrecognized command 'sort'
[main] unrecognized command 'merge'
[main] unrecognized command 'view'
cp: cannot stat '/home/iqra/Downloads//tmp//genome/./all.sam': No such file or directory
[main] unrecognized command 'view'
[main] unrecognized command 'aln'
[main] unrecognized command 'samse'
[main] unrecognized command 'view'
[main] unrecognized command 'sort'
[main] unrecognized command 'view'
cp: cannot stat '/home/iqra/Downloads//tmp//transcript/./all.sam': No such file or directory
[main] unrecognized command 'view'
[main] unrecognized command 'aln'
[main] unrecognized command 'samse'
[main] unrecognized command 'view'
[main] unrecognized command 'sort'
[main] unrecognized command 'view'
cp: cannot stat '/home/iqra/Downloads//tmp//genome_mskAG/./all.sam': No such file or directory
[main] unrecognized command 'view'
[main] unrecognized command 'aln'
[main] unrecognized command 'samse'
[main] unrecognized command 'view'
[main] unrecognized command 'sort'
[main] unrecognized command 'view'
cp: cannot stat '/home/iqra/Downloads//tmp//genome_mskTC/./all.sam': No such file or directory
[main] unrecognized command 'view'
[main] unrecognized command 'aln'
[main] unrecognized command 'samse'
[main] unrecognized command 'view'
[main] unrecognized command 'sort'
[main] unrecognized command 'view'
cp: cannot stat '/home/iqra/Downloads//tmp//transcript_mskAG/./all.sam': No such file or directory
[main] unrecognized command 'aln'
[main] unrecognized command 'samse'
[main] unrecognized command 'view'
[main] unrecognized command 'sort'
[main] unrecognized command 'view'
cp: cannot stat '/home/iqra/Downloads//tmp//transcript_mskTC/./all.sam': No such file or directory
Traceback (most recent call last):
File "run.py", line 7, in
File "sprint/pipeline.py", line 42, in pipeline
File "sprint/sprint_main.py", line 458, in main
File "sprint/tools_sam/recover_sam.py", line 39, in recover_sam
IOError: [Errno 2] No such file or directory: '/home/iqra/Downloads//tmp/transcript_mskAG_all.sam'
Failed to execute script run
from sprint.
It should be "./sprint main -1 R1.fq -2 R2.fq buffalo_reference_genome.fa /home/iqra/Downloads ./bwa-0.7.12/bwa ./samtools-1.2/samtools".
"./bwa-0.7.12/bwa" should be in front of "./samtools-1.2/samtools"
from sprint.
please tell me what should be the specifications of system/PC/laptop to run Sprint?
My laptop has Intel(R) Core(TM) i7-2670QM CPU @ 2.20GHz 2201 Mhz, 4 core(s), 8 Logical... processor.
RAM is 4 GB. Available virtual memory is 10.6 GB.
I am working on buffalo genome. Forward and reverse reads file size is 6GB each and reference genome file is 3GB in size.
from sprint.
please tell me what should be the specifications of system/PC/laptop to run Sprint?
My laptop has Intel(R) Core(TM) i7-2670QM CPU @ 2.20GHz 2201 Mhz, 4 core(s), 8 Logical... processor.
RAM is 4 GB. Available virtual memory is 10.6 GB.
I am working on buffalo genome. Forward and reverse reads file size is 6GB each and reference genome file is 3GB in size.
-
We've tested SPRINT on Centos7 and Ubuntu.
-
You may need more memory. For a 6GB unzipped FASTQ file (single end), SPRINT, SAMTOOLS, and BWA may need around 6GB +3GB (reference genome) memory to process the data (rough estimation).
from sprint.
Related Issues (20)
- # HOT 19
- How to set the parameter -ss for non-strand-specific RNA-seq? Thank you. HOT 2
- Is the trimming first 6 bases step included in your pipeline? HOT 2
- Why the rate of A-to-G deteced by SPRINT is very low ? HOT 3
- Generated binary files not working HOT 6
- zz2sam.py hard-codes strandedness HOT 5
- how to calculate the no. of editing sites present in 3' UTRs and CDS and 5'TRS??? HOT 3
- Effect of editing sites on the condon changes HOT 3
- Differential RNA Editing HOT 3
- Error during run HOT 6
- Execution problem HOT 3
- No output after execution HOT 4
- import error HOT 3
- reverse strandedness -ss 1 or -ss 2 HOT 4
- No results in final result files HOT 2
- calculation time HOT 1
- What ref .fa file to use for sprint main after prepare? HOT 1
- Main command causing issue with getA2I.py HOT 8
- Some editing sites can not be identified but it has editing reads when viewing with IGV. HOT 3
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from sprint.