SPRINT installation Error about sprint

[jumphone]

1. Please directly download and use the executable binary file "sprint": https://github.com/jumphone/SPRINT/tree/master/bin
2. Please use “chmod” to change the permission: "chmod 777 sprint"
   Best,
   Feng

[iqraishtiaq]

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

[jumphone]

1. You can download executable binary file "samtools" from : https://github.com/jumphone/SPRINT/tree/master/samtools_and_bwa
2. 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.))

[iqraishtiaq]

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

[jumphone]

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"

[iqraishtiaq]

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.

[jumphone]

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.

1. We've tested SPRINT on Centos7 and Ubuntu.

2. 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).