Comments (6)
SPRINT will generate a "tmp" folder to store some files when processing sequencing data.
Please attach the full error log.
from sprint.
SPRINT will generate a "tmp" folder to store some files when processing sequencing data.
Please attach the full error log.
from sprint.
We have tested sprint in multiple servers, and the "/" will not cause error.
from sprint.
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 21939744 sequences have been processed.
[main] Version: 0.7.17-r1188
[main] CMD: /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa samse -n4 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/read2.sai /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp/cut_read2.fastq
[main] Real time: 311.477 sec; CPU: 308.874 sec
[main] Version: 0.7.17-r1188
[main] CMD: /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa samse -n4 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/read1.sai /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp/cut_read1.fastq
[main] Real time: 312.621 sec; CPU: 310.092 sec
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-u Output uncompressed data (equivalent to -l 0)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-M Use minimiser for clustering unaligned/unplaced reads
-K INT Kmer size to use for minimiser [20]
-n Sort by read name (not compatible with samtools index command)
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--write-index
Automatically index the output files [off]
--verbosity INT
Set level of verbosity
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-u Output uncompressed data (equivalent to -l 0)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-M Use minimiser for clustering unaligned/unplaced reads
-K INT Kmer size to use for minimiser [20]
-n Sort by read name (not compatible with samtools index command)
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--write-index
Automatically index the output files [off]
--verbosity INT
Set level of verbosity
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/name_read1_sorted.bam" : No such file or directory
samtools merge: fail to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/name_read1_sorted.bam": No such file or directory
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/all.bam" for reading: No such file or directory
sh: 0: getcwd() failed: No such file or directory
cp: cannot stat '/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/./all.sam': No such file or directory
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome/all.bam" for reading: No such file or directory
sh: 0: getcwd() failed: No such file or directory
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[main] Version: 0.7.17-r1188
[main] CMD: /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa aln -t 20 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa.mskAG.fa /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//regular_unmapped_A_to_G.fq
[main] Real time: 1.459 sec; CPU: 1.438 sec
sh: 0: getcwd() failed: No such file or directory
[main] Version: 0.7.17-r1188
[main] CMD: /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa samse -n4 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa.mskAG.fa /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskAG/read1.sai /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//regular_unmapped_A_to_G.fq
[main] Real time: 0.020 sec; CPU: 0.002 sec
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-u Output uncompressed data (equivalent to -l 0)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-M Use minimiser for clustering unaligned/unplaced reads
-K INT Kmer size to use for minimiser [20]
-n Sort by read name (not compatible with samtools index command)
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--write-index
Automatically index the output files [off]
--verbosity INT
Set level of verbosity
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskAG/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskAG/all.bam" for reading: No such file or directory
sh: 0: getcwd() failed: No such file or directory
cp: cannot stat '/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskAG/./all.sam': No such file or directory
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskAG/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskAG/all.bam" for reading: No such file or directory
sh: 0: getcwd() failed: No such file or directory
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[main] Version: 0.7.17-r1188
[main] CMD: /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa aln -t 20 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa.mskTC.fa /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//regular_unmapped_A_to_G.fq
[main] Real time: 1.440 sec; CPU: 1.410 sec
sh: 0: getcwd() failed: No such file or directory
[main] Version: 0.7.17-r1188
[main] CMD: /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa samse -n4 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa.mskTC.fa /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/read1.sai /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//regular_unmapped_A_to_G.fq
[main] Real time: 0.020 sec; CPU: 0.002 sec
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-u Output uncompressed data (equivalent to -l 0)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-M Use minimiser for clustering unaligned/unplaced reads
-K INT Kmer size to use for minimiser [20]
-n Sort by read name (not compatible with samtools index command)
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--write-index
Automatically index the output files [off]
--verbosity INT
Set level of verbosity
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" for reading: No such file or directory
sh: 0: getcwd() failed: No such file or directory
cp: cannot stat '/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/./all.sam': No such file or directory
sh: 0: getcwd() failed: No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" for reading: No such file or directory
Traceback (most recent call last):
File "/media/kokyriakidis/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/sprint/bin/sprint", line 11, in <module>
load_entry_point('sprint==0.1.8', 'console_scripts', 'sprint')()
File "build/bdist.linux-x86_64/egg/sprint/__init__.py", line 18, in main
File "build/bdist.linux-x86_64/egg/sprint/pipeline.py", line 42, in pipeline
File "build/bdist.linux-x86_64/egg/sprint/sprint_main.py", line 476, in main
File "build/bdist.linux-x86_64/egg/sprint/tools_sam/recover_sam.py", line 39, in recover_sam
IOError: [Errno 2] No such file or directory: '/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp/genome_mskAG_all.sam'
(sprint) root@XAROS-WORKSTATION:/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E#
from sprint.
Please use SAMTOOLS == 1.2 & BWA == 0.7.12.
You can download binary "samtools 1.2" and "bwa 0.7.12" from: https://github.com/jumphone/SPRINT/tree/master/samtools_and_bwa
from sprint.
It works using these versions but I get a lot of these messages during runs
/home/kokyriakidis/anaconda3/envs/sprint/bin/samtools: /tmp/_MEI1ceDNd/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libncurses.so.5)
even though I have ncurses installed. But I guess it does not cause any problems. I get the final tables as expected.
Thanks for your help!
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
- SPRINT installation Error HOT 7
- Differential RNA Editing HOT 3
- 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.