Main command causing issue with getA2I.py about sprint

[jumphone]

Here are my scripts:

sprint  main  -p 10 -1  $FQ1 -2 $FQ2  $REF  $SPRINT_OUTPUT_FOLDER  $BWA  $SAMTOOLS
python    getA2I.py     0     $SPRINT_OUTPUT_FOLDER      $A_TO_I_PATH

"SPRINT_identified_all.res", "SPRINT_identified_hyper.res", and "SPRINT_identified_regular.res" should be in the "$SPRINT_OUTPUT_FOLDER"

[jumphone]

1. '//' and ‘/’ have the same function in linux;
2. You can directly download the executable program of SPRINT, BWA (0.7.12) and SAMTOOLS (1.2) from "https://github.com/jumphone/SPRINT/tree/master/bin/" and "https://github.com/jumphone/SPRINT/tree/master/samtools_and_bwa" . After clicking the file, there is a button for "download raw file". And please remember to make them executable “e.g. chmod 777 sprint”
3. python | getA2I.py | 0 | path_to_directory_of_sprint_output | path_to_A_to_I_result

[haydenshinn]

Hi there, I reran SPRINT using the correct versions of bwa and samtools and I definitely noticed more output files created so it fixed something but I'm not getting any .res files outputted.

Here is my out file:

$1: INT, 1 for strand-specific sequencing data. 
$2: OUTPUT_DIR of SPRINT
$3: OUTPUT_PATH of A-to-G RESs

Traceback (most recent call last):
  File "/home/user/github/SPRINT/utilities/getA2I.py", line 15, in <module>
    fi=open(regular)
IOError: [Errno 2] No such file or directory: 'path/SPRINT/Output/NO-01/tmp/SPRINT_identified_regular.res'

I have all sorts of output files in my designated output file from SPRINT main and I have run multiple different samples and none of them have outputted any sort of .res file. I thought maybe that was supposed to be an output from getA2I.py but I'm now seeing that that is part of what SPRINT main outputs. I looked into sprint main to try and figure out why the .res noticed in sprint_main.py around line 625 that there is good amount of lines commented out that involved the .res files so I thought maybe it had something to do with that. I could really use a bit more description as to what I could possibly be doing wrong or why I am not getting the expected output.

Here is what is contained in each of the output folders that I have "successfully" run with no error (copied from my SPRINT output directory).

all_combined.zz                hyper_mskAG.snv                              transcript_mskAG_all.zz.dedup.genome.zz
all_combined.zz.sorted         hyper_mskTC.snv                              transcript_mskAG_all.zz.dedup.snv
baseq.cutoff                   PARAMETER.txt                                transcript_mskAG_all.zz.dedup.snv.genome.snv
genome                         regular.snv                                  transcript_mskAG_all.zz.dedup.snv.genome.snv.sort
genome_all.zz.dedup            transcript                                   transcript_mskTC
genome_all.zz.dedup.snv        transcript_all.zz.dedup                      transcript_mskTC_all.zz.dedup
genome_mskAG                   transcript_all.zz.dedup.genome.zz            transcript_mskTC_all.zz.dedup.genome.zz
genome_mskAG_all.zz.dedup      transcript_all.zz.dedup.snv                  transcript_mskTC_all.zz.dedup.snv
genome_mskAG_all.zz.dedup.snv  transcript_all.zz.dedup.snv.genome.snv       transcript_mskTC_all.zz.dedup.snv.genome.snv
genome_mskTC                   transcript_all.zz.dedup.snv.genome.snv.sort  transcript_mskTC_all.zz.dedup.snv.genome.snv.sort
genome_mskTC_all.zz.dedup      transcript_mskAG
genome_mskTC_all.zz.dedup.snv  transcript_mskAG_all.zz.dedup

[jumphone]

Your input path of getA2I.py is the "tmp" folder. Please directly use the output folder "path/SPRINT/Output/NO-01/".

[haydenshinn]

Appreciate the quick response - I reran my script with your suggested path modification and came up with the same error.

Traceback (most recent call last):
  File "/path/github/SPRINT/utilities/getA2I.py", line 15, in <module>
    fi=open(regular)
IOError: [Errno 2] No such file or directory: '/path/SPRINT/Output/NO-01/SPRINT_identified_regular.res'

A .res file is supposed to be included in the output from sprint_main, correct? I was not seeing in the tmp directory but I am not seeing it in the parent directory either (the specified output dir).

[haydenshinn]

I got it working - thanks for your help :)