Fasta file not found, while I provide it

Dear Rafail,

there is an error in your command line.
-F option requires a string to create a directory inside the output folder.
you should try using: -o /Users/tasakis/Desktop/TEST -F RUN
This will create a TEST folder and inside a nested RUN folder containing results.

Regarding the genome fasta file, is it indexed? So, please check the presence of /Users/tasakis/Documents/mm10.fa.fai file.
Otherwise please run this command before:

samtools faidx /Users/tasakis/Documents/mm10.fa

For more details, please look at the documentation: http://srv00.recas.ba.infn.it/reditools/

Best,
Ernesto

Il giorno 12 dic 2017, alle ore 18:49, Rafail Tasakis tasakis@users.sf.net ha scritto:

[tickets:#10] https://sourceforge.net/p/reditools/tickets/10/ Fasta file not found, while I provide it

Status: New
Labels: fasta error
Created: Tue Dec 12, 2017 05:49 PM UTC by Rafail Tasakis
Last Updated: Tue Dec 12, 2017 05:49 PM UTC
Owner: nobody

Hi I am trying to run the REDItoolDnaRna.py (without a -j DNA BAM seq). My input is:
REDItoolDnaRna.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \ -I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \ -f /Users/tasakis/Documents/mm10.fa -F /Users/tasakis/Documents/mm10.2bit \ -o /Users/tasakis/Desktop

Output:
Script time --> START: 12/12/2017 18:44:54
Analysis ID: 634138550
Sorting RNA-Seq BAM file.
Indexing RNA-Seq BAM file.
Working without DNA-Seq BAM file(s).
.
.
.

Fasta file not found.

Any idea why that happens, as long as i provide the reference genome fasta sequence?

Thanks in advance!

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Dear Ernesto,
thank you very much for getting back to me.

I tried as you said. Also made sure that the fa.fai file of the reference genome is in the same directory with that. My input command it this now:
REDItoolDnaRna.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \
-I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \
-f /Users/tasakis/Documents/mm10.fa \
-o /Users/tasakis/Desktop/TEST -F RUN

However I still ge the same error.
In previous tickets of REDItools I found out that pysam plays a prominent role in the REDItools pipeline. So I changed the pysam version from 0.13 that I had (was problematic then) to 0.7.7 (works fine till this error). Do you think that pysam might be creating a problem again? I kinda doubt it, 'cause the error I get of not finding the Fasta file is not associated with that. Just saying...

Thanks in advance!
Rafail

Dear Ernesto,

I’ve tried what you pointed out on your last response. I got back the pysam 0.13 and tried to run the REDItoolDnaRna_1.1.py you provided me with last time. Unfortunately it doesn’t work again.
My input is:
python REDItoolDnaRna_1.1.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \
-I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \
-f /Users/tasakis/Documents/Mus_musculus.GRCm38.dna_sm.toplevel.fa \
-o /Users/tasakis/Desktop/TEST -F RUN
And I get this error:
Script time --> START: 27/12/2017 12:29:16
Analysis ID: 632969698
Sorting RNA-Seq BAM file.
Traceback (most recent call last):
File "REDItoolDnaRna_1.1.py", line 649, in <module>
pysam.sort(bamfile,'sorted_%s'%(pid))
File "/Users/tasakis/anaconda2/lib/python2.7/site-packages/pysam/utils.py", line 75, in call
stderr))
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\nUsage: samtools sort [options...] [in.bam]\nOptions:\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n -n Sort by read name\n -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)\n -o FILE Write final output to FILE rather than standard output\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n --input-fmt-option OPT[=VAL]\n Specify a single input file format option in the form\n of OPTION or OPTION=VALUE\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n Specify output format (SAM, BAM, CRAM)\n --output-fmt-option OPT[=VAL]\n Specify a single output file format option in the form\n of OPTION or OPTION=VALUE\n --reference FILE\n Reference sequence FASTA FILE [null]\n -@, --threads INT\n Number of additional threads to use [0]\n'</module>

Do you have any ideas why this happens?