Tophat on Cygwin error

[fchatonnet]

Hello and thank you to welcome me in the community. I have been a intensive user of seqanswers threads to answer my many problems with bioinformatics, but this time, I have found no solution.
I want to perform colorspace alignments using something else than LifeScope (the SOLiD dedicated out-of-date software). As I used tophat before for Illumina, I wanted to try a combination tophat2 / bowtie1 (bowtie2 does not handle colorspace). So after many problems, I finally got bowtie (v1.1.0) and tophat (2.0.12) running. Well bowtie runs, but not tophat, I get this error:

$ more tophat_out/logs/tophat.log

[2014-09-04 16:15:53] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-09-04 16:15:53] Checking for Bowtie
Bowtie version: 1.1.0.0
[2014-09-04 16:15:54] Checking for Samtools
Samtools version: 0.1.19.0
[2014-09-04 16:15:54] Checking for Bowtie index files (genome)..
[2014-09-04 16:15:54] Checking for reference FASTA file
[2014-09-04 16:15:54] Generating SAM header for mm10C
[2014-09-04 16:15:54] Preparing reads
left reads: min. length=50, max. length=50, 98 kept reads (2 discarded)
[2014-09-04 16:15:54] Mapping left_kept_reads to genome mm10C with Bowtie
[FAILED]
Error running bowtie:
Could not open single-ended aligned/unaligned-read file for writing: /dev/null

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'int'

Last lign of run.log says:

/usr/sbin/bam2fastx --all --color ./tophat_out/tmp/left_kept_reads.bam|/usr/sbin/bowtie -C --col-keepends -v 2 -k 20 -m 20 -S -p 1 --sam-nohead --max /dev/null mm10C -|/usr/sbin/fix_map_ordering --color --read-
mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads.mapped.bam.index --bowtie1 --sam-header ./tophat_out/tmp/mm10C_genome.bwt.samheade
r.sam - ./tophat_out/tmp/left_kept_reads.mapped.bam ./tophat_out/tmp/left_kept_reads_unmapped.bam

I decomposed the actions, bam2fastx runs well, bowtie also as long as I change /dev/null to something else. I suspect a permission problem.
I am under cygwin 2.850 64 bits, tried to move all my cygwin tree under an admin session and got the same problem. Any ideas?
If not I will try to install another colorspace-able aligner (any suggestion?)

Thanks a lot if you read the whole message and for your help (?!)

[WhatsOEver]

You just provide a folder and not a filename to the "max" parameter and that's what the program is complaining about

[FAILED]
Error running bowtie:
Could not open single-ended aligned/unaligned-read file for writing: /dev/null

/usr/sbin/bam2fastx --all --color ./tophat_out/tmp/left_kept_reads.bam|/usr/sbin/bowtie -C --col-keepends -v 2 -k 20 -m 20 -S -p 1 --sam-nohead --max /dev/null mm10C -|/usr/sbin/fix_map_ordering --color --read-
mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads.mapped.bam.index --bowtie1 --sam-header ./tophat_out/tmp/mm10C_genome.bwt.samheade
r.sam - ./tophat_out/tmp/left_kept_reads.mapped.bam ./tophat_out/tmp/left_kept_reads_unmapped.bam

[fchatonnet]

Except that --max is a bowtie option and I don't know how to specify it when I run tophat. As said in my previous most, if I specify --max with a file name when running the bowtie subroutine, everything goes well.

[WhatsOEver]

ok, sry, didn't got that before. Please paste the command you used to run tophat then.

[fchatonnet]

Here is the tophat command line

tophat -C -Q --bowtie1 --library-type fr-secondstrand mm10C toto.csfasta toto.QV.qual

Then, as I said, I decomposed the last line of the run.log: bam2fastx works fine, used the output as input for bowtie, works also fine with --max toto_unmapped.fq as option. fix_map_ordering was also tested, but not directly with bowtie output.
Thanks for your reply by the way.

[WhatsOEver]

Looks like a cygwin related problem then.
/dev/null should be accessible without special permissions.
Only thing that comes into my mind is to provide full paths to everything and specify also an output dir with fullpath ("-o") for tophat files. Using --keep-tmp tmp files created during the tophat run won't be deleted. Within those you may also find additional information about what is happening.