Error: number of labels must match number of conditions in cuffdiff

[bvk]

In a python script I gave a call in this way:

do.call([cfg.tool_cmd("cuffdiff"),
"-p", str(cfg.project["analysis"]["threads"]),
"-b", str(cfg.project["genome"]["fasta"]),
"-u", cfg.project["experiment"]["merged"],
"-L", str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7],
"-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] + ' ' + cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])

And this gives an Error: number of labels must match number of conditions

subprocess.CalledProcessError: Command '['/usr/local/bin/cuffdiff', '-p', '5', '-b', '/scratchsan/venkatesh/TuxedoProject/data/genome/ce10.fa', '-u', 'pipeline/merging/merged.gtf', '-L', 'embryo', 'larva', '-o', 'pipeline/degenes', 'pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam']' returned non-zero exit status 1

[dpryan]

When it's actually constructing the command, it's separating the labels by a space rather than a comma. You probably want something like:

do.call([cfg.tool_cmd("cuffdiff"),
"-p", str(cfg.project["analysis"]["threads"]),
"-b", str(cfg.project["genome"]["fasta"]),
"-u", cfg.project["experiment"]["merged"],
"-L", "%s,%s" % (str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7]),
"-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] + ' ' + cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])

[bvk]

When it's actually constructing the command, it's separating the labels by a space rather than a comma. You probably want something like:

do.call([cfg.tool_cmd("cuffdiff"),
"-p", str(cfg.project["analysis"]["threads"]),
"-b", str(cfg.project["genome"]["fasta"]),
"-u", cfg.project["experiment"]["merged"],
"-L", "%s,%s" % (str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7]),
"-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] + ' ' + cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])

Thank you !! Can you please tell what does "%s,%s" % this do?

[dpryan]

It's a formatted print (I have no clue what the python terminology for this is). "%s" means a string (%i is an integer, %f is a floating point value, etc.). There's probably a more "pythonic" way of doing that, but what I showed is simple enough.

[bvk]

It's a formatted print (I have no clue what the python terminology for this is). "%s" means a string (%i is an integer, %f is a floating point value, etc.). There's probably a more "pythonic" way of doing that, but what I showed is simple enough.

Thanks again It worked but now the error is:

Error: cuffdiff requires at least 2 SAM files

[dpryan]

You forgot the GTF file, so it's assuming the first BAM file is the GTF file.

Edit: I take that back, it's there, but try putting it before the BAM files in the command.

[bvk]

You forgot the GTF file, so it's assuming the first BAM file is the GTF file.

Nope. Here, merged is the merged.gtf file !!

[dpryan]

See the update to my previous reply it's possible that the command simply isn't being parsed correctly. In general, run the command manually from the command line and then fix it as needed to get it to work. Then make the python script construct that command.

[bvk]

See the update to my previous reply it's possible that the command simply isn't being parsed correctly. In general, run the command manually from the command line and then fix it as needed to get it to work. Then make the python script construct that command.

Yes, as you said I tried to run on command line and this gave:

.../usr/local/bin/cuffdiff -p 5 -b /scratchsan/venkatesh/TuxedoProject/data/genome/ce10.fa -u pipeline/merging/merged.gtf -L embryo,larva -o pipeline/degenes pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam

Here there is a space between bam files but bothe the bam files are taken as one string.

[bvk]

Yes, as you said I tried to run on command line and this gave:

.../usr/local/bin/cuffdiff -p 5 -b /scratchsan/venkatesh/TuxedoProject/data/genome/ce10.fa -u pipeline/merging/merged.gtf -L embryo,larva -o pipeline/degenes pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam

Here there is a space between bam files but bothe the bam files are taken as one string.

It is treating both the bam files as one bam file. this is the problem

[dpryan]

You can always just construct that exact command in python and then pass it as a string to subprocess.call(). That's often a bit easier to debug, since you can use a print() command first to be certain what the command that's being run is.

[bvk]

You can always just construct that exact command in python and then pass it as a string to subprocess.call(). That's often a bit easier to debug, since you can use a print() command first to be certain what the command that's being run is.

I tried with the print() command:

In that it gave 'pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam'. so eventhough there is a space between bam files both are taken as one file. (represented with single code)

I guess it should give like this:

'pipeline/SAMN00990702-1/mappings/accepted_hits.bam' 'pipeline/SAMN00990702-2/mappings/accepted_hits.bam'

[bvk]

You can always just construct that exact command in python and then pass it as a string to subprocess.call(). That's often a bit easier to debug, since you can use a print() command first to be certain what the command that's being run is.

Atlast it worked !! Thank you