Error executing tool: maximum recursion depth exceeded while calling a Python object

Question: Error executing tool: maximum recursion depth exceeded while calling a Python object

2.1 years ago by

US, Tufts University

Hi, I'm using a custom genome (in FASTA format) which I downloaded from EupathDB.org. I used User/Custom builds and edited the attributes per galaxy instructions. When I run tophat I get the following error message:

Error executing tool: maximum recursion depth exceeded while calling a Python object

In my history, the genome FASTA file shows the following description: 8 sequences, format: fasta, database: Cparvum

Info: uploaded fasta file

thanks for your help,

Giovanni

error tophat custom-genome • 902 views

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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by Widmer, Giovanni • 150

Hello - Where are you using Galaxy? If at http://usegalaxy.org, please send in a bug report and we can review. If working somewhere else, can the same issue be reproduced at http://usegalaxy.org? Please leave all input and output datasets undeleted for review.

https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks, Jen, Galaxy team

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

2.1 years ago by

Widmer, Giovanni • 150

US, Tufts University

Widmer, Giovanni • 150 wrote:

thanks Jen. I use a local galaxy at http://galaxy.med.tufts.edu/.

I re-loaded the genome FASTA file and ran TopHat again and now I get another error: Error in tophat:

[Fri Nov 4 13:10:25 2016] Beginning TopHat run (v1.4.1)

[Fri Nov 4 13:10:25 2016] Preparing output location ./tophat_out/ [Fri Nov 4 13:10:25 2016] Checking for Bowtie index files [Fri Nov 4 13:10:25 2016] Checking for reference FASTA file [Fri Nov 4 13:10:25 2016] Checking for Bowtie Bowtie version: 0.12.8.0 [Fri Nov 4 13:10:25 2016] Checking for Samtools Samtools Version: 0.1.15 [Fri Nov 4 13:10:26 2016] Generating SAM header for /storage/apps/galaxy_dist/database/tmp/tmpfKjZ3o/dataset_113208 Traceback (most recent call last): File "/export/bin/tophat", line 3063, in <module> sys.exit(main()) File "/export/bin/tophat", line 2937, in main params.read_params = check_reads_format(params, reads_list) File "/export/bin/tophat", line 1322, in check_reads_format zf = ZReader(f_name, params.system_params) File "/export/bin/tophat", line 1275, in __init__ self.file=open(filename) IOError: [Errno 2] No such file or directory: '/storage/apps/galaxy_dist/database/files/000/102/dataset_102410.dat'

It's obviously looking for a file, but what is dataset_102410.dat?

ADD COMMENT • link written 2.1 years ago by Widmer, Giovanni • 150

Giovanni, This looks like a server error now. Contacting the admins for this instance about the problem will help them to solve it. -Jen

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

[Fri Nov 4 13:10:25 2016] Beginning TopHat run (v1.4.1)

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