Cufflinks Error

Question: Cufflinks Error

7.1 years ago by

jh yu • 10

jh yu • 10 wrote:

Dear all: Recently I am using cufflinks to analyze differential expression between different conditions, but when using cufflinks an error occurred: An error occurred running this job:cufflinks v1.0.3 cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat Error running cufflinks. [bam_header_read] EOF marker is absent. [bam_header_read] invalid BAM binary header (this However, when I used the same parameters to analyze another file, it worked well: 19,904 lines format: gtf, database: rhodRHA1 Info: cufflinks v1.0.3 cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat The only difference is the size of each file, the failed one input file is 23 G, while the succeeded one input file is 3.5 G, is the size causing failure? Thank you in advance. Best wishes! Sincerely, Jinhai YU Jinhai YU, Ph.D Candidate 010-64888521 Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China

rna-seq cufflinks • 1.3k views

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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by jh yu • 10

7.1 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

Hello, Without seeing your analysis, it's difficult to determine what the problem is. My best guess is that: (a) your SAM/BAM dataset is not compatible with Cufflinks for some reason, perhaps due to sorting? (b) your gene annotation dataset is not compatible with Cufflinks. Perhaps looking at the Cufflinks documentation will help you determine the error: http://cufflinks.cbcb.umd.edu/ If that doesn't work, you can report the problem by clicking on the bug icon next to the failed datasets. Good luck, J.

ADD COMMENT • link written 7.1 years ago by Jeremy Goecks • 2.2k

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Jinhai YU, The error indicates that there was a problem with the BAM file/index. When you loaded the larger file into Galaxy, did you use FTP? Was it successful? Using a utility would allow you to track the progress, if you are not certain. An incomplete load could generate an error like the one you ran into. FTP help is at: http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP If the problem is confirmed to not be a data loading issue, it might be a good idea to go back to the SAM file and convert to BAM again (if the data was yours) or contact the owner/source of the BAM data and report the problem to see what they think. Apologies for the delay in reply, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

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