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ChristofferFlensburg / superFreq

Analysis pipeline for cancer sequencing data
MIT License
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Ok, I had a closer look at the latest Rsubread version, and they have indeed changed syntax for how to tell it to to count raw reads (not fragments) in PE samples. And that is most likely they cause of the bug. I made a change to superFreq that reads out the Rsubread version and does the appropriate call. Running tests and will push online, but will (hopefully) be next week. You can either backdate Rsubread if you're in a hurry, or wait for me to finish the testing and push changes online. #117

Closed duanshumeng closed 9 months ago

duanshumeng commented 9 months ago 
          Ok, I had a closer look at the latest Rsubread version, and they have indeed changed syntax for how to tell it to to count raw reads (not fragments) in PE samples. And that is most likely they cause of the bug. I made a change to superFreq that reads out the Rsubread version and does the appropriate call. Running tests and will push online, but will (hopefully) be next week. You can either backdate Rsubread if you're in a hurry, or wait for me to finish the testing and push changes online.

Originally posted by @ChristofferFlensburg in https://github.com/ChristofferFlensburg/superFreq/issues/74#issuecomment-786409614

duanshumeng commented 9 months ago

I also meet the trouble. The superFreq version 1.4.2 and Rsubread 2.8.2.

ERROR: Paired-end reads were detected in single-end read library : /cpfs01/projects-HDD/cfff-e44ef5cf7aa5_HDD/dsm_23110700129/HCC1395_DNA/HCC1395_WGS_bam/BGI_T20_WGS_2023_1_N.sorted.deduped.recaled.bam No counts were generated. Error in .stop_quietly() : In addition: Warning message: In read.table(sampleMetaDataFile, header = T, as.is = T, fill = T, : incomplete final line found by readTableHeader on '/cpfs01/projects-HDD/cfff-e44ef5cf7aa5_HDD/dsm_23110700129/HCC1395_DNA/HCC1395_clonality/matadata_hcc1395-WGS.txt' Error in featureCounts. Input was bamFiles: /cpfs01/projects-HDD/cfff-e44ef5cf7aa5_HDD/dsm_23110700129/HCC1395_DNA/HCC1395_WGS_bam/BGI_T20_WGS_2023_1_N.sorted.deduped.recaled.bam /cpfs01/projects-HDD/cfff-e44ef5cf7aa5_HDD/dsm_23110700129/HCC1395_DNA/HCC1395_WGS_bam/BGI_T20_WGS_2023_1_T.sorted.deduped.recaled.bam captureAnnotation[1:10,]: ? WASH7P WASH7P FAM138A ? ? OR4F5 ? ? ENST00000466430 1 10000 20000 30000 40000 50000 60000 70000 80000 90000 10000 20000 30000 40000 50000 60000 70000 80000 90000 100000 1 1 1 1 1 1 1 1 1 1 Error in runDE(bamFiles, sampleNames, externalNormalCoverageBams, captureRegions, : Error in featureCounts. Calls: superFreq -> superFreq -> analyse -> runDE Execution halted

I don't know how to deal this issue, please give me some advice. Thank you a lot!

ChristofferFlensburg commented 9 months ago

Hi! I believe that was fixed and should work in current superfreq version 1.5.1. Try updating superFreq and rerunning, and post a new issue if the problem persists in the current version.