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Question: Trouble sorting a BAM file
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gravatar for xpna01t
9 months ago by
xpna01t • 0
xpna01t • 0 wrote:

Hi

I have aligned reads to Brassica juncea genome 1.5 using HISAT2. Now i want to perform PCA analysis to check my replicates. For this i am sorting BAM files by chromosomal coordinates but I am getting error; SORT An error occurred setting the metadata for this dataset Set it manually or retry auto-detection

SortSAM Fatal error: Exit code 127 () /galaxy-repl/main/jobdir/018/286/18286619/tool_script.sh: line 9: picard: command not found

multiBAMSummary Fatal error: Exit code 1 () [bwHdrRead] There was an error while reading in the header! Traceback (most recent call last): File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/bin/multiBamSummary", line 11, in <module> main(args) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/multiBamSummary.py", line 224, in main num_reads_per_bin = c.run(allArgs=args) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 244, in run y = pyBigWig.open(x) RuntimeError: Received an error during file opening!
pca analysis sortsam sort samtools • 280 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by xpna01t • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The public Main Galaxy server at https://usegalaxy.org is presenting with job errors across many tools at this time. We are actively working to correct the issues.

Please follow this ticket for updates: https://biostar.usegalaxy.org/p/26580/

Once the server is corrected, retest your specific issue and comment here in your original post if the problems persist and we can troubleshoot the use case.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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