Default target region bed file in test run #146
Comments
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Hi Mamoon, Please use Best, |
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Thanks a lot Yunfei,
Please let me know any troubleshooting. I will be thankful to you. On Thu, Aug 11, 2016 at 1:02 AM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Hi Rashid, Could you please provide the contents of Thanks. Best, On Mon, Aug 15, 2016 at 12:47 AM, rashidma [email protected] wrote:
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Hi Yunfei, On Mon, Aug 15, 2016 at 4:05 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD NOTICE: unable to check for updates. Results will not be affected. [ => SeqMule Execution Status: step 36 is finished at Thu Aug 11 21:19:46 AST 2016, Extract variants in custom regions] NOTICE: Output written to NIST7086_result/NIST7086_bwamem.merge.realn.0_gatklite.multi-call_var_stat.txt NOTICE: Output written to NIST7035_result/NIST7035_bwamem.merge.0_samtools.multi-call_var_stat.txt NOTICE: Output written to NIST7035_result/NIST7035_bwamem.merge.0_freebayes.multi-call_var_stat.txt ----------NOTICE---------- Current version: 1.2.5 ----------NOTICE---------- Current version: 1.2.5 ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- NOTICE: unable to download '/work/rashidma/software/seqmule_by_admin/SeqMule-master/bin/secondary/../../version' from http://www.openbioinformatics.org/seqmule. Bad Internet connection? ----------ERROR---------- ----------ERROR---------- ----------NOTICE---------- [ => SeqMule Execution Status: step 2 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 3 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 4 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 5 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 6 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 7 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 8 is finished at Sun Aug 14 09:39:35 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 9 is finished at Sun Aug 14 09:39:35 AST 2016, Generate QC stat] [ => SeqMule Execution Status: step 10 is finished at Sun Aug 14 09:39:35 AST 2016, Generate QC stat] [ => SeqMule Execution Status: step 11 is finished at Sun Aug 14 09:39:35 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 12 is finished at Sun Aug 14 09:39:35 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 13 is finished at Sun Aug 14 09:39:35 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 14 is finished at Sun Aug 14 09:39:35 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 15 is finished at Sun Aug 14 09:39:35 AST 2016, Remove duplicates in NIST7035_result/NIST7035.0.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 16 is finished at Sun Aug 14 09:39:35 AST 2016, Remove duplicates in NIST7035_result/NIST7035.1.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 17 is finished at Sun Aug 14 09:39:35 AST 2016, Remove duplicates in NIST7086_result/NIST7086.0.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 18 is finished at Sun Aug 14 09:39:35 AST 2016, Remove duplicates in NIST7086_result/NIST7086.1.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 19 is finished at Sun Aug 14 09:39:35 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 20 is finished at Sun Aug 14 09:39:35 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 21 is finished at Sun Aug 14 09:39:35 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 22 is finished at Sun Aug 14 09:39:35 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 23 is finished at Sun Aug 14 09:39:35 AST 2016, Merge BAM by bwamem and NIST7035] [ => SeqMule Execution Status: step 24 is finished at Sun Aug 14 09:39:35 AST 2016, Merge BAM by bwamem and NIST7086] Current version: 1.2.5 [ => SeqMule Execution Status: step 26 is finished at Sun Aug 14 09:39:35 AST 2016, gatklite realn] [ => SeqMule Execution Status: step 27 is finished at Sun Aug 14 09:39:35 AST 2016, gatklite.multi-call variant calling] [ => SeqMule Execution Status: step 28 is finished at Sun Aug 14 09:39:35 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 29 is finished at Sun Aug 14 09:39:35 AST 2016, gatklite.multi-call variant filtering] [ => SeqMule Execution Status: step 30 is finished at Sun Aug 14 09:39:35 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 31 is finished at Sun Aug 14 09:39:35 AST 2016, samtools.multi-call variant calling] [ => SeqMule Execution Status: step 32 is finished at Sun Aug 14 09:39:35 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 33 is finished at Sun Aug 14 09:39:35 AST 2016, freebayes.multi-call variant calling] [ => SeqMule Execution Status: step 34 is finished at Sun Aug 14 09:39:35 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 35 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 36 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 37 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 38 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 39 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 40 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 41 is finished at Sun Aug 14 09:39:35 AST 2016, Extract variants in custom regions] Check for upgrade ... ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- NOTICE: unable to download '/work/rashidma/software/seqmule_by_admin/SeqMule-master/bin/secondary/../../version' from http://www.openbioinformatics.org/seqmule. Bad Internet connection? ----------ERROR---------- ----------NOTICE---------- [ => SeqMule Execution Status: step 2 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 3 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 4 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 5 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 6 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 7 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 8 is finished at Sun Aug 14 13:17:16 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 9 is finished at Sun Aug 14 13:17:16 AST 2016, Generate QC stat] [ => SeqMule Execution Status: step 10 is finished at Sun Aug 14 13:17:16 AST 2016, Generate QC stat] [ => SeqMule Execution Status: step 11 is finished at Sun Aug 14 13:17:16 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 12 is finished at Sun Aug 14 13:17:16 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 13 is finished at Sun Aug 14 13:17:16 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 14 is finished at Sun Aug 14 13:17:16 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 15 is finished at Sun Aug 14 13:17:16 AST 2016, Remove duplicates in NIST7035_result/NIST7035.0.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 16 is finished at Sun Aug 14 13:17:16 AST 2016, Remove duplicates in NIST7035_result/NIST7035.1.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 17 is finished at Sun Aug 14 13:17:16 AST 2016, Remove duplicates in NIST7086_result/NIST7086.0.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 18 is finished at Sun Aug 14 13:17:16 AST 2016, Remove duplicates in NIST7086_result/NIST7086.1.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 19 is finished at Sun Aug 14 13:17:16 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 20 is finished at Sun Aug 14 13:17:16 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 21 is finished at Sun Aug 14 13:17:16 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 22 is finished at Sun Aug 14 13:17:16 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 23 is finished at Sun Aug 14 13:17:16 AST 2016, Merge BAM by bwamem and NIST7035] [ => SeqMule Execution Status: step 24 is finished at Sun Aug 14 13:17:16 AST 2016, Merge BAM by bwamem and NIST7086] [ => SeqMule Execution Status: step 25 is finished at Sun Aug 14 13:17:16 AST 2016, gatklite realn] Current version: 1.2.5 [ => SeqMule Execution Status: step 27 is finished at Sun Aug 14 13:17:16 AST 2016, gatklite.multi-call variant calling] [ => SeqMule Execution Status: step 28 is finished at Sun Aug 14 13:17:16 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 29 is finished at Sun Aug 14 13:17:16 AST 2016, gatklite.multi-call variant filtering] [ => SeqMule Execution Status: step 30 is finished at Sun Aug 14 13:17:16 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 31 is finished at Sun Aug 14 13:17:16 AST 2016, samtools.multi-call variant calling] [ => SeqMule Execution Status: step 32 is finished at Sun Aug 14 13:17:16 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 33 is finished at Sun Aug 14 13:17:16 AST 2016, freebayes.multi-call variant calling] [ => SeqMule Execution Status: step 34 is finished at Sun Aug 14 13:17:16 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 35 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 36 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 37 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 38 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 39 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 40 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 41 is finished at Sun Aug 14 13:17:16 AST 2016, Extract variants in custom regions] Check for upgrade ... ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- NOTICE: unable to download '/work/rashidma/software/seqmule_by_admin/SeqMule-master/bin/secondary/../../version' from http://www.openbioinformatics.org/seqmule. Bad Internet connection? ----------ERROR---------- ----------NOTICE---------- [ => SeqMule Execution Status: step 2 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 3 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 4 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 5 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 6 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 7 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 8 is finished at Mon Aug 15 08:29:29 AST 2016, QC assesment on input] [ => SeqMule Execution Status: step 9 is finished at Mon Aug 15 08:29:29 AST 2016, Generate QC stat] [ => SeqMule Execution Status: step 10 is finished at Mon Aug 15 08:29:29 AST 2016, Generate QC stat] [ => SeqMule Execution Status: step 11 is finished at Mon Aug 15 08:29:29 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 12 is finished at Mon Aug 15 08:29:29 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 13 is finished at Mon Aug 15 08:29:29 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 14 is finished at Mon Aug 15 08:29:29 AST 2016, bwamem alignment] [ => SeqMule Execution Status: step 15 is finished at Mon Aug 15 08:29:29 AST 2016, Remove duplicates in NIST7035_result/NIST7035.0.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 16 is finished at Mon Aug 15 08:29:29 AST 2016, Remove duplicates in NIST7035_result/NIST7035.1.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 17 is finished at Mon Aug 15 08:29:29 AST 2016, Remove duplicates in NIST7086_result/NIST7086.0.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 18 is finished at Mon Aug 15 08:29:29 AST 2016, Remove duplicates in NIST7086_result/NIST7086.1.0_bwamem.sort.bam] [ => SeqMule Execution Status: step 19 is finished at Mon Aug 15 08:29:29 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 20 is finished at Mon Aug 15 08:29:29 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 21 is finished at Mon Aug 15 08:29:29 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 22 is finished at Mon Aug 15 08:29:29 AST 2016, Filter BAM file by mapping quality] [ => SeqMule Execution Status: step 23 is finished at Mon Aug 15 08:29:29 AST 2016, Merge BAM by bwamem and NIST7035] [ => SeqMule Execution Status: step 24 is finished at Mon Aug 15 08:29:29 AST 2016, Merge BAM by bwamem and NIST7086] [ => SeqMule Execution Status: step 25 is finished at Mon Aug 15 08:29:29 AST 2016, gatklite realn] Current version: 1.2.5 [ => SeqMule Execution Status: step 27 is finished at Mon Aug 15 08:29:29 AST 2016, gatklite.multi-call variant calling] [ => SeqMule Execution Status: step 28 is finished at Mon Aug 15 08:29:29 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 29 is finished at Mon Aug 15 08:29:29 AST 2016, gatklite.multi-call variant filtering] [ => SeqMule Execution Status: step 30 is finished at Mon Aug 15 08:29:29 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 31 is finished at Mon Aug 15 08:29:29 AST 2016, samtools.multi-call variant calling] [ => SeqMule Execution Status: step 32 is finished at Mon Aug 15 08:29:29 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 33 is finished at Mon Aug 15 08:29:29 AST 2016, freebayes.multi-call variant calling] [ => SeqMule Execution Status: step 34 is finished at Mon Aug 15 08:29:29 AST 2016, Copy results to other samples] [ => SeqMule Execution Status: step 35 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 36 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 37 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 38 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 39 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 40 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] [ => SeqMule Execution Status: step 41 is finished at Mon Aug 15 08:29:29 AST 2016, Extract variants in custom regions] Check for upgrade ... ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- NOTICE: unable to download '/work/rashidma/software/seqmule_by_admin/SeqMule-master/bin/secondary/../../version' from http://www.openbioinformatics.org/seqmule. Bad Internet connection? |
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Hi, 2 sample(s) in this analysis: NIST7035 NIST7086All input is merged on a NIST7086_result/NIST7086.extract_consensus.vcfNIST7086_result/NIST7086_bwamem.merge.realn.0_gatklite.multi-call.extract.vcfNIST7086_result/NIST7086_bwamem.merge.realn.0_gatklite.multi-call.extract.vcfNIST7086_result/NIST7086_bwamem.merge.0_samtools.multi-call.extract.vcfNIST7086_result/NIST7086_bwamem.merge.0_freebayes.multi-call.extract.vcf Thanks On Tue, Aug 16, 2016 at 8:07 AM, Mamoon Rashid [email protected]
Mamoon Rashid, PhD |
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Hi MR, I noticed that there was an error "ERROR: not all VCFs have the same number command to check # of samples: for i in *multi-call.extract.vcf; do echo $i; perl -ne 'if On Tue, Aug 16, 2016 at 4:33 AM, rashidma [email protected] wrote:
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Hi VCFs number of samples NIST7086_bwamem.merge.0_freebayes.multi-call.extract.vcf 1 I noticed frrebayes processed only one sample. Is this a known bug in I am trying to understand the system well so that I can use seqmule on my On Tue, Aug 16, 2016 at 5:46 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Thanks, Mamoon. Let me test the latest freebayes and get back to you later. On Wed, Aug 17, 2016 at 10:05 PM, rashidma [email protected] wrote:
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Thanks a lot for your reply. The log file contains the *gatk-multicall-extract.vcf twice for second I could not understand the behavior. regards On Thu, Aug 18, 2016 at 5:43 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Is it because you tried to rerun the analysis?
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I re-run the analysis in a completely new directory. So both runs should Thanks
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I mean for each analysis, did you run it twice (probably with 'seqmule run' On Thu, Aug 18, 2016 at 7:13 PM, rashidma [email protected] wrote:
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Yes I did run the analysis multiple times with "seqmule run *.script" in The analysis takes a lot of time so seqmule run saves a lot of time. Does it affect the result after rerunning seqmule? Thanks
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This should not affect the results, however, it may be the reason why you On Fri, Aug 19, 2016 at 7:56 AM, rashidma [email protected] wrote:
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Hi Yunfei, On Fri, Aug 19, 2016 at 7:53 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Hi Mamoon, Sorry, our servers are temporarily unavailable right now. We are still Instructions:
Thanks. On Sun, Aug 21, 2016 at 4:28 AM, rashidma [email protected] wrote:
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I installed freebayes from github as you mentioned. [33]JOBID=0PID=14673command=/work/rashidma/software/seqmule_by_admin/SeqMule-master/bin/secondary/../../bin/secondary/worker What should i do now? On Mon, Aug 22, 2016 at 2:15 AM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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33 is the step number. seqmule run -n 33 yourseqmule.script On Mon, Aug 22, 2016 at 6:27 AM, rashidma [email protected] wrote:
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Hi Yunfei, I would like to know --
Thanks you so much for your time. On Mon, Aug 22, 2016 at 7:53 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Hi Mamoon,
Thanks. On Mon, Aug 22, 2016 at 10:23 PM, rashidma [email protected] wrote:
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Thanks a ton Does seqmule support parallel processing using MPI? Thanks On Tue, Aug 23, 2016 at 8:42 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Hi Mamoon, That is weird. If you could provide a small portion of your bam file so SeqMule does not support MPI. Best, On Tue, Aug 23, 2016 at 12:30 PM, rashidma [email protected] wrote:
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Hi Yunfei,
Now, i want to know about the "average coverage in target region". Is this waiting for reply On Wed, Aug 24, 2016 at 6:09 AM, Yunfei Guo [email protected]
Mamoon Rashid, PhD |
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Hi Mamoon, I am out of town right now. Could you please send me the files you were using (perhaps a small portion of it) along with the command and configurations you used? I would be glad to figure out where is the problem and help you get the results once I come back. Thanks!
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Hi Yunfei, This time I am writing you on a separate note. On Tue, Aug 30, 2016 at 6:20 AM, Yunfei Guo [email protected]
Mamoon Rashid, PhD WARN 00:12:44,667 Interpreter - ![0,14]: 'ReadPosRankSum < -20.0;' undefined variable ReadPosRankSum |
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Hi @rashidma, Thanks for using SeqMule! GATK VQSR will not work well for a number of variants (e.g. in a small region) because it requires a relatively large sample for sampling. Regarding variant extraction, is your BED file compatible with UCSC hg19, i.e. has a subset of UCSC hg19 chromosomal names? Also I cannot find the log file. Best, |
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Hi Yunfei, The chromosome name is consistent in bed file and reference file. Please NOTICE: checking contig(chromosome) name consistency in I realised that seqmule is reading VCF.pm from another installations of Many thanks for your time. Mamoon On Tue, Oct 25, 2016 at 10:55 PM, Yunfei Guo [email protected]
Mamoon Rashid, PhD "WARN 00:12:53,217 Interpreter - ![0,14]: 'ReadPosRankSum < -20.0;' undefined variable ReadPosRankSum " ----------NOTICE---------- ----------NOTICE---------- Current version: 1.2.5 ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- ----------NOTICE---------- at /work/rashidma/software/VCFTOOLS/vcftools-vcftools-4a4e953/src/perl/Vcf.pm line 172 ----------ERROR---------- real 444m46.571s |
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VQSR is a better filtering method than hard filters. You can disable it in You are right about vcf module loading. I will fix it asap when I got time. On Wed, Oct 26, 2016 at 8:51 AM, rashidma [email protected] wrote:
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Hi Yun,
I recently run seqmule in quick mode with the following commands to test the installation-
seqmule pipeline -a normal_R1.fastq.gz -b normal_R2.fastq.gz -prefix example -N 2 -capture default -threads 10 -e
The report I got is matched with http://www.openbioinformatics.org/seqmule/example/example_report/example/example.html
There are differences which I assume is due to the target regions from bed file. In my run the bed (by default) is -
hg19_exonPlus5bp_UCSCrefGene.bed
But on your website the default bed is hg19_exome.bed
Can you provide me that hg19_exome.bed in order to reproduce the same result mentioned on your website.
Please comment overall.
Regards
Mamoon
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