haoziyeung
commented
6 years ago Traceback (most recent call last):
File "iCallSV.py", line 380, in
Closed haoziyeung closed 6 years ago
haoziyeung
commented
6 years ago Traceback (most recent call last):
File "iCallSV.py", line 380, in
rhshah
commented
6 years ago Are you trying to run scripts individually? Also are the two errors that you mentioned are related to the same run.
The Calculate Confidence Score feature is not validated and doesn't work in all cases, I tried to take advantage of targetSeqView to do this but it does not run successfully in all scenarios, thus I use the value '0' in cases it fails.
haoziyeung
commented
6 years ago can i remove targetSeqView,and run all the pipeline of iCallSV?
rhshah
commented
6 years ago No you cannot. iCallSV should be able to continue even if targetSeqView fails.
haoziyeung
commented
6 years ago First,i run iCallSV,
python iCallSV.py -sc configuration/template.ini -abam /gpfs/users/yanghao/project/shi-jian-zhi-ping/t_n_20171030/illumina/Illumina-B1701.bam -bbam /gpfs/users/yanghao/project/shi-jian-zhi-ping/t_n_20171030/illumina/Illumina-B17NC.bam -aId Illumina-B1701-sm -bId Illumina-B17NC-sm -o /gpfs/users/yanghao/test/iCallSV -op prefix_for_the_output_files -v
it occurs error:
i realize maybe it's because targetSeqView,so i run R individually
rhshah
commented
6 years ago Thanks for the detailed explanation. Would you mind pasting the header of the Illumina-B17NC-sm_allSVFiltered.vcf. The issue most likely looks like is the ID of the samples in the VCF and ID of the samples provided by you on the command line. If they are not the same then you can fix this by making the readgroup in BAM file as same ID as what you are using in command line using AddOrReplaceReadGroups and then rerun. This happens because delly uses readgroup from BAM to assign sample ID.
haoziyeung
commented
6 years ago sorry for reply you so slow,here is my header in Illumina-B1701-sm_allSVFiltered.vcf:
rhshah
commented
6 years ago Than you for pasting the header of vcf as you can see from the header the
Sample ID has _ after Illumina in the sample ID and what you have provided to the script does not as you can see below:
-aId Illumina-B1701-sm -bId Illumina-B17NC-sm
Can you please try running it with the:
-aId Illumina_B1701-sm -bId Illumina_B17NC-sm
Do let me know if you see any issue further.
haoziyeung
commented
6 years ago thanks a lot,i'll try again with the right sample ID
haoziyeung
commented
6 years ago Hi,@rhshah,it's all right now ,thank you ,it's a great software.
rhshah
commented
6 years ago I am glad it worked and it is useful.
Hello,@rhshah,sorry for bother you again,when i run iCallSV,i met a error like below:
command: R --slave --vanilla --args 5 /gpfs/users/yanghao/project/shi-jian-zhi-ping/t_n_20171030/illumina /gpfs/users/yanghao/test/iCallSV/StructuralVariantAnalysis/DellyDir/Illumina-B1701-sm/Illumina-B1701-sm_allSVFiltered_tsvInput.txt hg19 150 /gpfs/users/yanghao/test/iCallSV/StructuralVariantAnalysis/DellyDir/Illumina-B1701-sm Illumina-B1701-sm_allSVFiltered_cScore.txt < /gpfs/users/yanghao/software/iCallSV/iCallSV/R/Rscripts/calculateConfidenceScore.R
stdout/stderr: [1] "mismatch limit increased to 136 to capture reads on both references" [1] "mismatch limit increased to 137 to capture reads on both references" [1] "Working on event 20 of 24" [1] "mismatch limit increased to 138 to capture reads on both references" [1] "mismatch limit increased to 139 to capture reads on both references" [1] "mismatch limit increased to 140 to capture reads on both references" [1] "mismatch limit increased to 141 to capture reads on both references" [1] "mismatch limit increased to 142 to capture reads on both references" [1] "mismatch limit increased to 143 to capture reads on both references" [1] "mismatch limit increased to 144 to capture reads on both references" [1] "mismatch limit increased to 7 to capture reads on both references" [1] "mismatch limit increased to 145 to capture reads on both references" [1] "mismatch limit increased to 8 to capture reads on both references" [1] "mismatch limit increased to 146 to capture reads on both references" [1] "mismatch limit increased to 9 to capture reads on both references" [1] "mismatch limit increased to 147 to capture reads on both references" [1] "mismatch limit increased to 10 to capture reads on both references" [1] "mismatch limit increased to 148 to capture reads on both references" [1] "mismatch limit increased to 11 to capture reads on both references" [1] "mismatch limit increased to 149 to capture reads on both references" [1] "mismatch limit increased to 150 to capture reads on both references" [1] "mismatch limit increased to 151 to capture reads on both references" [1] "Working on event 22 of 24" [1] "Working on event 16 of 24" [1] "mismatch limit increased to 7 to capture reads on both references" [1] "mismatch limit increased to 8 to capture reads on both references" [1] "mismatch limit increased to 9 to capture reads on both references" [1] "mismatch limit increased to 10 to capture reads on both references" [1] "Working on event 24 of 24" [1] "mismatch limit increased to 7 to capture reads on both references" [1] "mismatch limit increased to 8 to capture reads on both references" [1] "mismatch limit increased to 9 to capture reads on both references" [1] "Working on event 21 of 24" Error in { : task 1 failed - "'unlist' is not an exported object from 'namespace:Biostrings'" Calls: calculateConfidenceScore ... ViewAndScoreFull -> alignViewFull -> %dopar% ->
Execution halted
can you help me ?