Closed highwire2021 closed 1 year ago
I am sorry for my late response.
Would you share the VCF file in 30_vcf with the command line that you ran?
Thank you.
The command and result as follows:
~/mutmap$ mutmap -r ref.fasta -c P7_CleanData_R1.fastq.gz,P7_CleanData_R1.fastq.gz -b R151_L2_137A37.R1.fastq.gz,R151_L2_137A37.R2.fastq.gz -n 30 -o outR151 -t 12 --species Rice
[MutMap:2022-06-09 16:17:47] start to run MutMap.
[MutMap:2022-06-09 16:17:47] maximum number of threads which you can use is up to 16.
[MutMap:2022-06-09 16:17:47] start to index reference fasta.
[MutMap:2022-06-09 16:21:27] indexing of reference successfully finished.
[MutMap:2022-06-09 16:21:27] start to align reads of cultivar.0000 by BWA.
[MutMap:2022-06-09 16:53:04] alignment cultivar.0000 successfully finished.
[MutMap:2022-06-09 16:53:04] start to align reads of bulk.0000 by BWA.
[MutMap:2022-06-09 17:41:21] alignment bulk.0000 successfully finished.
[MutMap:2022-06-09 17:41:21] start to merge BAMs.
[MutMap:2022-06-09 17:42:50] merging process successfully finished.
[MutMap:2022-06-09 17:42:50] start to call variants.
[MutMap:2022-06-09 17:46:47] variant calling successfully finished.
[MutMap:2022-06-09 17:46:47] start to index VCF.
[MutMap:2022-06-09 17:46:47] indexing VCF successfully finished.
[MutMap:2022-06-09 17:46:48] start to run MutPlot.
!!WARNING!! Number of replicates for simulation is not enough to consider multiple testing correction. Therefore, the highest SNP-index and the second highest SNP-index were selected for p99 and p95, respectively.
[MutMap:2022-06-09 17:46:48] start to calculate SNP-index.
[MutMap:2022-06-09 17:46:48] SNP-index successfully finished.
[MutMap:2022-06-09 17:46:48] start to smooth SNP-index.
[MutMap:2022-06-09 17:46:48] smoothing process successfully finished.
[MutMap:2022-06-09 17:46:48] plotting now...
Traceback (most recent call last):
File "/home/wdk/miniconda3/envs/mutmap/bin/mutplot", line 10, in
Sorry for my late response.
Would you remove the option "--species Rice" and try mutplot from VCF file? We implemented that option into QTL-seq, but the results may change from what we expect.
Hi, Many thanks to the developers. I used use the mutmap v2.3.3 and showed "MutMap successfully finished". But the message "SystemError: tile cannot extend outside image" showed in the last line. I don't know how to deal with it.
Could you help me?
Best wishes!