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grenaud / schmutzi

Maximum a posteriori estimate of contamination for ancient samples
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Calmd problem #20

Open anaa94 opened 1 year ago

anaa94 commented 1 year ago

Hi, I am aware this is an issue caused by not producing a proper calmd bam, but maybe you have some ideas?
I ran the calmd file without any issues in the rmdupped bam file. Then I ran the Cont.deam command without any issues as well. But then I ran the schmutzi command it gave an error:

/home/ubuntu/programs/schmutzi/src/schmutzi.pl --notusepredC --uselength --lengthMT 16389 --ref /home/ubuntu/reference/mtDNA_orang_NC_001646.1.fa --out 653_npred 653/653 653 653_sorted_alignment.rmdup_MD.bam Found the following freq files:

copying 653/653.endo.5p.prof to 653_npred_1_endo.5p.prof copying 653/653.endo.3p.prof to 653_npred_1_endo.3p.prof copying 653/653.cont.est to 653_npred_1_cont.est

############################

reading the contamination estimate file: 653_npred_1_cont.est

############################

ITERATION # 1

Contamination rate: 0.00

############################ running cmd /home/ubuntu/programs/schmutzi/src/endoCaller -seq 653_npred_1_endo.fa -log 653_npred_1_endo.log -name MT -qual 0 -logindel 50 -deamread -deam5p 653_npred_1_endo.5p.prof -deam3p 653_npred_1_endo.3p.prof -cont 0.01 -deam5pc 653_npred_1_cont.5p.prof -deam3pc 653_npred_1_cont.3p.prof -single -seqc 653_npred_1_cont.fa -logc 653_npred_1_cont.log -namec MTc -l 1 /home/ubuntu/reference/mtDNA_orang_NC_001646.1.fa 653_sorted_alignment.rmdup_MD.bam Reading genome file ... ... done Reading BAM file ... Read 100,000 reads Read 200,000 reads (continues) Read 10,500,000 reads ... done Reading BAM to set priors for each read ... Query reference base is not the same for read A00500:383:H27FTDSX3:1:1160:21323:17503 pos 2 This can be normally solved by calling samtools' calmd on your bam file 2 T M T T R= C= A00500:383:H27FTDSX3:1:1160:21323:17503

Then I checked the calmd files and realized it was the same file size, then md5sum and it was the same file content as well. Has this happened before to any schmutzi user? I have already searched over the internet but I haven't found this calmd problem anywhere.

Thank you in advance!

grenaud commented 1 year ago

Hello! I think with calmd, it should be slightly larger as you add information, I would be worried about the intial value of 0.0, are you sture you have some damage?