moabs and bismark

[Awni Mousa]

Hi, 

I successfully installed moabs and it runs very smoothly with the test run.

I’m trying to run mcall on a bismark.sam alignment file and bumped into the following error:

$ mcall -m 415_test.sam --sampleName=OX --fullMode=1 --genome=mm10 --reportCpX=H --reportCHX=H --reference=mm10.fa -p 50

Options are saved in file run.config and printed here:
cytosineMinScore=20
excludedFlag=0
fullMode=1
genome=mm10
keepTemp=0
mappedFiles=415_test.sam 
minFragSize=0
minMMFragSize=0
nextBaseMinScore=3
processPEOverlapSeq=1
qualityScoreBase=0
reference=mm10.fa
reportCHX=H
reportCpX=H
requiredFlag=0
sampleName=OX
skipRandomChrom=1
statsOnly=0
threads=50
trimRRBSEndRepairSeq=2
trimWGBSEndRepairPE1Seq=3
trimWGBSEndRepairPE2Seq=3
Program started
From the extension of file 415_test.sam, program is parsing file according to SAM foramt
XR:Z or ZR:Z:, or ZS:Z: field not found, please enable -R option in bsmap
For file 415_test.sam, the quality score format is Sanger format based at 33!
Protocol and read length are detected as WGBS and 101 bases for file 415_test.sam
For file 415_test.sam the number of all reads is 99976 and the number of mapped reads is 99976
Start processing file 415_test.sam on chrom chrM
No read is found in file 415_test.sam
Writing strand specific statistics for file 415_test.sam and chrom chrM
Writing strand combined statistics for file 415_test.sam and chrom chrM
Finished processing file 415_test.sam on chrom chrM

All files done for chrom chrM
Start processing file 415_test.sam on chrom chr10
HISEQ1:483:H88B5ADXX:1:1101:1367:2140_1:N:0: 99 chr10 54030180 255 101M = 54030237 157 AATGGATTATAGGTGGTAGAATTAGGTGGGAAGGATTATGAGGTTTGTTTTTTATTGGGGTAGGTTTTTTTTGTTTTTTAATTTAGGTTATTATTAGTTAG CCCFFFFFHHHHGACGCGHIIIIJJIAFGGIJICFIIJJJGIJ?FHIFGIJIIDIJJJJJ:AEFCDFFDDDDDACDDDDDDCEECDD@ACDDCEEDDDDDC NM:i:18 XX:Z:6CC13C26C1C3C9C1CCC7CC3CCC3CC4C7 XM:Z:......hh.............h..........................h.h...x.........h.hhh.......hh...hhx...hh....h....... XR:Z:CT XG:Z:CT
18446744073709551615
ZS:Z:<str> field not found; Is it BAM/SAM format?

Any advice?

Thank you,

Awni Mousa

[franck ladam]

Hi Mousa,

I ran into the same problem. Have you found a solution? can you share?
Thanks!