no output from abbababa

[zyxplus]

Ran a test to calculate D statistics as followings, ANGSD -doAbbababa2 1 -bam test.bam.list -sizeFile test.bam.size -doCounts 1 -out test.bam.Angsd.1240k_test -anc $chimpFasta -rf 1240k.regio.test.v1 -useLast 1 -minQ 20 -minMapQ 13 -p 1 -nThreads 1

the output log is: ...... -> Region lookup 999/1000 -> Region lookup 1000/1000

    -> Done reading data waiting for calculations to finish
    -> Done waiting for threads
    -> Output filenames:
            ->"test.bam.Angsd.1240k_test.arg"
            ->"test.bam.Angsd.1240k_test.abbababa2"
    -> Sat Jan 25 23:01:45 2020
    -> Arguments and parameters for all analysis are located in .arg file
    -> Total number of sites analyzed: 185109
    -> Number of sites retained after filtering: 1870 
    [ALL done] cpu-time used =  53.75 sec
    [ALL done] walltime used =  54.00 sec

"test.bam.Angsd.1240k_test.abbababa2" only shows one line: CHR BLOCKstart BLOCKend Numer Denom numSites 0000 .... 3333

I checked the region file, bam file header, fasta file, they all name cheomosome as "chr1..23" . Any clue, please?

[SamueleSoraggi]

The error might be the use of -useLast 1 option, because you provide a fasta file as outgroup and not the last group of individuals in the list of bam files. Try to set -useLast 0 instead.

lør. 25. jan. 2020 4.08 PM skrev zyxplus notifications@github.com:

Ran a test to calculate D statistics as followings, ANGSD -doAbbababa2 1 -bam test.bam.list -sizeFile test.bam.size -doCounts 1 -out test.bam.Angsd.1240k_test -anc $chimpFasta -rf 1240k.regio.test.v1 -useLast 1 -minQ 20 -minMapQ 13 -p 1 -nThreads 1

the output log is: ...... -> Region lookup 999/1000 -> Region lookup 1000/1000

-> Done reading data waiting for calculations to finish
-> Done waiting for threads
-> Output filenames:
        ->"test.bam.Angsd.1240k_test.arg"
        ->"test.bam.Angsd.1240k_test.abbababa2"
-> Sat Jan 25 23:01:45 2020
-> Arguments and parameters for all analysis are located in .arg file
-> Total number of sites analyzed: 185109
-> Number of sites retained after filtering: 1870
[ALL done] cpu-time used =  53.75 sec
[ALL done] walltime used =  54.00 sec

"test.bam.Angsd.1240k_test.abbababa2" only shows one line: CHR BLOCKstart BLOCKend Numer Denom numSites 0000 .... 3333

I checked the region file, bam file header, fasta file, they all name cheomosome as "chr1..23" . Any clue, please?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANGSD/angsd/issues/281?email_source=notifications&email_token=ACC66UOODQ4DA74Y3I45FYLQ7RIXRA5CNFSM4KLRJUZ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIWC5JA, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACC66ULEVW7WDG5QG5QBFCLQ7RIXRANCNFSM4KLRJUZQ .

[ANGSD]

Im am closing this issue feel free to reopen if needed.