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tony-kuo / eagle

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Empty output file from eagle run #2

Closed huguanjing closed 4 years ago

huguanjing commented 4 years ago

Hi @tony-kuo! I followed the tetraploid_analysis.sh to prepare vcf and run Star mapping. When it came to the EAGLE step running below script, the run finished but output is empty. Would you please help me to trouble shoot? Thanks a lot!

$time eagle -t 8 -a A2-10-R1.refsort.bam -r ../A2Du_13.fasta -v ../A.vs.D.gtf.vcf --splice --rc 1> A2-10-R1.A.vs.D.txt 2> A2-10-R1.A.vs.D.readinfo.txt

real    27m26.761s
user    50m44.891s
sys 1m26.995s

ls -lh
-rw-rw-r--+ 1 hugj2006 domain users    0 Jan 16 17:13 A2-10-R1.A.vs.D.list
-rw-rw-r--+ 1 hugj2006 domain users 817M Jan 16 17:42 A2-10-R1.A.vs.D.readinfo.txt

head A2-10-R1.A.vs.D.readinfo.txt
# Read VCF: ../A.vs.D.gtf.vcf   630309 entries  Fri Jan 17 09:08:17 2020
# Variants within 10 (max window: 0) bp: 503284 entries Fri Jan 17 09:08:17 2020
# Options: maxh=1024 mvh=1 pao=0 isc=1 nodup=0 splice=1 bs=0 lowmem=1 phred64=0
#          dp=0 gap_op=6 gap_ex=1
#          hetbias=0.5 omega=1e-40 cq=0
#          verbose=1
# Start: 8 threads  A2-10-R1.refsort.bam    Fri Jan 17 09:08:17 2020
HWI-ST412:220:D0L5UACXX:4:1207:13770:68011  Chr13   123831951   -0.030616   -8.727259   -92.123863  23M84N91M   1       [Chr13,123832117,C,A;]
HWI-ST412:220:D0L5UACXX:4:1207:13770:68011  Chr13   123831951   -0.030616   -9.418283   -92.123863  23M84N91M   1       [Chr13,123832138,T,C;]
HWI-ST412:220:D0L5UACXX:4:1207:13770:68011  Chr13   123831951   -0.030616   -10.569748  -92.123863  23M84N91M   1       [Chr13,123832076,G,A;]
tony-kuo commented 4 years ago

Hi,

The readinfo.txt file looks fine. What is the content of A2-10-R1.A.vs.D.txt?

The A2-10-R1.A.vs.D.list file would be generated with the next command, running eagle-rc.

In your case it would be: eagle-rc -a A2-10-R1.refsort.bam -o A2-10-R1.A.vs.D -v A2-10-R1.A.vs.D.txt \ A2-10-R1.A.vs.D.readinfo.txt > A2-10-R1.A.vs.D.list

Did you run this step?

huguanjing commented 4 years ago

Thank you for the speedy response! I tried both eagle and eagle-rc scripts again and they worked. It turned out my original job was somehow killed halfway so it didn't output 'A2-10-R1.A.vs.D.txt'. Thanks again!