Empty sam file

[mrb20045]

hi I used bs3 and every things goes well as follow. But at the end sam file is empty. I found out some other people faced to the same problem. I think that the main code has some problem. Let me know can it be my fault.

python '/home/bs3/bs3-align.py' -1 '/home/Data/R1_1.fq.gz' -2 '/home/Data/R1_2.fq.gz' -g '/home/ARS-UCD1/bt_ref_ARS-UCD1.2.fa' -d '/media/reference_genome' -o aex

 BS-Seeker3 beta

Welcome to SNAP version 1.0beta.23.

Loading index from directory... 59s. 961853050 bases, seed size 20 Aligning. Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s) 400,000 325,572 (81.39%) 36,032 (9.01%) 27,723 (6.93%) 10,673 (2.67%) 45.33% 78,724 5 (None, None)

BS-seeker3 Result

Final Alignment Report

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Number of reads in total: 400000 Number of unique-hits reads (before post-filtering): 0 Number of reads mapped after post-filtering 0

Alignment Time: 79.7409200668secs

Final Cytosine Report

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Total Number of Cytosines: 0 Total Number of Cs in CpG context: 0 Total Number of Cs in CHG context: 0 Total Number of Cs in CHH context: 0

Rate of Methylation mCG 0.000% mCHG 0.000% mCHH 0.000%