Erro in SOAPfuse-v1.27

[liuco...@gmail.com]

Dear MIss\Sir，

When I used SOAPfuse-v1.27, I  always got this error message,while this erro did not happen  when I used another data:

1. 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Step s03 finishes at Mon Jun 19 05:05:01 CST 2017

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Step s04 starts at Mon Jun 19 05:05:11 CST 2017

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Step s04 didnot finish successfully!

2. The fusion.s04.singlefork.sh.log file is:

change_SE_tmp_ok

Wrong change_SE format2:

SOAPfuse-v1.27/simu-results/change_SE/simu.final.100.rep1/simu.final.100.rep1-library/simu.final.100.rep1.Combined.SESoap.tmp.gz_Sf_SD1_Sf_AACS_ACSBG1-112/1 TCTGCCAGAGGGTGGGCAGCAGAGCCACCACAGTGTCCGAGATCATAGAGAAGAAGGATGAGGCCTTGTACCAGGCCATCGAAGAGGGGATCCGGAGGGT CDB@D;CF?DDDCDID>DC(D9HFB5BDHFF@J@IIJI@HC:GHHHF

@JD7JIJI(DIJIJHGAE)IFI<AIIJFHJA?:IEFJJJEHHGFHDEFFFC>C 5 a 100 - ACSBG1-001 2110 1 G->65T5 100M 65G34 p

3. The computer system I used:

Linux ZlabN 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4. The fastq file I used:

simu.final.100.rep1_1.fq.gz  

@ENST00000255152.2-540/1

GTGGTATGGTCCCAAACACAGGCCAGCCTGAGAAGCAAGGACGGAACGACATGATTCAGGACCTAAGCAGGGAGTTAGCAAACCTGCTCATGCAGACCGA

+

BCBFFF>FHHHH?JIJIIJIIJJJJHAIJFJGJCEJ)GDIBIIDI3=AIJIAIFJGI;7GDIJBJ?)(DAEEJ>IC?1EEFDGDEE8D(>>CE4DE@DED

@ENST00000255152.2-538/1

TCCGCTTCCCAGAGAATCTCTTGCTACACCGGGTGGAGAACACCCAGGGCCACATCCTCTATGCTTTCTTGGTCGAGAACAAGGAACGAGAAAGTCGAGT

+

@C4FDEFFH)HHHIIHJJJIJIJJJ+HICGIIAI?HJ+GJ0JIHF?J9&JIIDHFJHIFI3JEAEFGDE-CEI(>?<9C>F(E?D@;@FD&+...@4.DCD

simu.final.100.rep1_2.fq.gz

 

@ENST00000255152.2-540/2

TCAGCTAAAGTGCTTCAATAATGCATCACAGCTGTAGCAGGAGGGAATCCCTCCCCTTCTTCTTGCTTTCCCCAGAGGAAAGGGAGGCGGCCCACGTCCT

+

CC@FFEF1HFHFHJJJJJGJBI<AIJ?JG<IDI)<HGIHJJF?I?0FJ.IFABIEJFGHIHAJCA:IFGDDEFDBHDDEDCCFD.@BCDE>A8>DAABD(

@ENST00000255152.2-538/2

AGAGTCGGGTTGTGTGGTAGATGGAAAGGAGGATGCGGGCAGCAGGAAAGATCTCCTGCTGGATAGCCCGGTAATGGAATGAAGGGTCCACAAAGACCAC

+

CC@FFFB,HHDHH)JBEJGDHGEJJH1JGIIGGJCFGGFJJHGGHBHI4JIGCAG:IGJ)5GDFDFIHJ=HHEBA?DFHDDF3H+D.D()D5D4DFDCDD

The folder of align_trim_unmap_Tran:

lSOAPfuse-v1.27/simu-results/align_trim_unmap_Tran$ ls -lht

drwxrwxr-x 3 liuc liuc 4.0K Jun 19 02:25 simu.final.100.rep1

The filder of change_SE:

SOAPfuse-v1.27/simu-results/change_SE/simu.final.100.rep1/simu.final.100.rep1-library$ ls -lht

total 16M

-rw-rw-r-- 1 liuc liuc 1.3K Jun 19 16:45 simu.final.100.rep1.Combined.SESoap.gz

-rw-rw-r-- 1 liuc liuc  16M Jun 19 05:05 simu.final.100.rep1.Combined.SESoap.tmp.gz

Thank you!

[Yifang Tan]

It's hard to tell what's wrong with your information provided.
The error tells you: Wrong change_SE format2!

My suggest:

1) Compare the two datasets: worked vs not_worked

2) The config files of the two tests, and the corresponding files including the path to the files

3) Look into the reads of FASTQ files including the quality scores and seq length. I had a bug of unequal string lengths of the quality score and the sequence due to the processing at the sequencer, which took me days to find it out.

Good luck!

--
You received this message because you are subscribed to the Google Groups "BGI-SOAP" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bgi-soap+unsubscribe@googlegroups.com.
To post to this group, send email to bgi-...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/bgi-soap/02239e71-1b1c-425d-99d1-23dd14481b19%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.