mothur

Make.sra command

Dear all, sorry to interrupt.

Can anyone help me with the Make.sra command. I have been trying since morning but it’s night now no output.

Some command I used:

mothur > make.sra(sff=AP.sff, oligos=AP.txt, pdiffs=2, bdiffs=1, project=test.project, mimark=MIMarksData.txt)

/******************************************/
Running command: sffinfo(sff=C:\mothur\AP.sff, oligos=C:\mothur\AP.txt, pdiffs=2, bdiffs=1, tdiffs=3)
Extracting info from C:\mothur\AP.sff …
10000
20000
30000
40000
50000
60000
70000
80000
90000
100000
110000
119813
It took 483 secs to extract 119813.

Output File Names:
C:\mothur\AP.Treatment.24.1_AACGTATC.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.24.1_AACGTATG.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Treatment.48.1_AACGTATT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.48.1_AACGTCAC.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Treatment.48.2_CAGTCATT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.R.0_CATATGGT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Treatment.24.3_TAATTGGA.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.0_TCCGTCAT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.48.3_TCTACGTT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Treatment.24.2_TCTCTTCT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.48.2_TGGCGAGA.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.24.3_TGGTAAGT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Treatment.48.3_TTACCAAT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.Control.24.2_TTCAGGCT.GAGTTTGATCCTGGCTCA.sff
C:\mothur\AP.fasta
C:\mothur\AP.qual
C:\mothur\AP.flow
C:\mothur\AP.scrap.sff

/******************************************/
[ERROR]: MIMarks file is missing group Control.0_TCCGTCAT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.24.1_AACGTATG.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.24.2_TTCAGGCT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.24.3_TGGTAAGT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.48.1_AACGTCAC.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.48.2_TGGCGAGA.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.48.3_TCTACGTT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Control.R.0_CATATGGT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Treatment.24.1_AACGTATC.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Treatment.24.2_TCTCTTCT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Treatment.24.3_TAATTGGA.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Treatment.48.1_AACGTATT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Treatment.48.2_CAGTCATT.GAGTTTGATCCTGGCTCA, please correct.
[ERROR]: MIMarks file is missing group Treatment.48.3_TTACCAAT.GAGTTTGATCCTGGCTCA, please correct.

Actually, there is no output in the folder.

The command in the released version of mothur is not ready for prime time. The next release should have our first working version of the function.

Dear Dr. Pat, thanks a lot for your clarification. I will wait for the next release.