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Hi there,
What could be the reason why no alignable_1.fq is generated and all reads are written to GSM1272882_un_1.fq and GSM1272882_un_2.fq?
Here is the stderr,
[samopen] SAM header is present: 93312 sequences. # reads processed: 8792495 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 8792495 (100.00%) No alignments Cannot open GSM1272882.temp/GSM1272882_alignable_1.fq! It may not exist.
./rsem-1.2.5/rsem-build-read-index 32 1 0 GSM1272882.temp/GSM1272882_alignable_1.fq GSM1272882.temp/GSM1272882_alignable_2.fq "./rsem-1.2.5/rsem-build-read-index 32 1 0 GSM1272882.temp/GSM1272882_alignable_1.fq GSM1272882.temp/GSM1272882_alignable_2.fq" failed! Plase check if you provide correct parameters/options for the pipeline!
Thanks! Zhuyi
Summer Rae
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Dec 8, 2014, 5:10:20 PM12/8/14
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I'm getting the same error.. did you ever get any help on this?
Bo Li
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Dec 9, 2014, 2:43:14 PM12/9/14
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Hi Summer,
The error message suggested that you set '--paired-end' option for an
single-end data set.
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Hi! I am getting the same error. You mention that the error message suggests that it's a single end data set but
the original post has paired end data as inputs
my dataset is paired end reads as well.
I am running RSEM on multiple samples with paired-end reads and one of the sample is giving me the same error:
rsem-build-read-index 32 1 0 AA3_KP1_Neo_3.temp/AA3_KP1_Neo_3_alignable_1.fq AA3_KP1_Neo_3.temp/AA3_KP1_Neo_3_alignable_2.fq Cannot open AA3_KP1_Neo_3.temp/AA3_KP1_Neo_3_alignable_1.fq! It may not exist. "rsem-build-read-index 32 1 0 AA3_KP1_Neo_3.temp/AA3_KP1_Neo_3_alignable_1.fq AA3_KP1_Neo_3.temp/AA3_KP1_Neo_3_alignable_2.fq" failed! Plase check if you provide correct parameters/options for the pipeline!
Will highly appreciate your input on this. Thanks!