Comments (2)
I encountered similar problem, but dealing with KNIFE output.
Logs will be written to /home/jshi/disks/diskd/circRNA_0929/101N/quant_circular/logs
there is 1 lib
[2018-09-30 09:18:26.861] [jointLog] [info] parsing read library format
Loading 32-bit quasi index[2018-09-30 09:18:26.930] [jointLog] [info] Loading Quasi index
[2018-09-30 09:18:26.939] [stderrLog] [info] Loading Suffix Array
[2018-09-30 09:18:26.939] [stderrLog] [info] Loading Position Hash
[2018-09-30 09:18:27.653] [stderrLog] [info] Loading Transcript Info
[2018-09-30 09:18:27.842] [stderrLog] [info] Loading Rank-Select Bit Array
[2018-09-30 09:18:27.925] [stderrLog] [info] There were 51530 set bits in the bit array
[2018-09-30 09:18:27.944] [stderrLog] [info] Computing transcript lengths
[2018-09-30 09:18:27.947] [stderrLog] [info] Waiting to finish loading hash
Index contained 51530 targets
[2018-09-30 09:18:33.868] [stderrLog] [info] Done loading index
[2018-09-30 09:18:33.868] [jointLog] [info] done
Loaded targets
Done Quasi-Mapping
[2018-09-30 09:27:17.666] [jointLog] [info] Gathered fragment lengths from all threads
[2018-09-30 09:27:17.666] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction
[2018-09-30 09:27:17.666] [jointLog] [info] Estimating effective lengths
[2018-09-30 09:27:17.702] [jointLog] [info] Computed 0 rich equivalence classes for further processing
[2018-09-30 09:27:17.702] [jointLog] [info] Counted 0 total reads in the equivalence classes
[2018-09-30 09:27:17.702] [jointLog] [info] Starting optimizer:
[2018-09-30 09:27:17.705] [jointLog] [info] Optimizing over 0 equivalence classes
[2018-09-30 09:27:17.705] [jointLog] [error] It seems that no transcripts are expressed; something is likely wrong!
[2018-09-30 09:27:17.705] [jointLog] [error] Encountered error during optimization.
This should not happen.
Please file a bug report on GitHub.
Can you figure out the problem for us please? Thank you in advance!
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I have observed the same issue mentioned, if I call sailfish_cir
as suggested for sailfish kingsfordgroup/sailfish#11 using sailfish_cir [options] -r <(unzip -c <fastq>.gz)
.
This didn't happen to me when I unzip the fastq files beforehand.
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