Hello, I have illumina Data: Trying to use kallisto and Salmon for alignment. 12 PE samples Both are failing to process my data:
Can some one try advising where and what is the problem? Thank you, Prasad.
The errors are pasted below:
*****************************************KALLISTO error on 2nd Sample*********
drsarat@saratngs:~/Downloads/PD_Analysis_4Jun2017/UsingKallisto$ ../../kallisto_linux-v0.43.1/kallisto quant -i ./KallistoDmel.idx -o 2TD -b 100 <(bunzip2 ../NGSData/2-Td_R1.fastq_filtered_trimmed.bz2) <(bunzip2 ../NGSData/2-Td_R2.fastq_filtered_trimmed.bz2)
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 30,485
[index] number of k-mers: 33,122,546
[index] number of equivalence classes: 57,764
[quant] running in paired-end mode
[quant] will process pair 1: /dev/fd/63
/dev/fd/62
[quant] finding pseudoalignments for the reads ... done
[quant] processed 0 reads, 0 reads pseudoaligned
[~warn] no reads pseudoaligned.
[quant] estimated average fragment length: 0
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 52 rounds
terminate called after throwing an instance of 'std::domain_error'
what(): nsamp must be -1 or >=1
Aborted (core dumped)
*********************************************************************
************SALMON error on 1st Sample which is successful with Kallisto** Logs will be written to quants/salmon_1CTR_quant/logs [2017-06-04 06:59:37.477] [jointLog] [info] parsing read library format [2017-06-04 06:59:37.477] [jointLog] [info] There is 1 library. [2017-06-04 06:59:37.549] [stderrLog] [info] Loading Suffix Array [2017-06-04 06:59:37.541] [jointLog] [info] Loading Quasi index [2017-06-04 06:59:37.549] [jointLog] [info] Loading 32-bit quasi index [2017-06-04 06:59:59.952] [stderrLog] [info] Loading Transcript Info [2017-06-04 07:00:05.466] [stderrLog] [info] Loading Rank-Select Bit Array [2017-06-04 07:00:06.385] [stderrLog] [info] There were 30485 set bits in the bit array [2017-06-04 07:00:06.407] [stderrLog] [info] Computing transcript lengths [2017-06-04 07:00:06.408] [stderrLog] [info] Waiting to finish loading hash [2017-06-04 07:00:08.624] [stderrLog] [info] Done loading index
[2017-06-04 07:00:08.624] [jointLog] [info] done
[2017-06-04 07:00:08.624] [jointLog] [info] Index contained 30485 targets
[2017-06-04 07:03:41.142] [jointLog] [info] Computed 0 rich equivalence classes for further p
rocessing
[2017-06-04 07:03:41.142] [jointLog] [info] Counted 0 total reads in the equivalence classes
[2017-06-04 07:03:41.146] [jointLog] [warning] Only 0 fragments were mapped, but the number o
f burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.
[2017-06-04 07:03:41.146] [jointLog] [warning] Something seems to be wrong with the calculati
on of the mapping rate. The recorded ratio is likely wrong. Please file this as a bug repor
t.
[2017-06-04 07:03:41.146] [jointLog] [info] Mapping rate = 0%
[2017-06-04 07:03:41.146] [jointLog] [info] finished quantifyLibrary()
[2017-06-04 07:03:41.158] [jointLog] [info] Starting optimizer
[2017-06-04 07:03:41.188] [jointLog] [info] Marked 0 weighted equivalence classes as degenera
te
[2017-06-04 07:03:41.188] [jointLog] [info] iteration = 0 | max rel diff. = 0.315097
[2017-06-04 07:03:41.191] [jointLog] [info] iteration = 50 | max rel diff. = -1.79769e+308
[2017-06-04 07:03:41.191] [jointLog] [error] Total alpha weight was too small! Make sure you
ran salmon correclty.
[2017-06-04 07:03:41.191] [jointLog] [error] The optimization algorithm failed. This is likel
y the result of bad input (or a bug). If you cannot track down the cause, please report this
issue on GitHub.
