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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Salmon (0.6.0) [jointLog] [warning] [Sampler.hpp]: Failed to sample an alignment #210

Open XinpengQi opened 7 years ago

XinpengQi commented 7 years ago

Hi @blahah any updates for Transrate v1.0.3?

my snap.log seems fine:

Loading index from directory... 2s. 384271831 bases, seed size 23 Aligning. Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns Extra Alignments %Pairs Reads/s Time in Aligner (s) 693,340,846 280,486,471 (40.45%) 330,208,110 (47.63%) 78,660,098 (11.35%) 3,986,167 (0.57%) 620,752,208 78.36% 124,387 5,574 Welcome to SNAP version 1.0dev.96.

While salmon.log gives warning:

[2017-05-17 13:45:11.509] [jointLog] [warning] [Sampler.hpp]: Failed to sample an alignment for this read; this shouldn't happen currentMass = -nan, r = 0.694954

Detail salmon.log: ...... [2017-05-17 13:40:55.996] [fileLog] [info] quantification processed 354000000 fragments so far [2017-05-17 13:41:01.787] [jointLog] [info] Completed first pass through the alignment file. Total # of mapped reads : 354762625 of uniquely mapped reads : 144015998 ambiguously mapped reads : 210746627 [2017-05-17 13:41:01.761] [fileLog] [info] quantification processed 354762625 fragments so far [2017-05-17 13:41:33.214] [jointLog] [info] Computed 9628374 rich equivalence classes for further processing [2017-05-17 13:41:33.214] [jointLog] [info] Counted 354762625 total reads in the equivalence classes [2017-05-17 13:41:33.227] [jointLog] [info] starting optimizer [2017-05-17 13:41:39.341] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2017-05-17 13:41:39.618] [jointLog] [info] iteration = 0 | max rel diff. = 800.763 [2017-05-17 13:41:53.311] [jointLog] [info] iteration 50, recomputing effective lengths [2017-05-17 13:42:09.716] [jointLog] [info] iteration = 100 | max rel diff. = 0.358082 [2017-05-17 13:42:40.040] [jointLog] [info] iteration = 200 | max rel diff. = 0.305365 [2017-05-17 13:43:10.754] [jointLog] [info] iteration = 300 | max rel diff. = 0.0754343 [2017-05-17 13:43:41.135] [jointLog] [info] iteration = 400 | max rel diff. = 0.0490107 [2017-05-17 13:44:09.308] [jointLog] [info] iteration 500, recomputing effective lengths [2017-05-17 13:44:10.037] [jointLog] [info] iteration = 500 | max rel diff. = 0.0219555 [2017-05-17 13:44:39.741] [jointLog] [info] iteration = 600 | max rel diff. = 0.127602 [2017-05-17 13:45:09.829] [jointLog] [info] iteration = 699 | max rel diff. = 0.0077808 [2017-05-17 13:45:09.864] [jointLog] [info] finished optimizer [2017-05-17 13:45:10.734] [jointLog] [info] Sampling alignments; outputting results to ./postSample.bam [2017-05-17 13:45:11.509] [jointLog] [warning] [Sampler.hpp]: Failed to sample an alignment for this read; this shouldn't happen currentMass = -nan, r = 0.694954 ......

XinpengQi commented 7 years ago

I mean, Transrate v1.0.3 finished run: [ INFO] 2017-05-17 15:11:51 : Writing contig metrics for each contig to /mnt/nfs/nfs2/xinpeng.qi/blueberry/TransRate/transrate_results/trinity_version4/contigs.csv [ INFO] 2017-05-17 15:13:35 : Writing analysis results to assemblies.csv However, the "p fragments mapped" is only 0.37.

XinpengQi commented 7 years ago

@blahah confirmed Salmon0.8.2 works fine in my data!

matthewabirk commented 5 years ago

@XinpengQi, how did you get the updated Salmon to run within Transrate? I have encountered the same issue.

XinpengQi commented 5 years ago

Not yet solved :-(