I am using SALMON for my RNASeq project. Currently, I used SALMON to get the quantification value for my RNASeq samples. I got an message: "Greater than 5% of the fragments disagreed with the provided library type; check the file: /runjobs/SP00011781/34781/R38-6_S30/lib_format_counts.json for details".
Is this a very important error message and it is telling me that something is wrong with my processing.
The message comes like this:
Observed 32569645 total fragments (32569645 in most recent round)
[2017-06-20 16:57:32.847] [jointLog] [info] Computed 85307 rich equivalence classes for further processing
[2017-06-20 16:57:32.847] [jointLog] [info] Counted 26923981 total reads in the equivalence classes
[2017-06-20 16:57:32.878] [jointLog] [info] Mapping rate = 82.6659%
[2017-06-20 16:57:32.878] [jointLog] [info] finished quantifyLibrary()
[2017-06-20 16:57:32.879] [jointLog] [info] Starting optimizer
[2017-06-20 16:57:34.285] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2017-06-20 16:57:34.517] [jointLog] [info] iteration = 0 | max rel diff. = 66.205
[2017-06-20 16:57:57.521] [jointLog] [info] iteration = 100 | max rel diff. = 0.114067
[2017-06-20 16:58:18.699] [jointLog] [info] iteration = 200 | max rel diff. = 0.0611144
[2017-06-20 16:58:40.676] [jointLog] [info] iteration = 300 | max rel diff. = 0.0405679
[2017-06-20 16:59:02.968] [jointLog] [info] iteration = 400 | max rel diff. = 0.039969
[2017-06-20 16:59:25.304] [jointLog] [info] iteration = 500 | max rel diff. = 0.0460572
[2017-06-20 16:59:48.197] [jointLog] [info] iteration = 600 | max rel diff. = 0.0208071
[2017-06-20 17:00:10.401] [jointLog] [info] iteration = 700 | max rel diff. = 0.0189551
[2017-06-20 17:00:32.842] [jointLog] [info] iteration = 800 | max rel diff. = 0.0178634
[2017-06-20 17:00:56.286] [jointLog] [info] iteration = 900 | max rel diff. = 0.0139147
[2017-06-20 17:01:19.603] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0126367
[2017-06-20 17:01:44.383] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0124511
[2017-06-20 17:02:09.674] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0105276
[2017-06-20 17:02:34.535] [jointLog] [info] iteration = 1300 | max rel diff. = 0.0105277
[2017-06-20 17:02:41.125] [jointLog] [info] iteration = 1328 | max rel diff. = 0.00955
[2017-06-20 17:02:41.367] [jointLog] [info] Finished optimizer
[2017-06-20 17:02:41.367] [jointLog] [info] writing output
[2017-06-20 17:02:43.996] [jointLog] [warning] NOTE: Read Lib [( /runjobs/SP00011781/34776/R38-77_S28_R1.fastq.gz, /runjobs/SP00011781/34776/R38-77_S28_R2.fastq.gz )] :
****Greater than 5% of the fragments disagreed with the provided library type; check the file: /runjobs/SP00011781/34776/R38-77_S28/lib_format_counts.json for details****
It never helps to try and post the actual error messages in the title of a post. Consider something simpler like "Salmon error".
Have you looked at the suggested file to see what could be wrong:
/runjobs/SP00011781/34776/R38-77_S28/lib_format_counts.json
?You also seem to be specifying an incorrect library type:
Greater than 5% of the fragments disagreed with the provided library type