SALMON's warning library type

Question

[biks.kestro]

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****

[GenoMax]

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

Answer 1

[Rob]

Hi biks.kestro,

I just had a chance to respond to this on the salmon/sailfish user group here. Please note that I moved your original post there since it was submitted as a response to our survey announcement rather than as its own thread. Basically, this warning is not necessarily serious, but it means you should check the output in the JSON file, and make sure you're providing the correct library type.