STEP 6: Error in geneIndexList[[i]] : subscript out of bounds #26
Description
HERE IS THE ERROR. Salmon and Cutadapt works fine but when i follow your protocol i keep getting this error. Please help me resolve this issue.
determining read length
Trimming reads
This is cutadapt 4.2 with Python 3.10.8
Command line parameters: -m 30 -u 18 -u -17 -o ./subset_SRR12820270_trimmed.fq subset_SRR12820270.fastq
Processing single-end reads on 1 core ...
Finished in 103.257 s (2.988 µs/read; 20.08 M reads/minute).
=== Summary ===
Total reads processed: 34,554,336
== Read fate breakdown ==
Reads that were too short: 778,286 (2.3%)
Reads written (passing filters): 33,776,050 (97.7%)
Total basepairs processed: 2,555,642,890 bp
Total written (filtered): 1,335,316,421 bp (52.2%)
Salmon
Version Info: This is the most recent version of salmon.
salmon (selective-alignment-based) v1.10.0
[ program ] => salmon
[ command ] => quant
[ threads ] => { 5 }
[ index ] => { ref//default }
[ libType ] => { U }
[ unmatedReads ] => { subset_SRR12820270_trimmed.fq }
[ output ] => { salmonRes_SRR12820270 }
Logs will be written to salmonRes_SRR12820270/logs
[2023-02-28 11:41:51.239] [jointLog] [info] setting maxHashResizeThreads to 5
[2023-02-28 11:41:51.240] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2023-02-28 11:41:51.240] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-02-28 11:41:51.241] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-02-28 11:41:51.241] [jointLog] [info] parsing read library format
[2023-02-28 11:41:51.242] [jointLog] [info] There is 1 library.
[2023-02-28 11:41:51.243] [jointLog] [info] Loading pufferfish index
[2023-02-28 11:41:51.243] [jointLog] [info] Loading dense pufferfish index.
| Loading contig table | Time = 13.375 s
size = 36981178
| Loading contig offsets | Time = 223.69 ms
| Loading reference lengths | Time = 5.5834 ms
| Loading mphf table | Time = 2.765 s
size = 3784352032
Number of ones: 36981177
Number of ones per inventory item: 512
Inventory entries filled: 72229
| Loading contig boundaries | Time = 6.5841 s
size = 3784352032
| Loading sequence | Time = 1.6722 s
size = 2674916722
| Loading positions | Time = 19.596 s
size = 3401221626
| Loading reference sequence | Time = 2.5547 s
| Loading reference accumulative lengths | Time = 71.449 ms
[2023-02-28 11:42:38.364] [jointLog] [info] done
[2023-02-28 11:42:38.896] [jointLog] [info] Index contained 177,651 targets
[2023-02-28 11:42:39.060] [jointLog] [info] Number of decoys : 195
[2023-02-28 11:42:39.060] [jointLog] [info] First decoy index : 177,412
processed 500,005 fragments
processed 1,000,021 fragmentsg: 3.51056
processed 1,500,006 fragmentsg: 3.57137
processed 2,000,010 fragmentsg: 3.50785
processed 2,500,000 fragmentsg: 3.52013
processed 3,000,002 fragmentsg: 3.51665
processed 3,500,005 fragmentsag: 3.51738
processed 4,000,005 fragmentsag: 3.49182
processed 4,500,001 fragmentsag: 3.49594
processed 5,000,003 fragmentsag: 3.50565
processed 5,500,002 fragmentsag: 3.4983
processed 6,000,002 fragmentsag: 3.49189
processed 6,500,004 fragmentsag: 3.49138
processed 7,000,003 fragmentsag: 3.4895
processed 7,500,008 fragmentsag: 3.48928
processed 8,000,002 fragmentsag: 3.49037
processed 8,500,001 fragmentsag: 3.4896
processed 9,000,010 fragmentsag: 3.48465
processed 9,500,001 fragmentsag: 3.48998
processed 10,000,003 fragmentsg: 3.48525
processed 10,500,010 fragmentsg: 3.48806
processed 11,000,015 fragmentsg: 3.48831
processed 11,500,005 fragmentsg: 3.48911
processed 12,000,014 fragmentsg: 3.48969
processed 12,500,006 fragmentsg: 3.48973
processed 13,000,013 fragmentsg: 3.49159
processed 13,500,002 fragmentsg: 3.49334
processed 14,000,008 fragmentsg: 3.49106
processed 14,500,014 fragmentsg: 3.49369
processed 15,000,006 fragmentsg: 3.49404
processed 15,500,003 fragmentsg: 3.49327
processed 16,000,006 fragmentsg: 3.49111
processed 16,500,000 fragmentsg: 3.49389
processed 17,000,008 fragmentsg: 3.49389
processed 17,500,003 fragmentsg: 3.49404
processed 18,000,008 fragmentsg: 3.49595
processed 18,500,007 fragmentsg: 3.49517
processed 19,000,004 fragmentsg: 3.4917
processed 19,500,005 fragmentsg: 3.49187
processed 20,000,016 fragmentsg: 3.49191
processed 20,500,001 fragmentsg: 3.49566
processed 21,000,002 fragmentsg: 3.49412
processed 21,500,005 fragmentsg: 3.49473
processed 22,000,003 fragmentsg: 3.49406
processed 22,500,008 fragmentsg: 3.49372
processed 23,000,001 fragmentsg: 3.49317
processed 23,500,001 fragmentsg: 3.49268
processed 24,000,009 fragmentsg: 3.49015
processed 24,500,012 fragmentsg: 3.49356
processed 25,000,000 fragmentsg: 3.49292
processed 25,500,005 fragmentsg: 3.49137
processed 26,000,007 fragmentsg: 3.49166
processed 26,500,018 fragmentsg: 3.49258
processed 27,000,004 fragmentsg: 3.49206
processed 27,500,007 fragmentsg: 3.49304
processed 28,000,004 fragmentsg: 3.49252
processed 28,500,003 fragmentsg: 3.49275
processed 29,000,006 fragmentsg: 3.4934
processed 29,500,011 fragmentsag: 3.49361
processed 30,000,010 fragmentsag: 3.49353
processed 30,500,009 fragmentsag: 3.4931
processed 31,000,008 fragmentsag: 3.49452
processed 31,500,010 fragmentsag: 3.4932
processed 32,000,004 fragmentsag: 3.4953
processed 32,500,012 fragmentsag: 3.4926
processed 33,000,009 fragmentsag: 3.49283
processed 33,500,004 fragmentsag: 3.49281
hits: 116,993,925; hits per frag: 3.49287
[2023-03-02 14:09:05.703] [jointLog] [info] Computed 342,989 rich equivalence classes for further processing
[2023-03-02 14:09:05.706] [jointLog] [info] Counted 20,405,708 total reads in the equivalence classes
[2023-03-02 14:09:05.778] [jointLog] [warning] 0.106504% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 30.
[2023-03-02 14:09:05.781] [jointLog] [info] Number of mappings discarded because of alignment score : 6,166,684
[2023-03-02 14:09:05.781] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 549,711
[2023-03-02 14:09:05.781] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 538,143
[2023-03-02 14:09:05.781] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-03-02 14:09:05.781] [jointLog] [info] Mapping rate = 60.4147%
[2023-03-02 14:09:05.781] [jointLog] [info] finished quantifyLibrary()
[2023-03-02 14:09:05.793] [jointLog] [info] Starting optimizer
[2023-03-02 14:09:21.937] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-03-02 14:09:21.966] [jointLog] [info] iteration = 0 | max rel diff. = 6800.09
[2023-03-02 14:09:23.764] [jointLog] [info] iteration = 100 | max rel diff. = 18.8774
[2023-03-02 14:09:25.676] [jointLog] [info] iteration = 200 | max rel diff. = 12.666
[2023-03-02 14:09:27.747] [jointLog] [info] iteration = 300 | max rel diff. = 5.09729
[2023-03-02 14:09:30.090] [jointLog] [info] iteration = 400 | max rel diff. = 1.4944
[2023-03-02 14:09:32.487] [jointLog] [info] iteration = 500 | max rel diff. = 0.441993
[2023-03-02 14:09:34.927] [jointLog] [info] iteration = 600 | max rel diff. = 1.02472
[2023-03-02 14:09:37.425] [jointLog] [info] iteration = 700 | max rel diff. = 0.682443
[2023-03-02 14:09:39.923] [jointLog] [info] iteration = 800 | max rel diff. = 9.14076
[2023-03-02 14:09:42.654] [jointLog] [info] iteration = 900 | max rel diff. = 3.03266
[2023-03-02 14:09:45.419] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.527561
[2023-03-02 14:09:48.060] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0268382
[2023-03-02 14:09:50.716] [jointLog] [info] iteration = 1,200 | max rel diff. = 2.66146
[2023-03-02 14:09:53.844] [jointLog] [info] iteration = 1,300 | max rel diff. = 1.04132
[2023-03-02 14:09:56.847] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.199233
[2023-03-02 14:09:59.859] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.131681
[2023-03-02 14:10:02.856] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0744955
[2023-03-02 14:10:05.860] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.028298
[2023-03-02 14:10:08.580] [jointLog] [info] iteration = 1,800 | max rel diff. = 0.0700855
[2023-03-02 14:10:11.169] [jointLog] [info] iteration = 1,900 | max rel diff. = 0.036263
[2023-03-02 14:10:13.713] [jointLog] [info] iteration = 2,000 | max rel diff. = 0.0731979
[2023-03-02 14:10:15.059] [jointLog] [info] iteration = 2,055 | max rel diff. = 0.00890234
[2023-03-02 14:10:15.065] [jointLog] [info] Finished optimizer
[2023-03-02 14:10:15.065] [jointLog] [info] writing output
[2023-03-02 14:10:15.401] [jointLog] [warning] NOTE: Read Lib [[ subset_SRR12820270_trimmed.fq ]] :
Detected a potential strand bias > 1% in an unstranded protocol check the file: salmonRes_SRR12820270/lib_format_counts.json for details
./salmonRes_SRR12820270/quant.sf
Error in geneIndexList[[i]] : subscript out of bounds