STEP 6: Error in geneIndexList[[i]] : subscript out of bounds

[wiafridi]

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