nan values in quant files

[Tzachi]

Hi Rob,

Thank you very much for developing Salmon.

I ran salmon -0.6.0 on many libraries and in a few cases I got nan values in all the TPMs and in some of the read counts, e.g.:
ENST00000448914    13    13    -nan    0
ENST00000415118    8    8    -nan    0
ENST00000631435    12    12    -nan    0
ENST00000632684    12    12    -nan    0
ENST00000631471    344    154.532    -nan    1
ENST00000417977    447    255.41    -nan    0
ENST00000617347    406    214.371    -nan    55.6802
ENST00000611462    368    191.302    -nan    0
ENST00000620569    409    211.974    -nan    2.1599
ENST00000390344    552    350.379    -nan    -nan
ENST00000613175    2233    1865.46    -nan    -nan
ENST00000390348    465    273.274    -nan    0

I am running Salmon on 8 paired-end fastq files that were trimmed using trim galore:

SalmonBeta-0.6.0_DebianSqueeze_tcmalloc/bin/salmon quant -i **human_hg38_index** -l ISR  -p 8 --biasCorrect --sensitive --extraSensitive  -o **output_directory** -1 ** 8_first_mates**  -2 **8_second_mates**   -g **transcript_to_gene_file**  --useFSPD  --useVBOpt --numBootstraps 100


It seems that the problem only happens when I am mapping some of the files to the human transcriptome (I am using cdna.fa from the most recent ENSEMBL assembly- v84), but this does not happen with most of the human files and in none of the other species I am running (with other files that contain non-human sequences).
The problem repeats itself if I am trying to rerun the problematic files. I think the files I am having this issue with, were also having issues when I used the --useVBOpt  flag (I am no longer using it since the problem I had with it was mentioned earlier by someone else).


While running it, I got:
Version Info: This is the most recent version of Salmon.
# salmon (mapping-based) v0.6.0
# [ program ] => salmon
# [ command ] => quant
# [ index ] => { /panfs/nobackup/research/saraht/tzachi/genomes/Homo_sapiens/hg38/indices/ENSEMBL_Salmon_coding/ }
# [ libType ] => { ISR }
# [ threads ] => { 8 }
# [ biasCorrect ] => { }
# [ sensitive ] => { }
# [ extraSensitive ] => { }
# [ output ] => { salmonQuantCoding/26/ }
# [ mates1 ] => { 18982_1#26_R1_val_1.fq 18982_2#26_R1_val_1.fq 18982_3#26_R1_val_1.fq 18982_4#26_R1_val_1.fq 18982_5#26_R1_val_1.fq 18982_6#26_R1_val_1.fq 18982_7#26_R1_val_1.fq 18982_8#26_R1_val_1.fq }
# [ mates2 ] => { 18982_1#26_R2_val_2.fq 18982_2#26_R2_val_2.fq 18982_3#26_R2_val_2.fq 18982_4#26_R2_val_2.fq 18982_5#26_R2_val_2.fq 18982_6#26_R2_val_2.fq 18982_7#26_R2_val_2.fq 18982_8#26_R2_val_2.fq }
# [ geneMap ] => { mart_export_human_v84_clean.txt }
# [ useFSPD ] => { }
# [ numBootstraps ] => { 100 }
Logs will be written to salmonQuantCoding/26/logs
there is 1 lib
[2016-05-02 14:22:53.981] [jointLog] [info] parsing read library format
Loading 32-bit quasi indextcmalloc: large alloc 1140842496 bytes == 0x2016c000 @
[2016-05-02 14:22:54.796] [jointLog] [info] Loading Quasi index
tcmalloc: large alloc 4294967296 bytes == 0x6416e000 @
[2016-05-02 14:22:54.796] [stderrLog] [info] Loading Suffix Array
[2016-05-02 14:22:54.797] [stderrLog] [info] Loading Position Hash
[2016-05-02 14:22:59.999] [stderrLog] [info] Loading Transcript Info
[2016-05-02 14:23:01.257] [stderrLog] [info] Loading Rank-Select Bit Array
[2016-05-02 14:23:01.643] [stderrLog] [info] There were 176241 set bits in the bit array
[2016-05-02 14:23:01.927] [stderrLog] [info] Computing transcript lengths
[2016-05-02 14:23:01.928] [stderrLog] [info] Waiting to finish loading hash
Index contained 176241 targets
[2016-05-02 14:23:12.217] [stderrLog] [info] Done loading index
[2016-05-02 14:23:12.217] [jointLog] [info] done



processed 28000000 fragments
hits: 117173084, hits per frag:  4.18758



[2016-05-02 14:25:14.441] [jointLog] [info] Computed 347673 rich equivalence classes for further processing
[2016-05-02 14:25:14.441] [jointLog] [info] Counted 26850150 total reads in the equivalence classes




[2016-05-02 14:25:14.467] [jointLog] [info] Mapping rate = 95.8053%

[2016-05-02 14:25:14.467] [jointLog] [info] finished quantifyLibrary()
[2016-05-02 14:25:14.467] [jointLog] [info] Starting optimizer
project to polytope: 5000[2016-05-02 14:25:23.621] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2016-05-02 14:25:23.638] [jointLog] [info] iteration = 0 | max rel diff. = 55.4378
[2016-05-02 14:25:24.500] [jointLog] [info] iteration 50, recomputing effective lengths
[2016-05-02 14:25:31.784] [jointLog] [info] iteration = 100 | max rel diff. = 0.652823
[2016-05-02 14:25:33.483] [jointLog] [info] iteration = 200 | max rel diff. = 0.381744
**
[2016-05-02 14:28:31.273] [jointLog] [info] iteration = 9900 | max rel diff. = 0.0562637
[2016-05-02 14:28:33.025] [jointLog] [info] iteration = 10000 | max rel diff. = 0.0106865
[2016-05-02 14:28:33.035] [jointLog] [info] Finished optimizer
[2016-05-02 14:28:33.035] [jointLog] [info] writing output

[2016-05-02 14:28:33.674] [jointLog] [info] Staring Bootstrapping
[2016-05-02 14:28:33.806] [jointLog] [info] Will draw 100 bootstrap samples
[2016-05-02 14:28:33.806] [jointLog] [info] Optimizing over 347673 equivalence classes
[2016-05-02 14:28:33.840] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2016-05-02 14:29:31.950] [jointLog] [info] wrote 1 bootstraps
[2016-05-02 14:29:32.049] [jointLog] [info] wrote 2 bootstraps
**
[2016-05-02 14:43:34.224] [jointLog] [info] wrote 100 bootstraps
[2016-05-02 14:43:34.265] [jointLog] [info] Finished Bootstrapping
Computing gene-level abundance estimates
There were 217533 transcripts mapping to 66203 genes
Parsed 176000 expression lines
done
Aggregating expressions to gene level . . . done



The output log also does not show any issue:
[2016-05-02 14:22:53.981] [jointLog] [info] parsing read library format
[2016-05-02 14:22:54.796] [jointLog] [info] Loading Quasi index
[2016-05-02 14:23:12.217] [jointLog] [info] done
[2016-05-02 14:25:14.441] [jointLog] [info] Computed 347673 rich equivalence classes for further processing
[2016-05-02 14:25:14.441] [jointLog] [info] Counted 26850150 total reads in the equivalence classes
[2016-05-02 14:25:14.467] [jointLog] [info] Mapping rate = 95.8053%

[2016-05-02 14:25:14.467] [jointLog] [info] finished quantifyLibrary()
[2016-05-02 14:25:14.467] [jointLog] [info] Starting optimizer
[2016-05-02 14:25:14.441] [fileLog] [info]
At end of round 0
==================
Observed 28025750 total fragments (28025750 in most recent round)

[2016-05-02 14:25:23.621] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2016-05-02 14:25:23.638] [jointLog] [info] iteration = 0 | max rel diff. = 55.4378
[2016-05-02 14:25:24.500] [jointLog] [info] iteration 50, recomputing effective lengths
[2016-05-02 14:25:31.784] [jointLog] [info] iteration = 100 | max rel diff. = 0.652823
[2016-05-02 14:25:33.483] [jointLog] [info] iteration = 200 | max rel diff. = 0.381744
[2016-05-02 14:25:35.206] [jointLog] [info] iteration = 300 | max rel diff. = 0.376109
[2016-05-02 14:25:36.915] [jointLog] [info] iteration = 400 | max rel diff. = 0.173246
[2016-05-02 14:25:38.570] [jointLog] [info] iteration 500, recomputing effective lengths
[2016-05-02 14:25:44.130] [jointLog] [info] iteration = 500 | max rel diff. = 949.688
[2016-05-02 14:25:45.685] [jointLog] [info] iteration = 600 | max rel diff. = 1.49474
[2016-05-02 14:25:47.256] [jointLog] [info] iteration = 700 | max rel diff. = 1.121
[2016-05-02 14:25:48.914] [jointLog] [info] iteration = 800 | max rel diff. = 2.13462
[2016-05-02 14:25:50.586] [jointLog] [info] iteration = 900 | max rel diff. = 0.469437
[2016-05-02 14:25:52.300] [jointLog] [info] iteration 1000, recomputing effective lengths
[2016-05-02 14:25:57.520] [jointLog] [info] iteration = 1000 | max rel diff. = 309.556
[2016-05-02 14:25:59.178] [jointLog] [info] iteration = 1100 | max rel diff. = 2.29611
[2016-05-02 14:26:00.845] [jointLog] [info] iteration = 1200 | max rel diff. = 0.915045
[2016-05-02 14:26:02.581] [jointLog] [info] iteration = 1300 | max rel diff. = 0.602349
[2016-05-02 14:26:04.315] [jointLog] [info] iteration = 1400 | max rel diff. = 0.332307
[2016-05-02 14:26:06.038] [jointLog] [info] iteration = 1500 | max rel diff. = 0.459863
[2016-05-02 14:26:07.714] [jointLog] [info] iteration = 1600 | max rel diff. = 0.31548
[2016-05-02 14:26:09.375] [jointLog] [info] iteration = 1700 | max rel diff. = 0.153252
[2016-05-02 14:26:11.039] [jointLog] [info] iteration = 1800 | max rel diff. = 0.344269
[2016-05-02 14:26:12.687] [jointLog] [info] iteration = 1900 | max rel diff. = 0.227084
[2016-05-02 14:26:14.339] [jointLog] [info] iteration = 2000 | max rel diff. = 0.16708
[2016-05-02 14:26:15.999] [jointLog] [info] iteration = 2100 | max rel diff. = 0.328591
[2016-05-02 14:26:17.654] [jointLog] [info] iteration = 2200 | max rel diff. = 0.12263
[2016-05-02 14:26:19.320] [jointLog] [info] iteration = 2300 | max rel diff. = 0.141096
[2016-05-02 14:26:20.982] [jointLog] [info] iteration = 2400 | max rel diff. = 0.226438
[2016-05-02 14:26:22.571] [jointLog] [info] iteration = 2500 | max rel diff. = 0.108267
[2016-05-02 14:26:24.225] [jointLog] [info] iteration = 2600 | max rel diff. = 0.121027
[2016-05-02 14:26:25.893] [jointLog] [info] iteration = 2700 | max rel diff. = 0.278897
[2016-05-02 14:26:27.556] [jointLog] [info] iteration = 2800 | max rel diff. = 0.131106
[2016-05-02 14:26:29.209] [jointLog] [info] iteration = 2900 | max rel diff. = 0.202072
[2016-05-02 14:26:30.840] [jointLog] [info] iteration = 3000 | max rel diff. = 0.116548
[2016-05-02 14:26:32.476] [jointLog] [info] iteration = 3100 | max rel diff. = 0.131677
[2016-05-02 14:26:34.152] [jointLog] [info] iteration = 3200 | max rel diff. = 0.0718831
[2016-05-02 14:26:35.811] [jointLog] [info] iteration = 3300 | max rel diff. = 0.162116
[2016-05-02 14:26:37.484] [jointLog] [info] iteration = 3400 | max rel diff. = 0.160175
[2016-05-02 14:26:39.211] [jointLog] [info] iteration = 3500 | max rel diff. = 0.0480432
[2016-05-02 14:26:40.932] [jointLog] [info] iteration = 3600 | max rel diff. = 0.0564495
[2016-05-02 14:26:42.635] [jointLog] [info] iteration = 3700 | max rel diff. = 0.0762822
[2016-05-02 14:26:44.343] [jointLog] [info] iteration = 3800 | max rel diff. = 0.284971
[2016-05-02 14:26:46.060] [jointLog] [info] iteration = 3900 | max rel diff. = 0.0670502
[2016-05-02 14:26:47.765] [jointLog] [info] iteration = 4000 | max rel diff. = 0.195777
[2016-05-02 14:26:49.452] [jointLog] [info] iteration = 4100 | max rel diff. = 0.0753004
[2016-05-02 14:26:51.104] [jointLog] [info] iteration = 4200 | max rel diff. = 0.068551
[2016-05-02 14:26:52.815] [jointLog] [info] iteration = 4300 | max rel diff. = 0.0773514
[2016-05-02 14:26:54.484] [jointLog] [info] iteration = 4400 | max rel diff. = 0.120333
[2016-05-02 14:26:56.144] [jointLog] [info] iteration = 4500 | max rel diff. = 0.0395703
[2016-05-02 14:26:57.810] [jointLog] [info] iteration = 4600 | max rel diff. = 0.040292
[2016-05-02 14:26:59.471] [jointLog] [info] iteration = 4700 | max rel diff. = 0.0907263
[2016-05-02 14:27:01.139] [jointLog] [info] iteration = 4800 | max rel diff. = 0.109302
[2016-05-02 14:27:02.801] [jointLog] [info] iteration = 4900 | max rel diff. = 0.158817
[2016-05-02 14:27:04.511] [jointLog] [info] iteration = 5000 | max rel diff. = 0.115082
[2016-05-02 14:27:06.251] [jointLog] [info] iteration = 5100 | max rel diff. = 0.152047
[2016-05-02 14:27:07.988] [jointLog] [info] iteration = 5200 | max rel diff. = 0.126965
[2016-05-02 14:27:09.672] [jointLog] [info] iteration = 5300 | max rel diff. = 0.112203
[2016-05-02 14:27:11.410] [jointLog] [info] iteration = 5400 | max rel diff. = 0.0920364
[2016-05-02 14:27:13.144] [jointLog] [info] iteration = 5500 | max rel diff. = 0.115881
[2016-05-02 14:27:14.813] [jointLog] [info] iteration = 5600 | max rel diff. = 0.122474
[2016-05-02 14:27:16.513] [jointLog] [info] iteration = 5700 | max rel diff. = 0.0831998
[2016-05-02 14:27:18.307] [jointLog] [info] iteration = 5800 | max rel diff. = 0.0847048
[2016-05-02 14:27:20.064] [jointLog] [info] iteration = 5900 | max rel diff. = 0.0659741
[2016-05-02 14:27:21.839] [jointLog] [info] iteration = 6000 | max rel diff. = 0.0712979
[2016-05-02 14:27:23.622] [jointLog] [info] iteration = 6100 | max rel diff. = 0.0392044
[2016-05-02 14:27:25.400] [jointLog] [info] iteration = 6200 | max rel diff. = 0.0453104
[2016-05-02 14:27:27.175] [jointLog] [info] iteration = 6300 | max rel diff. = 0.0710722
[2016-05-02 14:27:28.951] [jointLog] [info] iteration = 6400 | max rel diff. = 0.0727045
[2016-05-02 14:27:30.743] [jointLog] [info] iteration = 6500 | max rel diff. = 0.0765219
[2016-05-02 14:27:32.513] [jointLog] [info] iteration = 6600 | max rel diff. = 0.0613105
[2016-05-02 14:27:34.284] [jointLog] [info] iteration = 6700 | max rel diff. = 0.0287056
[2016-05-02 14:27:36.073] [jointLog] [info] iteration = 6800 | max rel diff. = 0.0760347
[2016-05-02 14:27:37.842] [jointLog] [info] iteration = 6900 | max rel diff. = 0.0747864
[2016-05-02 14:27:39.617] [jointLog] [info] iteration = 7000 | max rel diff. = 0.0354574
[2016-05-02 14:27:41.399] [jointLog] [info] iteration = 7100 | max rel diff. = 0.0150185
[2016-05-02 14:27:43.185] [jointLog] [info] iteration = 7200 | max rel diff. = 0.0140724
[2016-05-02 14:27:44.944] [jointLog] [info] iteration = 7300 | max rel diff. = 0.0347549
[2016-05-02 14:27:46.715] [jointLog] [info] iteration = 7400 | max rel diff. = 0.0345347
[2016-05-02 14:27:48.492] [jointLog] [info] iteration = 7500 | max rel diff. = 0.0982676
[2016-05-02 14:27:50.280] [jointLog] [info] iteration = 7600 | max rel diff. = 0.041789
[2016-05-02 14:27:52.065] [jointLog] [info] iteration = 7700 | max rel diff. = 0.0301308
[2016-05-02 14:27:53.858] [jointLog] [info] iteration = 7800 | max rel diff. = 0.0733047
[2016-05-02 14:27:55.645] [jointLog] [info] iteration = 7900 | max rel diff. = 0.0797163
[2016-05-02 14:27:57.432] [jointLog] [info] iteration = 8000 | max rel diff. = 0.0619056
[2016-05-02 14:27:59.200] [jointLog] [info] iteration = 8100 | max rel diff. = 0.0783558
[2016-05-02 14:28:00.981] [jointLog] [info] iteration = 8200 | max rel diff. = 0.0711454
[2016-05-02 14:28:02.775] [jointLog] [info] iteration = 8300 | max rel diff. = 0.0223476
[2016-05-02 14:28:04.563] [jointLog] [info] iteration = 8400 | max rel diff. = 0.0732376
[2016-05-02 14:28:06.355] [jointLog] [info] iteration = 8500 | max rel diff. = 0.0284521
[2016-05-02 14:28:08.135] [jointLog] [info] iteration = 8600 | max rel diff. = 0.043727
[2016-05-02 14:28:09.922] [jointLog] [info] iteration = 8700 | max rel diff. = 0.0257719
[2016-05-02 14:28:11.710] [jointLog] [info] iteration = 8800 | max rel diff. = 0.0403604
[2016-05-02 14:28:13.491] [jointLog] [info] iteration = 8900 | max rel diff. = 0.0265571
[2016-05-02 14:28:15.276] [jointLog] [info] iteration = 9000 | max rel diff. = 0.0163102
[2016-05-02 14:28:17.059] [jointLog] [info] iteration = 9100 | max rel diff. = 0.0685639
[2016-05-02 14:28:18.842] [jointLog] [info] iteration = 9200 | max rel diff. = 0.0184039
[2016-05-02 14:28:20.630] [jointLog] [info] iteration = 9300 | max rel diff. = 0.0149301
[2016-05-02 14:28:22.419] [jointLog] [info] iteration = 9400 | max rel diff. = 0.0448498
[2016-05-02 14:28:24.192] [jointLog] [info] iteration = 9500 | max rel diff. = 0.0326261
[2016-05-02 14:28:25.969] [jointLog] [info] iteration = 9600 | max rel diff. = 0.032242
[2016-05-02 14:28:27.742] [jointLog] [info] iteration = 9700 | max rel diff. = 0.0484218
[2016-05-02 14:28:29.504] [jointLog] [info] iteration = 9800 | max rel diff. = 0.013808
[2016-05-02 14:28:31.273] [jointLog] [info] iteration = 9900 | max rel diff. = 0.0562637
[2016-05-02 14:28:33.025] [jointLog] [info] iteration = 10000 | max rel diff. = 0.0106865
[2016-05-02 14:28:33.035] [jointLog] [info] Finished optimizer
[2016-05-02 14:28:33.035] [jointLog] [info] writing output

[2016-05-02 14:28:33.674] [jointLog] [info] Staring Bootstrapping
[2016-05-02 14:28:33.806] [jointLog] [info] Will draw 100 bootstrap samples
[2016-05-02 14:28:33.806] [jointLog] [info] Optimizing over 347673 equivalence classes
[2016-05-02 14:28:33.840] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2016-05-02 14:29:31.950] [jointLog] [info] wrote 1 bootstraps
[2016-05-02 14:29:32.049] [jointLog] [info] wrote 2 bootstraps
[2016-05-02 14:29:32.360] [jointLog] [info] wrote 3 bootstraps
[2016-05-02 14:29:33.033] [jointLog] [info] wrote 4 bootstraps
[2016-05-02 14:29:33.331] [jointLog] [info] wrote 5 bootstraps
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[2016-05-02 14:32:40.428] [jointLog] [info] wrote 28 bootstraps
[2016-05-02 14:33:26.400] [jointLog] [info] wrote 29 bootstraps
[2016-05-02 14:33:30.687] [jointLog] [info] wrote 30 bootstraps
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[2016-05-02 14:33:33.398] [jointLog] [info] wrote 32 bootstraps
[2016-05-02 14:33:37.562] [jointLog] [info] wrote 33 bootstraps
[2016-05-02 14:33:37.795] [jointLog] [info] wrote 34 bootstraps
[2016-05-02 14:33:38.570] [jointLog] [info] wrote 35 bootstraps
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[2016-05-02 14:36:37.511] [jointLog] [info] wrote 55 bootstraps
[2016-05-02 14:36:39.570] [jointLog] [info] wrote 56 bootstraps
[2016-05-02 14:37:28.005] [jointLog] [info] wrote 57 bootstraps
[2016-05-02 14:37:32.710] [jointLog] [info] wrote 58 bootstraps
[2016-05-02 14:37:33.395] [jointLog] [info] wrote 59 bootstraps
[2016-05-02 14:37:35.374] [jointLog] [info] wrote 60 bootstraps
[2016-05-02 14:37:35.413] [jointLog] [info] wrote 61 bootstraps
[2016-05-02 14:37:37.007] [jointLog] [info] wrote 62 bootstraps
[2016-05-02 14:37:45.254] [jointLog] [info] wrote 63 bootstraps
[2016-05-02 14:38:29.811] [jointLog] [info] wrote 64 bootstraps
[2016-05-02 14:38:31.544] [jointLog] [info] wrote 65 bootstraps
[2016-05-02 14:38:34.179] [jointLog] [info] wrote 66 bootstraps
[2016-05-02 14:38:34.395] [jointLog] [info] wrote 67 bootstraps
[2016-05-02 14:38:34.439] [jointLog] [info] wrote 68 bootstraps
[2016-05-02 14:38:34.926] [jointLog] [info] wrote 69 bootstraps
[2016-05-02 14:38:50.073] [jointLog] [info] wrote 70 bootstraps
[2016-05-02 14:39:28.076] [jointLog] [info] wrote 71 bootstraps
[2016-05-02 14:39:29.537] [jointLog] [info] wrote 72 bootstraps
[2016-05-02 14:39:34.873] [jointLog] [info] wrote 73 bootstraps
[2016-05-02 14:39:36.059] [jointLog] [info] wrote 74 bootstraps
[2016-05-02 14:39:36.120] [jointLog] [info] wrote 75 bootstraps
[2016-05-02 14:39:41.498] [jointLog] [info] wrote 76 bootstraps
[2016-05-02 14:39:50.579] [jointLog] [info] wrote 77 bootstraps
[2016-05-02 14:40:26.188] [jointLog] [info] wrote 78 bootstraps
[2016-05-02 14:40:29.796] [jointLog] [info] wrote 79 bootstraps
[2016-05-02 14:40:33.766] [jointLog] [info] wrote 80 bootstraps
[2016-05-02 14:40:35.481] [jointLog] [info] wrote 81 bootstraps
[2016-05-02 14:40:38.068] [jointLog] [info] wrote 82 bootstraps
[2016-05-02 14:40:39.897] [jointLog] [info] wrote 83 bootstraps
[2016-05-02 14:40:49.628] [jointLog] [info] wrote 84 bootstraps
[2016-05-02 14:41:29.651] [jointLog] [info] wrote 85 bootstraps
[2016-05-02 14:41:30.790] [jointLog] [info] wrote 86 bootstraps
[2016-05-02 14:41:30.852] [jointLog] [info] wrote 87 bootstraps
[2016-05-02 14:41:36.189] [jointLog] [info] wrote 88 bootstraps
[2016-05-02 14:41:40.933] [jointLog] [info] wrote 89 bootstraps
[2016-05-02 14:41:42.208] [jointLog] [info] wrote 90 bootstraps
[2016-05-02 14:41:48.809] [jointLog] [info] wrote 91 bootstraps
[2016-05-02 14:42:28.642] [jointLog] [info] wrote 92 bootstraps
[2016-05-02 14:42:29.324] [jointLog] [info] wrote 93 bootstraps
[2016-05-02 14:42:32.212] [jointLog] [info] wrote 94 bootstraps
[2016-05-02 14:42:37.246] [jointLog] [info] wrote 95 bootstraps
[2016-05-02 14:42:41.116] [jointLog] [info] wrote 96 bootstraps
[2016-05-02 14:42:47.020] [jointLog] [info] wrote 97 bootstraps
[2016-05-02 14:42:48.503] [jointLog] [info] wrote 98 bootstraps
[2016-05-02 14:43:25.713] [jointLog] [info] wrote 99 bootstraps
[2016-05-02 14:43:34.224] [jointLog] [info] wrote 100 bootstraps
[2016-05-02 14:43:34.265] [jointLog] [info] Finished Bootstrapping

And in the libParam I get:

# of consistent alignments: 112092653
# of inconsistent alignments: 5188087

(for some reason I always seem to get ~5% inconsistent alignments)

Can you please let me know what you think went wrong?

Thank you very much
Tzachi

[Jonathan Manning]

I'm also experiencing this problem, when running Salmon with a command like:

bash -c "salmon quant -i salmon/index -p 4 --biasCorrect --useFSPD -l U --fldMean 300 -r <(zcat trimmed.fastq.gz) -o /output/directory"

It only happens on 1 of 12 files, and I can't see anything obviously different with that file, all the QC looks fine etc. 

The top of the quant.sf looks like:

Name Length EffectiveLength TPM NumReads

ENSMUST00000178537.1 12 12 -nan 0

ENSMUST00000178862.1 14 14 -nan 0

ENSMUST00000177564.1 16 16 -nan 0

ENSMUST00000196221.1 9 9 -nan 0

ENSMUST00000179664.1 11 11 -nan 0

ENSMUST00000179520.1 11 11 -nan 0

ENSMUST00000179883.1 16 16 -nan 0

ENSMUST00000195858.1 10 10 -nan 0

ENSMUST00000179932.1 12 12 -nan 0

ENSMUST00000180001.1 17 17 -nan 0

ENSMUST00000178815.1 10 10 -nan 0

ENSMUST00000177965.1 17 17 -nan 0

ENSMUST00000178909.1 29 29 -nan 0

ENSMUST00000177646.1 10 10 -nan 0

ENSMUST00000178230.1 17 17 -nan 0

ENSMUST00000178483.1 29 29 -nan 0

ENSMUST00000179262.1 10 10 -nan 0

ENSMUST00000178549.1 17 17 -nan 0

ENSMUST00000193012.1 29 29 -nan 0

ENSMUST00000179166.1 10 10 -nan 0

ENSMUST00000179560.1 17 17 -nan 0

ENSMUST00000177839.1 17 17 -nan 0

ENSMUST00000103439.1 23 23 -nan 0

ENSMUST00000180266.1 17 17 -nan 0

ENSMUST00000103441.1 23 23 -nan 0

ENSMUST00000181728.2 451 152.856 -nan 0.5

ENSMUST00000103643.3 328 48.4624 -nan 0

ENSMUST00000103581.5 398 103.125 -nan 0

ENSMUST00000181210.2 375 83.2961 -nan 0

ENSMUST00000183488.1 335 53.0659 -nan 0

ENSMUST00000103583.4 406 110.333 -nan 0

Any suggestions as to what might be wrong?

Many thanks,

Jon

[Jonathan Manning]

If anyone else encounters this, it was fixed for me by a reinstall of Salmon. I think some server maintenance had disrupted some library paths, or something along those lines.

Jon

On Monday, 2 May 2016 14:57:29 UTC+1, Tzachi wrote:

[Rob]

Hi Jon,

  Thanks for reporting this solution back here!  I'm sorry for not replying more quickly, but I've been rather swamped with other work this week, and so have been less responsive than usual.  I do wonder what library was the culprit, though.  Almost everything is statically linked, so there are only a few potential suspects.

--Rob