
################################################################################
Started ShapeMapper v2.1.5 at 2021-03-26 13:24:41
Running from directory: /pine/scr/p/s/psirving/20210326-rnasep-acid-resequenced
args:  --target rnasep.fa --name Acid-API --modified --folder Sample_6 --untreated --folder Sample_10 --amplicon --output-parsed-mutations --overwrite --per-read-histograms
Created pipeline at 2021-03-26 13:24:41
Running PrimerLocator at 2021-03-26 13:24:41 . . .
. . . done at 2021-03-26 13:24:41
Running FastaFormatChecker at 2021-03-26 13:24:41 . . .
. . . done at 2021-03-26 13:24:41
Running BowtieIndexBuilder at 2021-03-26 13:24:41 . . .
. . . done at 2021-03-26 13:24:42
Running process group 4 at 2021-03-26 13:24:42 . . .
  Including these components:
    ProgressMonitor . . . started at 2021-03-26 13:24:42
    QualityTrimmer1 . . . started at 2021-03-26 13:24:42
    QualityTrimmer2 . . . started at 2021-03-26 13:24:42
    Interleaver . . . started at 2021-03-26 13:24:42
    Merger . . . started at 2021-03-26 13:24:42
    Tab6Interleaver . . . started at 2021-03-26 13:24:42
    BowtieAligner . . . started at 2021-03-26 13:24:42
    MutationParser_Modified . . . started at 2021-03-26 13:24:42
    SplitToFile1 . . . started at 2021-03-26 13:24:42
    MutationCounter_Modified . . . started at 2021-03-26 13:24:42
  /`````````````````````````````````````````````````````````````````````````````
  |Merger (sample: Modified) output message: 
  |----------------------------------------- 
  | 
  | java -Djava.library.path=/nas/longleaf/home/psirving/shapemapper-2.1.5/internals/thirdparty/miniconda/opt/bbmap-37.78/jni/ -ea -Xmx1000m -Xmx1000m -cp /nas/longleaf/home/psirving/shapemapper-2.1.5/internals/thirdparty/miniconda/opt/bbmap-37.78/current/ jgi.BBMerge vstrict=t in=stdin out=stdout outu=stdout interleaved=t usejni=t t=4
  | Executing jgi.BBMerge [vstrict=t, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4]
  | Version 37.78 [vstrict=t, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4]
  | 
  | Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4]
  | 
  | Set INTERLEAVED to true
  | Set threads to 4
  | Writing mergable reads merged.
  | Unspecified format for output stdout; defaulting to fastq.
  | Unspecified format for output stdout; defaulting to fastq.
  | Started output threads.
  | Unspecified format for input stdin; defaulting to fastq.
  | Total time: 1511.719 seconds.
  | 
  | Pairs:               	1024080
  | Joined:              	864170   	84.385%
  | Ambiguous:           	155809   	15.215%
  | No Solution:         	4101       	0.400%
  | Too Short:           	0       	0.000%
  | 
  | Avg Insert:          	322.6
  | Standard Deviation:  	47.1
  | Mode:                	335
  | 
  | Insert range:        	37 - 558
  | 90th percentile:     	336
  | 75th percentile:     	335
  | 50th percentile:     	334
  | 25th percentile:     	332
  | 10th percentile:     	303
  \_____________________________________________________________________________
  /`````````````````````````````````````````````````````````````````````````````
  |BowtieAligner (sample: Modified) output message: 
  |------------------------------------------------ 
  | 
  | 1024080 reads; of these:
  |   159910 (15.61%) were paired; of these:
  |     61678 (38.57%) aligned concordantly 0 times
  |     98095 (61.34%) aligned concordantly exactly 1 time
  |     137 (0.09%) aligned concordantly >1 times
  |     ----
  |     61678 pairs aligned concordantly 0 times; of these:
  |       245 (0.40%) aligned discordantly 1 time
  |     ----
  |     61433 pairs aligned 0 times concordantly or discordantly; of these:
  |       122866 mates make up the pairs; of these:
  |         82032 (66.77%) aligned 0 times
  |         40801 (33.21%) aligned exactly 1 time
  |         33 (0.03%) aligned >1 times
  |   864170 (84.39%) were unpaired; of these:
  |     32378 (3.75%) aligned 0 times
  |     830063 (96.05%) aligned exactly 1 time
  |     1729 (0.20%) aligned >1 times
  | 90.34% overall alignment rate
  \_____________________________________________________________________________
  /`````````````````````````````````````````````````````````````````````````````
  |MutationCounter_Modified (RNA: rnasep) (sample: Modified) output message: 
  |------------------------------------------------------------------------- 
  | 
  | Read lengths
  | --------------------
  | bin_range	frequency
  | [0,49]	0.114126
  | [50,99]	0.056399
  | [100,149]	0.041808
  | [150,199]	0.035825
  | [200,249]	0.029511
  | [250,299]	0.028137
  | [300,349]	0.694194
  | [350,399]	0.000000
  | [400,449]	0.000000
  | [450,499]	0.000000
  | [500,549]	0.000000
  | [550,599]	0.000000
  | [600,649]	0.000000
  | [650,699]	0.000000
  | [700,749]	0.000000
  | [750,799]	0.000000
  | [800,849]	0.000000
  | [850,899]	0.000000
  | [900,949]	0.000000
  | [950,999]	0.000000
  | >=1000	0.000000
  | --------------------
  | 
  | Mutations per read
  | --------------------
  | bin_left	frequency
  | 0	0.131544
  | 1	0.130763
  | 2	0.156648
  | 3	0.164545
  | 4	0.141690
  | 5	0.105147
  | 6	0.067949
  | 7	0.040146
  | 8	0.023267
  | 9	0.013789
  | 10	0.008742
  | 11	0.005854
  | 12	0.003752
  | 13	0.002392
  | 14	0.001513
  | 15	0.000949
  | 16	0.000557
  | 17	0.000309
  | 18	0.000188
  | 19	0.000120
  | 20	0.000137
  | --------------------
  \_____________________________________________________________________________
. . . done at 2021-03-26 13:49:55
Running process group 5 at 2021-03-26 13:49:55 . . .
  Including these components:
    ProgressMonitor . . . started at 2021-03-26 13:49:55
    QualityTrimmer1 . . . started at 2021-03-26 13:49:55
    QualityTrimmer2 . . . started at 2021-03-26 13:49:55
    Interleaver . . . started at 2021-03-26 13:49:55
    Merger . . . started at 2021-03-26 13:49:55
    Tab6Interleaver . . . started at 2021-03-26 13:49:55
    BowtieAligner . . . started at 2021-03-26 13:49:55
    MutationParser_Untreated . . . started at 2021-03-26 13:49:55
    SplitToFile1 . . . started at 2021-03-26 13:49:55
    MutationCounter_Untreated . . . started at 2021-03-26 13:49:55
  /`````````````````````````````````````````````````````````````````````````````
  |Merger (sample: Untreated) output message: 
  |------------------------------------------ 
  | 
  | java -Djava.library.path=/nas/longleaf/home/psirving/shapemapper-2.1.5/internals/thirdparty/miniconda/opt/bbmap-37.78/jni/ -ea -Xmx1000m -Xmx1000m -cp /nas/longleaf/home/psirving/shapemapper-2.1.5/internals/thirdparty/miniconda/opt/bbmap-37.78/current/ jgi.BBMerge vstrict=t in=stdin out=stdout outu=stdout interleaved=t usejni=t t=4
  | Executing jgi.BBMerge [vstrict=t, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4]
  | Version 37.78 [vstrict=t, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4]
  | 
  | Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4]
  | 
  | Set INTERLEAVED to true
  | Set threads to 4
  | Writing mergable reads merged.
  | Unspecified format for output stdout; defaulting to fastq.
  | Unspecified format for output stdout; defaulting to fastq.
  | Started output threads.
  | Unspecified format for input stdin; defaulting to fastq.
  | Total time: 1394.516 seconds.
  | 
  | Pairs:               	960965
  | Joined:              	828734   	86.240%
  | Ambiguous:           	129236   	13.449%
  | No Solution:         	2995       	0.312%
  | Too Short:           	0       	0.000%
  | 
  | Avg Insert:          	324.8
  | Standard Deviation:  	51.2
  | Mode:                	335
  | 
  | Insert range:        	35 - 542
  | 90th percentile:     	336
  | 75th percentile:     	335
  | 50th percentile:     	335
  | 25th percentile:     	335
  | 10th percentile:     	330
  \_____________________________________________________________________________
  /`````````````````````````````````````````````````````````````````````````````
  |BowtieAligner (sample: Untreated) output message: 
  |------------------------------------------------- 
  | 
  | 960965 reads; of these:
  |   132231 (13.76%) were paired; of these:
  |     57231 (43.28%) aligned concordantly 0 times
  |     74972 (56.70%) aligned concordantly exactly 1 time
  |     28 (0.02%) aligned concordantly >1 times
  |     ----
  |     57231 pairs aligned concordantly 0 times; of these:
  |       206 (0.36%) aligned discordantly 1 time
  |     ----
  |     57025 pairs aligned 0 times concordantly or discordantly; of these:
  |       114050 mates make up the pairs; of these:
  |         76067 (66.70%) aligned 0 times
  |         37979 (33.30%) aligned exactly 1 time
  |         4 (0.00%) aligned >1 times
  |   828734 (86.24%) were unpaired; of these:
  |     39366 (4.75%) aligned 0 times
  |     789219 (95.23%) aligned exactly 1 time
  |     149 (0.02%) aligned >1 times
  | 89.44% overall alignment rate
  \_____________________________________________________________________________
  /`````````````````````````````````````````````````````````````````````````````
  |MutationCounter_Untreated (RNA: rnasep) (sample: Untreated) output message: 
  |--------------------------------------------------------------------------- 
  | 
  | Read lengths
  | --------------------
  | bin_range	frequency
  | [0,49]	0.088702
  | [50,99]	0.045644
  | [100,149]	0.033110
  | [150,199]	0.031036
  | [200,249]	0.028484
  | [250,299]	0.027207
  | [300,349]	0.745816
  | [350,399]	0.000000
  | [400,449]	0.000000
  | [450,499]	0.000000
  | [500,549]	0.000000
  | [550,599]	0.000000
  | [600,649]	0.000000
  | [650,699]	0.000000
  | [700,749]	0.000000
  | [750,799]	0.000000
  | [800,849]	0.000000
  | [850,899]	0.000000
  | [900,949]	0.000000
  | [950,999]	0.000000
  | >=1000	0.000000
  | --------------------
  | 
  | Mutations per read
  | --------------------
  | bin_left	frequency
  | 0	0.449604
  | 1	0.277715
  | 2	0.139302
  | 3	0.077432
  | 4	0.030522
  | 5	0.013959
  | 6	0.006524
  | 7	0.002851
  | 8	0.001226
  | 9	0.000544
  | 10	0.000189
  | 11	0.000077
  | 12	0.000026
  | 13	0.000011
  | 14	0.000006
  | 15	0.000002
  | 16	0.000002
  | 17	0.000003
  | 18	0.000002
  | 19	0.000002
  | 20	0.000001
  | --------------------
  \_____________________________________________________________________________
. . . done at 2021-03-26 14:13:10
Running CalcProfile at 2021-03-26 14:13:10 . . .
. . . done at 2021-03-26 14:13:11
Running NormProfile at 2021-03-26 14:13:11 . . .
. . . done at 2021-03-26 14:13:11
Running TabToShape at 2021-03-26 14:13:11 . . .
. . . done at 2021-03-26 14:13:11
Running RenderFigures at 2021-03-26 14:13:11 . . .
/```````````````````````````````````````````````````````````````````````````````
|RenderFigures (RNA: rnasep) output message: 
|------------------------------------------- 
| 
| Quality control checks:
| 
| (See README.md for explanation)
| 
| Read depth check:
| 100.0% (294/294) nucleotides meet the minimum read depth of 5000
| PASS
| 
| Mutation rate check:
| 99.3% (292/294) nucleotides have positive mutation rates
| above background
| High background check:
| 0.0% (0/294) nucleotides have high background
| mutation rates.
| PASS: Not too many nucleotides with high background mutation rates.
| 
| Number highly reactive check:
| 43.5% (128/294) nucleotides show high apparent reactivity.
| PASS: The expected number of nucleotides or more are highly
|       reactive.
\_______________________________________________________________________________
. . . done at 2021-03-26 14:13:15
Running RenderMappedDepths at 2021-03-26 14:13:15 . . .
/```````````````````````````````````````````````````````````````````````````````
|RenderMappedDepths (RNA: rnasep) output message: 
|------------------------------------------------ 
| 
| Approximate maximum read depth for reads mapping near each amplicon primer pair
| (See *_mapped_depths.pdf for plots)
| (See *_per-amplicon_abundance.txt for exact numbers)
| 
| Modified:
|   pair forward                       left    right   reverse                       left    right   depth  
|   ---- ----------------------------- ------- ------- ----------------------------- ------- ------- ------ 
|   1    GGCCTTCGGGCCAA                0       13      GAACCGGACCGAAGCC              309     324     866k   
| 
| Untreated:
|   pair forward                       left    right   reverse                       left    right   depth  
|   ---- ----------------------------- ------- ------- ----------------------------- ------- ------- ------ 
|   1    GGCCTTCGGGCCAA                0       13      GAACCGGACCGAAGCC              309     324     831k   
| 
\_______________________________________________________________________________
. . . done at 2021-03-26 14:13:17
ShapeMapper run successfully completed at 2021-03-26 14:13:17.
