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aquaskyline / Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
BSD 3-Clause "New" or "Revised" License
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GetTruth.py: error: unrecognized arguments: --noGT 1 #30

Closed ghost closed 5 years ago

ghost commented 5 years ago

Hello, I am trying to launch Clairvoyante with a reference vcf. I get the following error 

GetTruth.py: error: unrecognized arguments: --noGT 1
Loading model ...
Traceback (most recent call last):
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 225, in <module>
    main()
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 221, in main
    Run(args)
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 138, in Run
    c.CVInstance.wait()
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 1384, in wait
    pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 476, in _eintr_retry_call
    return func(*args)
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 30, in CheckRtCode
    c.CTInstance.kill(); c.CVInstance.kill()
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 1564, in kill
    self.send_signal(signal.SIGKILL)
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 1554, in send_signal
    os.kill(self.pid, sig)
OSError: [Errno 3] No such process

Here is my command line /clairvoyante.py callVarBamParallel --chkpnt_fn trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn final.genome.scf.fasta --bam_fn $i --output_prefix masurca_$i --threshold 0.05 --minCoverage 1 --includingAllContigs --tensorflowThreads 4 --vcf_fn masurca.arc.sorted.bam.vcf.gz.vcf > commands.sh

And here is the vcf 

scf7180000001106    2018290 .   A   G   999 .   .   GT:GQ:DP:AF 0/1:999:114:0.4912
scf7180000001106    2018333 .   C   T   332 .   .   GT:GQ:DP:AF 0/1:332:105:0.4286
scf7180000001106    2018374 .   T   C   272 .   .   GT:GQ:DP:AF 0/1:272:100:0.38
scf7180000001106    2033413 .   C   A   39  .   .   GT:GQ:DP:AF 1/1:39:21:0.0476
scf7180000001106    2033415 .   T   A   198 .   .   GT:GQ:DP:AF 0/1:198:19:0.4737
scf7180000001106    2033421 .   T   C   134 .   .   GT:GQ:DP:AF 0/1:134:17:0.1765
scf7180000001106    2038817 .   C   T   115 .   .   GT:GQ:DP:AF 0/1:115:28:0.1071
scf7180000001106    2040532 .   A   T   60  .   .   GT:GQ:DP:AF 0/1:60:24:0.125
scf7180000001106    2045126 .   T   A   118 .   .   GT:GQ:DP:AF 1/1:118:2:0.5
scf7180000001106    2045147 .   G   A   153 .   .   GT:GQ:DP:AF 1/1:153:2:0.5

Note that Clairvoyante works well without the vcf_fn option.

Thank you

ghost commented 5 years ago

I tried to modify a line in callVarBam.py, line 120 from shlex.split("%s %s --vcf_fn %s --ctgName %s %s --noGT 1" %\ to shlex.split("%s %s --vcf_fn %s --ctgName %s %s" %\

Unfortunately Clairvoyante doesn't run then (it doesn't throw any error but nothing happens). Note that I don't know what the --noGT argument is actually doing.

aquaskyline commented 5 years ago

@chaklim please check and fix.

chaklim commented 5 years ago

@aderzelle I tried removing --noGT 1 and the variant calling process is fine. Does it terminates and output nothing or it keeps running forever? Besides, I would like to know what is the content of commands.sh

ghost commented 5 years ago

It terminates and returns nothing when I removed the --noGT Here is the content of commands.sh

python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001096 --ctgStart 0 --ctgEnd 1965920 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001096_0_1965920.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000971 --ctgStart 0 --ctgEnd 91420 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000971_0_91420.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000879 --ctgStart 0 --ctgEnd 4368 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000879_0_4368.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001031 --ctgStart 0 --ctgEnd 35387 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001031_0_35387.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000967 --ctgStart 0 --ctgEnd 47660 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000967_0_47660.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001082 --ctgStart 0 --ctgEnd 83914 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001082_0_83914.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000810 --ctgStart 0 --ctgEnd 84445 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000810_0_84445.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001003 --ctgStart 0 --ctgEnd 20029 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001003_0_20029.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000994 --ctgStart 0 --ctgEnd 13748 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000994_0_13748.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000789 --ctgStart 0 --ctgEnd 4688294 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000789_0_4688294.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001044 --ctgStart 0 --ctgEnd 10611 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001044_0_10611.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000796 --ctgStart 0 --ctgEnd 1588534 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000796_0_1588534.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001106 --ctgStart 0 --ctgEnd 2045162 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001106_0_2045162.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000906 --ctgStart 0 --ctgEnd 31170 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000906_0_31170.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001016 --ctgStart 0 --ctgEnd 15233 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001016_0_15233.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000920 --ctgStart 0 --ctgEnd 1231591 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000920_0_1231591.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001072 --ctgStart 0 --ctgEnd 85993 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001072_0_85993.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000933 --ctgStart 0 --ctgEnd 42309 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000933_0_42309.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000995 --ctgStart 0 --ctgEnd 38901 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000995_0_38901.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001075 --ctgStart 0 --ctgEnd 114460 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001075_0_114460.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000832 --ctgStart 0 --ctgEnd 261337 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000832_0_261337.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000875 --ctgStart 0 --ctgEnd 2906438 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000875_0_2906438.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001088 --ctgStart 0 --ctgEnd 2334408 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001088_0_2334408.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000861 --ctgStart 0 --ctgEnd 1060184 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000861_0_1060184.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000843 --ctgStart 0 --ctgEnd 165839 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000843_0_165839.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001059 --ctgStart 0 --ctgEnd 74448 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001059_0_74448.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001000 --ctgStart 0 --ctgEnd 47710 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001000_0_47710.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001056 --ctgStart 0 --ctgEnd 518624 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001056_0_518624.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000855 --ctgStart 0 --ctgEnd 46371 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000855_0_46371.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000988 --ctgStart 0 --ctgEnd 75753 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000988_0_75753.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000866 --ctgStart 0 --ctgEnd 523410 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000866_0_523410.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000948 --ctgStart 0 --ctgEnd 104656 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000948_0_104656.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001006 --ctgStart 0 --ctgEnd 35805 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001006_0_35805.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000996 --ctgStart 0 --ctgEnd 85560 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000996_0_85560.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001071 --ctgStart 0 --ctgEnd 5653122 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001071_0_5653122.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000804 --ctgStart 0 --ctgEnd 1609966 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000804_0_1609966.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001086 --ctgStart 0 --ctgEnd 3791123 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001086_0_3791123.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000898 --ctgStart 0 --ctgEnd 1206234 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000898_0_1206234.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000965 --ctgStart 0 --ctgEnd 3333 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000965_0_3333.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001087 --ctgStart 0 --ctgEnd 2167336 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001087_0_2167336.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001081 --ctgStart 0 --ctgEnd 55504 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001081_0_55504.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000925 --ctgStart 0 --ctgEnd 1382046 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000925_0_1382046.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001007 --ctgStart 0 --ctgEnd 70709 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001007_0_70709.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001051 --ctgStart 0 --ctgEnd 4615 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001051_0_4615.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001058 --ctgStart 0 --ctgEnd 50121 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001058_0_50121.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001077 --ctgStart 0 --ctgEnd 63372 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001077_0_63372.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000969 --ctgStart 0 --ctgEnd 67153 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000969_0_67153.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001035 --ctgStart 0 --ctgEnd 12112 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001035_0_12112.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000972 --ctgStart 0 --ctgEnd 120173 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000972_0_120173.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000793 --ctgStart 0 --ctgEnd 4852155 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000793_0_4852155.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000956 --ctgStart 0 --ctgEnd 297491 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000956_0_297491.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001004 --ctgStart 0 --ctgEnd 26476 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001004_0_26476.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001083 --ctgStart 0 --ctgEnd 39773 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001083_0_39773.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001076 --ctgStart 0 --ctgEnd 4825197 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001076_0_4825197.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000966 --ctgStart 0 --ctgEnd 216263 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000966_0_216263.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000990 --ctgStart 0 --ctgEnd 12627 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000990_0_12627.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001041 --ctgStart 0 --ctgEnd 20328 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001041_0_20328.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000868 --ctgStart 0 --ctgEnd 115583 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000868_0_115583.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000873 --ctgStart 0 --ctgEnd 4841037 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000873_0_4841037.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000991 --ctgStart 0 --ctgEnd 161077 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000991_0_161077.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000911 --ctgStart 0 --ctgEnd 454039 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000911_0_454039.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000831 --ctgStart 0 --ctgEnd 31273 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000831_0_31273.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000846 --ctgStart 0 --ctgEnd 1442103 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000846_0_1442103.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000825 --ctgStart 0 --ctgEnd 478707 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000825_0_478707.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000839 --ctgStart 0 --ctgEnd 114613 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000839_0_114613.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001093 --ctgStart 0 --ctgEnd 47251 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001093_0_47251.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000904 --ctgStart 0 --ctgEnd 63199 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000904_0_63199.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000981 --ctgStart 0 --ctgEnd 36986 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000981_0_36986.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000950 --ctgStart 0 --ctgEnd 81045 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000950_0_81045.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000913 --ctgStart 0 --ctgEnd 9152 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000913_0_9152.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000938 --ctgStart 0 --ctgEnd 32612 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000938_0_32612.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001027 --ctgStart 0 --ctgEnd 16554 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001027_0_16554.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001069 --ctgStart 0 --ctgEnd 29401 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001069_0_29401.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000834 --ctgStart 0 --ctgEnd 6113409 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000834_0_6113409.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000973 --ctgStart 0 --ctgEnd 164970 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000973_0_164970.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000803 --ctgStart 0 --ctgEnd 556756 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000803_0_556756.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000987 --ctgStart 0 --ctgEnd 44652 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000987_0_44652.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000891 --ctgStart 0 --ctgEnd 31187 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000891_0_31187.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000862 --ctgStart 0 --ctgEnd 980352 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000862_0_980352.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000915 --ctgStart 0 --ctgEnd 892666 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000915_0_892666.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000926 --ctgStart 0 --ctgEnd 25858 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000926_0_25858.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001048 --ctgStart 0 --ctgEnd 27552 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001048_0_27552.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001008 --ctgStart 0 --ctgEnd 12844 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001008_0_12844.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000899 --ctgStart 0 --ctgEnd 80162 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000899_0_80162.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001050 --ctgStart 0 --ctgEnd 8930 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001050_0_8930.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000961 --ctgStart 0 --ctgEnd 245267 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000961_0_245267.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000885 --ctgStart 0 --ctgEnd 156061 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000885_0_156061.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001040 --ctgStart 0 --ctgEnd 10287 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001040_0_10287.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000989 --ctgStart 0 --ctgEnd 48474 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000989_0_48474.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000923 --ctgStart 0 --ctgEnd 240259 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000923_0_240259.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000984 --ctgStart 0 --ctgEnd 35345 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000984_0_35345.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000934 --ctgStart 0 --ctgEnd 80346 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000934_0_80346.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001038 --ctgStart 0 --ctgEnd 22587 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001038_0_22587.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000886 --ctgStart 0 --ctgEnd 95711 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000886_0_95711.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000997 --ctgStart 0 --ctgEnd 24114 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000997_0_24114.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001103 --ctgStart 0 --ctgEnd 286456 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001103_0_286456.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000939 --ctgStart 0 --ctgEnd 200223 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000939_0_200223.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001101 --ctgStart 0 --ctgEnd 1551472 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001101_0_1551472.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001066 --ctgStart 0 --ctgEnd 69745 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001066_0_69745.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000944 --ctgStart 0 --ctgEnd 36874 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000944_0_36874.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001043 --ctgStart 0 --ctgEnd 8922 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001043_0_8922.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000802 --ctgStart 0 --ctgEnd 1395679 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000802_0_1395679.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001010 --ctgStart 0 --ctgEnd 41729 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001010_0_41729.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000975 --ctgStart 0 --ctgEnd 81188 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000975_0_81188.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000968 --ctgStart 0 --ctgEnd 29966 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000968_0_29966.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000820 --ctgStart 0 --ctgEnd 4020724 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000820_0_4020724.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001047 --ctgStart 0 --ctgEnd 45921 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001047_0_45921.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001049 --ctgStart 0 --ctgEnd 20955 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001049_0_20955.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000928 --ctgStart 0 --ctgEnd 117739 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000928_0_117739.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000889 --ctgStart 0 --ctgEnd 75413 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000889_0_75413.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001068 --ctgStart 0 --ctgEnd 106321 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001068_0_106321.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001002 --ctgStart 0 --ctgEnd 30977 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001002_0_30977.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001022 --ctgStart 0 --ctgEnd 39842 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001022_0_39842.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001014 --ctgStart 0 --ctgEnd 20649 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001014_0_20649.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000959 --ctgStart 0 --ctgEnd 109722 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000959_0_109722.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000884 --ctgStart 0 --ctgEnd 520944 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000884_0_520944.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000953 --ctgStart 0 --ctgEnd 83365 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000953_0_83365.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000816 --ctgStart 0 --ctgEnd 4497571 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000816_0_4497571.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000800 --ctgStart 0 --ctgEnd 589366 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000800_0_589366.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000897 --ctgStart 0 --ctgEnd 134791 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000897_0_134791.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000864 --ctgStart 0 --ctgEnd 47302 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000864_0_47302.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001025 --ctgStart 0 --ctgEnd 9954 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001025_0_9954.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001092 --ctgStart 0 --ctgEnd 17073 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001092_0_17073.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000801 --ctgStart 0 --ctgEnd 4422530 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000801_0_4422530.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000947 --ctgStart 0 --ctgEnd 78921 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000947_0_78921.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001021 --ctgStart 0 --ctgEnd 10892 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001021_0_10892.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000954 --ctgStart 0 --ctgEnd 43420 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000954_0_43420.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001018 --ctgStart 0 --ctgEnd 6076 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001018_0_6076.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001015 --ctgStart 0 --ctgEnd 31381 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001015_0_31381.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000940 --ctgStart 0 --ctgEnd 26819 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000940_0_26819.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001091 --ctgStart 0 --ctgEnd 18858 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001091_0_18858.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000942 --ctgStart 0 --ctgEnd 486799 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000942_0_486799.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001037 --ctgStart 0 --ctgEnd 9117 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001037_0_9117.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000847 --ctgStart 0 --ctgEnd 108607 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000847_0_108607.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000977 --ctgStart 0 --ctgEnd 30992 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000977_0_30992.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001019 --ctgStart 0 --ctgEnd 15807 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001019_0_15807.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000878 --ctgStart 0 --ctgEnd 198774 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000878_0_198774.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001029 --ctgStart 0 --ctgEnd 23324 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001029_0_23324.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000795 --ctgStart 0 --ctgEnd 1413189 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000795_0_1413189.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000931 --ctgStart 0 --ctgEnd 75942 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000931_0_75942.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001099 --ctgStart 0 --ctgEnd 5994770 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001099_0_5994770.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000883 --ctgStart 0 --ctgEnd 362273 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000883_0_362273.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001060 --ctgStart 0 --ctgEnd 77524 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001060_0_77524.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000824 --ctgStart 0 --ctgEnd 73373 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000824_0_73373.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001011 --ctgStart 0 --ctgEnd 67109 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001011_0_67109.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000881 --ctgStart 0 --ctgEnd 137589 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000881_0_137589.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000819 --ctgStart 0 --ctgEnd 103126 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000819_0_103126.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001046 --ctgStart 0 --ctgEnd 25809 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001046_0_25809.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000952 --ctgStart 0 --ctgEnd 257262 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000952_0_257262.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001028 --ctgStart 0 --ctgEnd 41721 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001028_0_41721.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000918 --ctgStart 0 --ctgEnd 218016 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000918_0_218016.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001104 --ctgStart 0 --ctgEnd 83280 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001104_0_83280.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000895 --ctgStart 0 --ctgEnd 85881 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000895_0_85881.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001045 --ctgStart 0 --ctgEnd 12839 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001045_0_12839.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001052 --ctgStart 0 --ctgEnd 25747 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001052_0_25747.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001026 --ctgStart 0 --ctgEnd 9616 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001026_0_9616.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000985 --ctgStart 0 --ctgEnd 97064 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000985_0_97064.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001090 --ctgStart 0 --ctgEnd 365875 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001090_0_365875.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000912 --ctgStart 0 --ctgEnd 30640 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000912_0_30640.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000805 --ctgStart 0 --ctgEnd 223212 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000805_0_223212.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000951 --ctgStart 0 --ctgEnd 963648 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000951_0_963648.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001005 --ctgStart 0 --ctgEnd 25631 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001005_0_25631.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000792 --ctgStart 0 --ctgEnd 6889606 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000792_0_6889606.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000830 --ctgStart 0 --ctgEnd 24712 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000830_0_24712.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001102 --ctgStart 0 --ctgEnd 10000000 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001102_0_10000000.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001102 --ctgStart 10000000 --ctgEnd 14108707 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001102_10000000_14108707.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001062 --ctgStart 0 --ctgEnd 48525 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001062_0_48525.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001039 --ctgStart 0 --ctgEnd 10517 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001039_0_10517.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000817 --ctgStart 0 --ctgEnd 119532 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000817_0_119532.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000860 --ctgStart 0 --ctgEnd 1565813 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000860_0_1565813.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001009 --ctgStart 0 --ctgEnd 23885 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001009_0_23885.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001024 --ctgStart 0 --ctgEnd 21193 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001024_0_21193.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001036 --ctgStart 0 --ctgEnd 13686 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001036_0_13686.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001084 --ctgStart 0 --ctgEnd 81847 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001084_0_81847.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000964 --ctgStart 0 --ctgEnd 114031 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000964_0_114031.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000998 --ctgStart 0 --ctgEnd 32892 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000998_0_32892.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000941 --ctgStart 0 --ctgEnd 85165 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000941_0_85165.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000905 --ctgStart 0 --ctgEnd 45349 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000905_0_45349.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001017 --ctgStart 0 --ctgEnd 36583 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001017_0_36583.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000935 --ctgStart 0 --ctgEnd 123357 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000935_0_123357.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001012 --ctgStart 0 --ctgEnd 40739 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001012_0_40739.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000814 --ctgStart 0 --ctgEnd 3323949 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000814_0_3323949.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000946 --ctgStart 0 --ctgEnd 38636 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000946_0_38636.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001089 --ctgStart 0 --ctgEnd 114657 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001089_0_114657.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001095 --ctgStart 0 --ctgEnd 457027 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001095_0_457027.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000993 --ctgStart 0 --ctgEnd 73061 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000993_0_73061.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001042 --ctgStart 0 --ctgEnd 31272 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001042_0_31272.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000916 --ctgStart 0 --ctgEnd 933839 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000916_0_933839.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000822 --ctgStart 0 --ctgEnd 2181579 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000822_0_2181579.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000919 --ctgStart 0 --ctgEnd 27109 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000919_0_27109.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000932 --ctgStart 0 --ctgEnd 99322 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000932_0_99322.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000958 --ctgStart 0 --ctgEnd 89052 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000958_0_89052.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001001 --ctgStart 0 --ctgEnd 74036 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001001_0_74036.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000979 --ctgStart 0 --ctgEnd 43699 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000979_0_43699.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001030 --ctgStart 0 --ctgEnd 29691 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001030_0_29691.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000818 --ctgStart 0 --ctgEnd 2886621 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000818_0_2886621.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001020 --ctgStart 0 --ctgEnd 15507 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001020_0_15507.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001023 --ctgStart 0 --ctgEnd 49883 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001023_0_49883.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000949 --ctgStart 0 --ctgEnd 866584 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000949_0_866584.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001098 --ctgStart 0 --ctgEnd 1101625 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001098_0_1101625.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000974 --ctgStart 0 --ctgEnd 92866 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000974_0_92866.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000876 --ctgStart 0 --ctgEnd 1273445 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000876_0_1273445.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000784 --ctgStart 0 --ctgEnd 10000000 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000784_0_10000000.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000784 --ctgStart 10000000 --ctgEnd 11325799 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000784_10000000_11325799.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000914 --ctgStart 0 --ctgEnd 195182 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000914_0_195182.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000877 --ctgStart 0 --ctgEnd 36108 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000877_0_36108.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001034 --ctgStart 0 --ctgEnd 3617 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001034_0_3617.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000809 --ctgStart 0 --ctgEnd 107773 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000809_0_107773.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000999 --ctgStart 0 --ctgEnd 3664 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000999_0_3664.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000000962 --ctgStart 0 --ctgEnd 19734 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000000962_0_19734.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001067 --ctgStart 0 --ctgEnd 76101 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001067_0_76101.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge 
python /media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py --chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 --ref_fn /media/urbe/MyBDrive/masurca_assembly_analysis/final.genome.scf.fasta --bam_fn /media/urbe/MyBDrive/masurca_assembly_analysis/GC031600.160503.sorted.bam --ctgName scf7180000001033 --ctgStart 0 --ctgEnd 14845 --call_fn masurca_GC031600.160503.sorted.bam.scf7180000001033_0_14845.vcf --threshold 0.050000 --minCoverage 1.000000 --pypy pypy --samtools samtools --delay 10 --threads 4 --sampleName SAMPLE --vcf_fn /media/urbe/MyBDrive/masurca_assembly_analysis/masurca.arc.sorted.bam.vcf.gz.vcf --considerleftedge
aquaskyline commented 5 years ago

Please run the commands in command.sh one by one to see if it if you get some vcf outputs per command.

ghost commented 5 years ago

Yes I get some vcf files as output if running one by one.

ghost commented 5 years ago

However so far they don't contain variant, just the spec lines of the vcf ... I am gonna run them all one by one and see.

Shouldn't the script cut the different chromosomal regions only at regions that have variants in the reference vcf?

EDIT: actually, running ./scripts.sh (so trying to run Clairvoyante with parallel) do produce a few .vcf ... they are empty except for the spec lines and seem to be "random" chunks. Then Clairvoyante exits. I am really confused lol. EDIT2: indeed, it runs as Calling variants ... Processed 0 tensors Total time elapsed: 0.06 s I guess it's so because the chunk is not one for which there is a variant in the reference vcf. It has stopped running it seems ... I don't see any clairvoyante process running it has produced some vcf but all empty, here is whole log (just an excerpt, the whole one is very log I could email it if necessary but it's basically a repetition of this chunk):

Traceback (most recent call last):
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 225, in <module>
    main()
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 221, in main
    Run(args)
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 138, in Run
    c.CVInstance.wait()
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 1384, in wait
    pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 476, in _eintr_retry_call
    return func(*args)
  File "/media/urbe/MyBDrive/masurca_assembly_analysis/Clairvoyante/clairvoyante/callVarBam.py", line 30, in CheckRtCode
    c.CTInstance.kill(); c.CVInstance.kill()
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 1564, in kill
    self.send_signal(signal.SIGKILL)
  File "/home/urbe/anaconda3/envs/python_clairvoyante/lib/python2.7/subprocess.py", line 1554, in send_signal
    os.kill(self.pid, sig)
OSError: [Errno 3] No such process
Restoring parameters from /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999
Calling variants ...
Processed 0 tensors
Total time elapsed: 0.06 s
aquaskyline commented 5 years ago

For debugging purpose, would you mind share with me a small part of your fasta file and vcf file. Ten sequences, as well as the variants in those ten sequences, will suffice.

ghost commented 5 years ago

I am checking with my boss and co-workers. I will send you the material per email if it's ok for you.

aquaskyline commented 5 years ago

Sure. please send to rbluo at cs.hku.hk. And you don't need to give me the whole file. Just 10 sequences and their corresponding variants will suffice.

On Thu, May 23, 2019 at 11:20 PM aderzelle notifications@github.com wrote:

I am checking with my boss and co-workers. I will send you the material per email if it's ok for you.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aquaskyline/Clairvoyante/issues/30?email_source=notifications&email_token=AAG2SOJN4QLFBHIEFRU7WPTPW2Y4PA5CNFSM4HK7JHCKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWCSEYI#issuecomment-495264353, or mute the thread https://github.com/notifications/unsubscribe-auth/AAG2SOO4FDH7F7QNHVIL7ELPW2Y4PANCNFSM4HK7JHCA .

-- Laurent

ghost commented 5 years ago

Ok, I am sending it through Wetransfer on your email.

aquaskyline commented 5 years ago

@aderzelle sorry, I forgot to mention the bam file. Could you please also provide the alignments on the ten sequences you sent me?

aquaskyline commented 5 years ago

I ran your files on my server with no problem.

May I suggest you run the following steps on your server:

  1. Run command "taskset", "samtools" and "pypy" to see if they could run properly.
  2. git clone another copy of the latest Clairvoyante code and try running the new code.

If still run into any problems, please send me via email the full copy of your error log. Thank you!