Malformed Output files - Githubissues

aaiezza commented 8 years ago

I've noticed it once before at the Find Quality Score recalibration spots step but now it is also occurring at the Proceed Quality Score recalibration step. The output of the RNAEditor at some steps includes the following:

------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------

This text has found itself at the top of my generated bam file as well as the recalSpots.grp GATK report rendering them useless for the succeeding step.

The physical locations of these steps are in MapFastq.py:201-204 and in CallEditingSites.py:342-348

-Alex

djhn75 commented 8 years ago

So the first line of your Sample.noDup.realigned.bam, Sample.noDup.realigned.recalibrated.bam and Sample.recalSpots.grp sometimes contain this text? Did i understand that correctly?

aaiezza commented 8 years ago

@djhn75 That's correct. I only seem to make progress in the pipeline by running each step manually.

djhn75 commented 8 years ago

So the pipeline fails at one of these steps and afterwards you have to run the steps manually?

What error message is apearing when the program fails?

And what machine and OS are you using for RNAEditor right now?

Greetings David

Am 19.10.2016 um 23:06 schrieb Alex Aiezza:

@djhn75 https://github.com/djhn75 That's correct. I only seem to make progress in the pipeline by running each step manually.

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David John Institute of Cardiovascular Regeneration Theodor-Stern-Kai 7 D-60590 Frankfurt am Main +49 69 6301 87952 John@med.uni-frankfurt.de

aaiezza commented 8 years ago

@djhn75, I've been doing sort of a quick evaluation of the tool so I cannot recall the exact step instances it has failed, but it has been several times so far.

In fact between our responses I've manually ran the GATK UnifiedGenotyper step which will output a vcf file. After that I did manage to get much further in the RNAEditor pipeline but still hit another error. The following are my commands and their outputs:

Manually run this step:

java -Xmx8G -jar /usr/bin/GATK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /cvri/data/ref_genome/human/Homo_sapiens.GRCh38.dna.primary_assembly.fa -glm SNP -I /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam -nt 4 -l ERROR -D /cvri/sb/RNAEditor/GRCH38/dbSNP.vcf -metrics /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.snp.metrics -o /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.vcf -stand_call_conf 0 -stand_emit_conf 0 -A Coverage -A AlleleBalance -A BaseCounts

Output:

------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------

Run RNAEditor again:

RNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq -c configuration.txt

Output:

*** INFO:    CHECK DEPENDENCIES ***
java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
*** INFO:    Dependencies satisfied ***
*** INFO:    *** Start RnaEditor with: *** ***
*** INFO:        FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq ***
*** INFO:        outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***
*** INFO:        refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO:        dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
*** INFO:        sourceDir:/usr/bin/ ***
*** INFO:        threads:4 ***
*** INFO:        maxDiff:0.04 ***
*** INFO:        seedDiff:2 ***
*** INFO:        paired:False ***
*** INFO:        keepTemp:False ***
*** INFO:        overwrite:False ***
*** INFO:     ***
*** INFO:    * * * [Skipping] Mapping result File already exists * * * ***
*** INFO:    *** CALL VARIANTS WITH FOLLOWING ATTRIBUTES *** ***
*** INFO:        Bam-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam ***
*** INFO:        outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***
*** INFO:        refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO:        dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
*** INFO:        HapMap:/cvri/sb/RNAEditor/GRCH38/HAPMAP.vcf ***
*** INFO:        1000G Omni:/cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf ***
*** INFO:        Alu-Regions:/cvri/sb/RNAEditor/GRCH38/repeats.bed ***
*** INFO:        sourceDir:/usr/bin/ ***
*** INFO:        threads:4 ***
*** INFO:        StandCall:0 ***
*** INFO:        standEmit:0 ***
*** INFO:        keepTemp:False ***
*** INFO:        intronDistance:5 ***
*** INFO:        minPts:5 ***
*** INFO:        eps:50 ***
*** INFO:        overwrite:False ***
*** INFO:    [Wed Oct 19 14:48:45 2016] * * * Call variants * * * ***
*** INFO:        [SKIP] File already exist ***
*** INFO:     [Wed Oct 19 14:48:45 2016] Parsing Variant Data from /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.vcf ***
        *** [DONE] Duration [0:00:00.234015] ***
*** INFO:     [Wed Oct 19 14:48:45 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
        *** [DONE] Duration [0:06:07.353301] ***
*** INFO:     [Wed Oct 19 14:54:53 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf ***
        *** [DONE] Duration [0:00:00.008447] ***
*** INFO:     [Wed Oct 19 14:54:53 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/ESP_filtered ***
        *** [DONE] Duration [0:00:00.510360] ***
*** INFO:    [Wed Oct 19 14:54:53 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSNPs.vcf ***
*** INFO:     [Wed Oct 19 14:54:53 2016] remove Missmatches from the first 3 bp from read edges ***
Traceback (most recent call last):
  File "./RNAEditor.py", line 75, in run
    self.startAnalysis()
  File "./RNAEditor.py", line 103, in startAnalysis
    result = self.callEditSites.startAnalysis()
  File "/cvri/sb/RNAEditor/CallEditingSites.py", line 386, in startAnalysis
    variants.removeEdgeMismatches(self.bamFile, self.rnaEdit.params.edgeDistance, 25)
  File "/cvri/sb/RNAEditor/VariantSet.py", line 816, in removeEdgeMismatches
    if not pileupread.is_del and not pileupread.is_refskip:
AttributeError: 'pysam.csamtools.PileupRead' object has no attribute 'is_refskip'

Traceback (most recent call last):
  File "./RNAEditor.py", line 77, in run
    Helper.error("RnaEditor Failed",self.logFile,self.textField)
  File "/cvri/sb/RNAEditor/Helper.py", line 749, in error
    raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
Exception:

*** ERROR:    RnaEditor Failed ***

I ran RNAEditor again from here though:

RNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq -c configuration.txt

And got a different output:

*** INFO:    CHECK DEPENDENCIES ***
java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
*** INFO:    Dependencies satisfied ***
*** INFO:    *** Start RnaEditor with: *** ***
*** INFO:        FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq ***
*** INFO:        outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***
*** INFO:        refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO:        dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
*** INFO:        sourceDir:/usr/bin/ ***
*** INFO:        threads:4 ***
*** INFO:        maxDiff:0.04 ***
*** INFO:        seedDiff:2 ***
*** INFO:        paired:False ***
*** INFO:        keepTemp:False ***
*** INFO:        overwrite:False ***
*** INFO:     ***
*** INFO:    * * * [Skipping] Mapping result File already exists * * * ***
*** INFO:    *** CALL VARIANTS WITH FOLLOWING ATTRIBUTES *** ***
*** INFO:        Bam-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam ***
*** INFO:        outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***
*** INFO:        refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO:        dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
*** INFO:        HapMap:/cvri/sb/RNAEditor/GRCH38/HAPMAP.vcf ***
*** INFO:        1000G Omni:/cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf ***
*** INFO:        Alu-Regions:/cvri/sb/RNAEditor/GRCH38/repeats.bed ***
*** INFO:        sourceDir:/usr/bin/ ***
*** INFO:        threads:4 ***
*** INFO:        StandCall:0 ***
*** INFO:        standEmit:0 ***
*** INFO:        keepTemp:False ***
*** INFO:        intronDistance:5 ***
*** INFO:        minPts:5 ***
*** INFO:        eps:50 ***
*** INFO:        overwrite:False ***
*** INFO:    [Wed Oct 19 15:25:30 2016] * * * Call variants * * * ***
*** INFO:        [SKIP] File already exist ***
*** INFO:     [Wed Oct 19 15:25:30 2016] Parsing Variant Data from /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSNPs.vcf ***
        *** [DONE] Duration [0:00:00.153624] ***
*** INFO:    [Wed Oct 19 15:25:30 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noReadEdges.vcf ***
*** INFO:    [Wed Oct 19 15:25:30 2016] Split Variants by Bed File /cvri/sb/RNAEditor/GRCH38/repeats.bed ***
*** STATUS:    100000 Bed Feautes parsed ***
*** STATUS:    200000 Bed Feautes parsed ***
*** STATUS:    300000 Bed Feautes parsed ***
*** STATUS:    400000 Bed Feautes parsed ***
*** STATUS:    500000 Bed Feautes parsed ***
*** STATUS:    600000 Bed Feautes parsed ***
*** STATUS:    700000 Bed Feautes parsed ***
*** STATUS:    800000 Bed Feautes parsed ***
*** STATUS:    900000 Bed Feautes parsed ***
*** STATUS:    1000000 Bed Feautes parsed ***
*** STATUS:    1100000 Bed Feautes parsed ***
*** STATUS:    1200000 Bed Feautes parsed ***
*** STATUS:    1300000 Bed Feautes parsed ***
*** STATUS:    1400000 Bed Feautes parsed ***
*** STATUS:    1500000 Bed Feautes parsed ***
*** STATUS:    1600000 Bed Feautes parsed ***
*** STATUS:    1700000 Bed Feautes parsed ***
*** STATUS:    1800000 Bed Feautes parsed ***
*** STATUS:    1900000 Bed Feautes parsed ***
*** STATUS:    2000000 Bed Feautes parsed ***
*** STATUS:    2100000 Bed Feautes parsed ***
*** STATUS:    2200000 Bed Feautes parsed ***
*** STATUS:    2300000 Bed Feautes parsed ***
*** STATUS:    2400000 Bed Feautes parsed ***
*** STATUS:    2500000 Bed Feautes parsed ***
*** STATUS:    2600000 Bed Feautes parsed ***
*** STATUS:    2700000 Bed Feautes parsed ***
*** STATUS:    2800000 Bed Feautes parsed ***
*** STATUS:    2900000 Bed Feautes parsed ***
*** STATUS:    3000000 Bed Feautes parsed ***
*** STATUS:    3100000 Bed Feautes parsed ***
*** STATUS:    3200000 Bed Feautes parsed ***
*** STATUS:    3300000 Bed Feautes parsed ***
*** STATUS:    3400000 Bed Feautes parsed ***
*** STATUS:    3500000 Bed Feautes parsed ***
*** STATUS:    3600000 Bed Feautes parsed ***
*** STATUS:    3700000 Bed Feautes parsed ***
*** STATUS:    3800000 Bed Feautes parsed ***
*** STATUS:    3900000 Bed Feautes parsed ***
*** STATUS:    4000000 Bed Feautes parsed ***
*** STATUS:    4100000 Bed Feautes parsed ***
*** STATUS:    4200000 Bed Feautes parsed ***
*** STATUS:    4300000 Bed Feautes parsed ***
*** STATUS:    4400000 Bed Feautes parsed ***
*** STATUS:    4500000 Bed Feautes parsed ***
*** STATUS:    4600000 Bed Feautes parsed ***
*** STATUS:    4700000 Bed Feautes parsed ***
*** STATUS:    4800000 Bed Feautes parsed ***
*** STATUS:    4900000 Bed Feautes parsed ***
*** STATUS:    5000000 Bed Feautes parsed ***
*** STATUS:    5100000 Bed Feautes parsed ***
*** STATUS:    5200000 Bed Feautes parsed ***
*** STATUS:    5300000 Bed Feautes parsed ***
*** STATUS:    5400000 Bed Feautes parsed ***
*** STATUS:    5500000 Bed Feautes parsed ***
*** INFO:    finished parsing Bed file ***
        *** [DONE] Duration [0:01:10.825262] ***
*** INFO:    finished creating overlaps ***
        *** [DONE] Duration [0:01:10.826497] ***
        *** [DONE] Duration [0:01:10.828455] ***
*** INFO:    [Wed Oct 19 15:26:41 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.alu.vcf ***
*** INFO:    [Wed Oct 19 15:26:41 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.nonAlu.vcf ***
*** INFO:     [Wed Oct 19 15:26:41 2016] Assembling Genome from /cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.83.gtf ***
        *** [DONE] Duration [0:02:22.236015] ***
*** INFO:     [Wed Oct 19 15:29:03 2016] remove Missmatches from the intronic splice junctions  ***
        *** [DONE] Duration [0:00:01.598600] ***
*** INFO:    [Wed Oct 19 15:29:05 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSpliceJunction.vcf ***
*** INFO:     [Wed Oct 19 15:29:05 2016] remove Missmatches from homopolymers  ***
*** INFO:                2973 out of 3169 passed the Homopolymer-Filter ***
        *** [DONE] Duration [0:00:22.079934] ***
*** INFO:    [Wed Oct 19 15:29:27 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noHomo.vcf ***
*** INFO:     [Wed Oct 19 15:29:27 2016] Search non uniquely mapped reads ***
*** INFO:     [Wed Oct 19 15:29:27 2016] Create fasta file for blat  ***
Traceback (most recent call last):
  File "./RNAEditor.py", line 75, in run
    self.startAnalysis()
  File "./RNAEditor.py", line 103, in startAnalysis
    result = self.callEditSites.startAnalysis()
  File "/cvri/sb/RNAEditor/CallEditingSites.py", line 453, in startAnalysis
    self.blatSearch(nonAluVariants, blatOutfile, 25, 2)
  File "/cvri/sb/RNAEditor/CallEditingSites.py", line 153, in blatSearch
    if not pileupread.is_del and not pileupread.is_refskip:
AttributeError: 'pysam.csamtools.PileupRead' object has no attribute 'is_refskip'

Traceback (most recent call last):
  File "./RNAEditor.py", line 77, in run
    Helper.error("RnaEditor Failed",self.logFile,self.textField)
  File "/cvri/sb/RNAEditor/Helper.py", line 749, in error
    raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
Exception:

*** ERROR:    RnaEditor Failed ***

Not sure how helpful this is. I will say I very much enjoy that the pipeline is able to pick up from where it left off! This is a very thoughtful feature. On another note, obviously the paper is practically published, but it might be more useful for this tool to be in the Java programming language. I know that is counter-intuitive to most Bioinformaticians to use anything but Python, but it would alleviate many of these issues including the dependencies issues I've also mentioned in another post. It would allow you to work directly with the GATK library as oppose to calling it's functionality in a more complicated way through: first Python, then Bash, then ultimately through Java anyways...

djhn75 commented 8 years ago

It seems like the attribute 'is_refskip' is missing. Could you send me the version of pysam you are using? Also it would be great if you could send me the vcf file which arised from variant calling. The one which ends with *.noSNPs.vcf

*Then i could directly check who the error occurs.

Am 20.10.2016 um 16:33 schrieb Alex Aiezza:

@djhn75 https://github.com/djhn75, I've been doing sort of a quick evaluation of the tool so I cannot recall the exact step instances it has failed, but it has been several times so far.

In fact between our responses I've manually ran the GATK UnifiedGenotyper step which will output a |vcf| file. After that I did manage to get much further in the RNAEditor pipeline but still hit another error. The following are my commands and their outputs:

Manually run this step:

java -Xmx8G -jar /usr/bin/GATK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /cvri/data/ref_genome/human/Homo_sapiens.GRCh38.dna.primary_assembly.fa -glm SNP -I /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam -nt 4 -l ERROR -D /cvri/sb/RNAEditor/GRCH38/dbSNP.vcf -metrics /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.snp.metrics -o /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.vcf -stand_call_conf 0 -stand_emit_conf 0 -A Coverage -A AlleleBalance -A BaseCounts

Output:

Done. There were no warn messages.

Run RNAEditor again:

RNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq -c configuration.txt

Output:

* INFO: CHECK DEPENDENCIES java version"1.8.0_101" Java(TM) SE Runtime Environment (build 1.8.0_101-b13) Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode) \ INFO: Dependencies satisfied \ INFO:* Start RnaEditor with:* * * INFO: FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq* * INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1* * INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa* * INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf* * INFO: sourceDir:/usr/bin/* * INFO: threads:4* * INFO: maxDiff:0.04* * INFO: seedDiff:2* * INFO: paired:False* * INFO: keepTemp:False* * INFO: overwrite:False* * INFO:* ** INFO:* * * [Skipping] Mapping result File already exists* * * *\ INFO:* CALL VARIANTS WITH FOLLOWING ATTRIBUTES* \ INFO: Bam-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam \ INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 \ INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa \ INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf \ INFO: HapMap:/cvri/sb/RNAEditor/GRCH38/HAPMAP.vcf \ INFO: 1000G Omni:/cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf \ INFO: Alu-Regions:/cvri/sb/RNAEditor/GRCH38/repeats.bed \ INFO: sourceDir:/usr/bin/ \ INFO: threads:4 \ INFO: StandCall:0 \ INFO: standEmit:0 \ INFO: keepTemp:False \ INFO: intronDistance:5 \ INFO: minPts:5 \ INFO: eps:50 \ INFO: overwrite:False * INFO: [Wed Oct 19 14:48:45 2016]* * * Call variants* * * * INFO: [SKIP] File already exist* * INFO: [Wed Oct 19 14:48:45 2016] Parsing Variant Data from /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.vcf* * [DONE] Duration [0:00:00.234015]* * INFO: [Wed Oct 19 14:48:45 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/dbSNP.vcf* * [DONE] Duration [0:06:07.353301]* * INFO: [Wed Oct 19 14:54:53 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf* * [DONE] Duration [0:00:00.008447]* * INFO: [Wed Oct 19 14:54:53 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/ESP_filtered* * [DONE] Duration [0:00:00.510360]* * INFO: [Wed Oct 19 14:54:53 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSNPs.vcf* * INFO: [Wed Oct 19 14:54:53 2016] remove Missmatches from the first 3 bp fromread edges* Traceback (most recent call last): File"./RNAEditor.py", line 75,in run self.startAnalysis() File"./RNAEditor.py", line 103,in startAnalysis result =self.callEditSites.startAnalysis() File"/cvri/sb/RNAEditor/CallEditingSites.py", line 386,in startAnalysis variants.removeEdgeMismatches(self.bamFile, self.rnaEdit.params.edgeDistance, 25) File"/cvri/sb/RNAEditor/VariantSet.py", line 816,in removeEdgeMismatches if not pileupread.is_del and not pileupread.is_refskip: AttributeError:'pysam.csamtools.PileupRead' object has no attribute'is_refskip'

Traceback (most recent call last): File"./RNAEditor.py", line 77,in run Helper.error("RnaEditor Failed",self.logFile,self.textField) File"/cvri/sb/RNAEditor/Helper.py", line 749,in error raise Exception("\n\n" + Helper.prefix +"ERROR: " + message + Helper.praefix +"\n\n") Exception:

* ERROR: RnaEditor Failed*

I ran RNAEditor again from here though:

RNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq -c configuration.txt

And got a different output:

* INFO: CHECK DEPENDENCIES java version"1.8.0_101" Java(TM) SE Runtime Environment (build 1.8.0_101-b13) Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode) \ INFO: Dependencies satisfied \ INFO:* Start RnaEditor with:* * * INFO: FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq* * INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1* * INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa* * INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf* * INFO: sourceDir:/usr/bin/* * INFO: threads:4* * INFO: maxDiff:0.04* * INFO: seedDiff:2* * INFO: paired:False* * INFO: keepTemp:False* * INFO: overwrite:False* * INFO:* ** INFO:* * * [Skipping] Mapping result File already exists* * * *\ INFO:* CALL VARIANTS WITH FOLLOWING ATTRIBUTES* \ INFO: Bam-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam \ INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 \ INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa \ INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf \ INFO: HapMap:/cvri/sb/RNAEditor/GRCH38/HAPMAP.vcf \ INFO: 1000G Omni:/cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf \ INFO: Alu-Regions:/cvri/sb/RNAEditor/GRCH38/repeats.bed \ INFO: sourceDir:/usr/bin/ \ INFO: threads:4 \ INFO: StandCall:0 \ INFO: standEmit:0 \ INFO: keepTemp:False \ INFO: intronDistance:5 \ INFO: minPts:5 \ INFO: eps:50 \ INFO: overwrite:False * INFO: [Wed Oct 19 15:25:30 2016]* * * Call variants* * * * INFO: [SKIP] File already exist* * INFO: [Wed Oct 19 15:25:30 2016] Parsing Variant Data from /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSNPs.vcf* * [DONE] Duration [0:00:00.153624]* * INFO: [Wed Oct 19 15:25:30 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noReadEdges.vcf* * INFO: [Wed Oct 19 15:25:30 2016] Split Variants by Bed File /cvri/sb/RNAEditor/GRCH38/repeats.bed* * STATUS: 100000 Bed Feautes parsed* * STATUS: 200000 Bed Feautes parsed* * STATUS: 300000 Bed Feautes parsed* * STATUS: 400000 Bed Feautes parsed* * STATUS: 500000 Bed Feautes parsed* * STATUS: 600000 Bed Feautes parsed* * STATUS: 700000 Bed Feautes parsed* * STATUS: 800000 Bed Feautes parsed* * STATUS: 900000 Bed Feautes parsed* * STATUS: 1000000 Bed Feautes parsed* * STATUS: 1100000 Bed Feautes parsed* * STATUS: 1200000 Bed Feautes parsed* * STATUS: 1300000 Bed Feautes parsed* * STATUS: 1400000 Bed Feautes parsed* * STATUS: 1500000 Bed Feautes parsed* * STATUS: 1600000 Bed Feautes parsed* * STATUS: 1700000 Bed Feautes parsed* * STATUS: 1800000 Bed Feautes parsed* * STATUS: 1900000 Bed Feautes parsed* * STATUS: 2000000 Bed Feautes parsed* * STATUS: 2100000 Bed Feautes parsed* * STATUS: 2200000 Bed Feautes parsed* * STATUS: 2300000 Bed Feautes parsed* * STATUS: 2400000 Bed Feautes parsed* * STATUS: 2500000 Bed Feautes parsed* * STATUS: 2600000 Bed Feautes parsed* * STATUS: 2700000 Bed Feautes parsed* * STATUS: 2800000 Bed Feautes parsed* * STATUS: 2900000 Bed Feautes parsed* * STATUS: 3000000 Bed Feautes parsed* * STATUS: 3100000 Bed Feautes parsed* * STATUS: 3200000 Bed Feautes parsed* * STATUS: 3300000 Bed Feautes parsed* * STATUS: 3400000 Bed Feautes parsed* * STATUS: 3500000 Bed Feautes parsed* * STATUS: 3600000 Bed Feautes parsed* * STATUS: 3700000 Bed Feautes parsed* * STATUS: 3800000 Bed Feautes parsed* * STATUS: 3900000 Bed Feautes parsed* * STATUS: 4000000 Bed Feautes parsed* * STATUS: 4100000 Bed Feautes parsed* * STATUS: 4200000 Bed Feautes parsed* * STATUS: 4300000 Bed Feautes parsed* * STATUS: 4400000 Bed Feautes parsed* * STATUS: 4500000 Bed Feautes parsed* * STATUS: 4600000 Bed Feautes parsed* * STATUS: 4700000 Bed Feautes parsed* * STATUS: 4800000 Bed Feautes parsed* * STATUS: 4900000 Bed Feautes parsed* * STATUS: 5000000 Bed Feautes parsed* * STATUS: 5100000 Bed Feautes parsed* * STATUS: 5200000 Bed Feautes parsed* * STATUS: 5300000 Bed Feautes parsed* * STATUS: 5400000 Bed Feautes parsed* * STATUS: 5500000 Bed Feautes parsed* * INFO: finished parsing Bed file* * [DONE] Duration [0:01:10.825262]* * INFO: finished creating overlaps* * [DONE] Duration [0:01:10.826497]* * [DONE] Duration [0:01:10.828455]* * INFO: [Wed Oct 19 15:26:41 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.alu.vcf* * INFO: [Wed Oct 19 15:26:41 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.nonAlu.vcf* * INFO: [Wed Oct 19 15:26:41 2016] Assembling Genome from /cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.83.gtf* * [DONE] Duration [0:02:22.236015]* * INFO: [Wed Oct 19 15:29:03 2016] remove Missmatches from the intronic splice junctions* * [DONE] Duration [0:00:01.598600]* * INFO: [Wed Oct 19 15:29:05 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSpliceJunction.vcf* * INFO: [Wed Oct 19 15:29:05 2016] remove Missmatches from homopolymers* * INFO: 2973 out of 3169 passed the Homopolymer-Filter* * [DONE] Duration [0:00:22.079934]* * INFO: [Wed Oct 19 15:29:27 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noHomo.vcf* * INFO: [Wed Oct 19 15:29:27 2016] Search non uniquely mapped reads* * INFO: [Wed Oct 19 15:29:27 2016] Create fasta filefor blat* Traceback (most recent call last): File"./RNAEditor.py", line 75,in run self.startAnalysis() File"./RNAEditor.py", line 103,in startAnalysis result =self.callEditSites.startAnalysis() File"/cvri/sb/RNAEditor/CallEditingSites.py", line 453,in startAnalysis self.blatSearch(nonAluVariants, blatOutfile, 25, 2) File"/cvri/sb/RNAEditor/CallEditingSites.py", line 153,in blatSearch if not pileupread.is_del and not pileupread.is_refskip: AttributeError:'pysam.csamtools.PileupRead' object has no attribute'is_refskip'

Traceback (most recent call last): File"./RNAEditor.py", line 77,in run Helper.error("RnaEditor Failed",self.logFile,self.textField) File"/cvri/sb/RNAEditor/Helper.py", line 749,in error raise Exception("\n\n" + Helper.prefix +"ERROR: " + message + Helper.praefix +"\n\n") Exception:

* ERROR: RnaEditor Failed*

Not sure how helpful this is. I will say I very much enjoy that the pipeline is able to pick up from where it left off! This is a very thoughtful feature. On another note, obviously the paper is practically published, but it might be more useful for this tool to be in the Java programming language. I know that is counter-intuitive to most Bioinformaticians to use anything but Python, but it would alleviate many of these issues including the dependencies issues I've also mentioned in another post. It would allow you to work directly with the GATK library as oppose to calling it's functionality in a more complicated way through: first Python, then Bash, then ultimately through Java anyways...

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After that I did manage to get much further in the RNAEditor pipeline but still hit another error.\r\nThe following are my commands and their outputs:\r\n\r\nManually run this step:\r\nbash\r\njava -Xmx8G -jar /usr/bin/GATK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /cvri/data/ref_genome/human/Homo_sapiens.GRCh38.dna.primary_assembly.fa -glm SNP -I /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam -nt 4 -l ERROR -D /cvri/sb/RNAEditor/GRCH38/dbSNP.vcf -metrics /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.snp.metrics -o /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.vcf -stand_call_conf 0 -stand_emit_conf 0 -A Coverage -A AlleleBalance -A BaseCounts\r\n\r\nOutput:\r\nbash\r\n------------------------------------------------------------------------------------------\r\nDone. There were no warn messages.\r\n------------------------------------------------------------------------------------------\r\n\r\n\r\nRun RNAEditor again:\r\nbash\r\nRNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq -c configuration.txt\r\n\r\n\r\nOutput:\r\nbash\r\n*** INFO: CHECK DEPENDENCIES ***\r\njava version \"1.8.0_101\"\r\nJava(TM) SE Runtime Environment (build 1.8.0_101-b13)\r\nJava HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)\r\n*** INFO: Dependencies satisfied ***\r\n*** INFO: *** Start RnaEditor with: *** ***\r\n*** INFO: FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq ***\r\n*** INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***\r\n*** INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***\r\n*** INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***\r\n*** INFO: sourceDir:/usr/bin/ ***\r\n*** INFO: threads:4 ***\r\n*** INFO: maxDiff:0.04 ***\r\n*** INFO: seedDiff:2 ***\r\n*** INFO: paired:False ***\r\n*** INFO: keepTemp:False ***\r\n*** INFO: overwrite:False ***\r\n*** INFO: ***\r\n*** INFO: * * * [Skipping] Mapping result File already exists * * * ***\r\n*** INFO: *** CALL VARIANTS WITH FOLLOWING ATTRIBUTES *** ***\r\n*** INFO: Bam-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam ***\r\n*** INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***\r\n*** INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***\r\n*** INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***\r\n*** INFO: HapMap:/cvri/sb/RNAEditor/GRCH38/HAPMAP.vcf ***\r\n*** INFO: 1000G Omni:/cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf ***\r\n*** INFO: Alu-Regions:/cvri/sb/RNAEditor/GRCH38/repeats.bed ***\r\n*** INFO: sourceDir:/usr/bin/ ***\r\n*** INFO: threads:4 ***\r\n*** INFO: StandCall:0 ***\r\n*** INFO: standEmit:0 ***\r\n*** INFO: keepTemp:False ***\r\n*** INFO: intronDistance:5 ***\r\n*** INFO: minPts:5 ***\r\n*** INFO: eps:50 ***\r\n*** INFO: overwrite:False ***\r\n*** INFO: [Wed Oct 19 14:48:45 2016] * * * Call variants * * * ***\r\n*** INFO: [SKIP] File already exist ***\r\n*** INFO: [Wed Oct 19 14:48:45 2016] Parsing Variant Data from /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.vcf ***\r\n *** [DONE] Duration [0:00:00.234015] ***\r\n*** INFO: [Wed Oct 19 14:48:45 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***\r\n *** [DONE] Duration [0:06:07.353301] ***\r\n*** INFO: [Wed Oct 19 14:54:53 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf ***\r\n *** [DONE] Duration [0:00:00.008447] ***\r\n*** INFO: [Wed Oct 19 14:54:53 2016] Delete overlapps from /cvri/sb/RNAEditor/GRCH38/ESP_filtered ***\r\n *** [DONE] Duration [0:00:00.510360] ***\r\n*** INFO: [Wed Oct 19 14:54:53 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSNPs.vcf ***\r\n*** INFO: [Wed Oct 19 14:54:53 2016] remove Missmatches from the first 3 bp from read edges ***\r\nTraceback (most recent call last):\r\n File \"./RNAEditor.py\", line 75, in run\r\n self.startAnalysis()\r\n File \"./RNAEditor.py\", line 103, in startAnalysis\r\n result = self.callEditSites.startAnalysis()\r\n File \"/cvri/sb/RNAEditor/CallEditingSites.py\", line 386, in startAnalysis\r\n variants.removeEdgeMismatches(self.bamFile, self.rnaEdit.params.edgeDistance, 25)\r\n File \"/cvri/sb/RNAEditor/VariantSet.py\", line 816, in removeEdgeMismatches\r\n if not pileupread.is_del and not pileupread.is_refskip:\r\nAttributeError: 'pysam.csamtools.PileupRead' object has no attribute 'is_refskip'\r\n\r\nTraceback (most recent call last):\r\n File \"./RNAEditor.py\", line 77, in run\r\n Helper.error(\"RnaEditor Failed\",self.logFile,self.textField)\r\n File \"/cvri/sb/RNAEditor/Helper.py\", line 749, in error\r\n raise Exception(\"\\n\\n\" + Helper.prefix + \"ERROR: \" + message + Helper.praefix + \"\\n\\n\")\r\nException:\r\n\r\n*** ERROR: RnaEditor Failed ***\r\n\r\n\r\n\r\nI ran RNAEditor again from here though:\r\nbash\r\nRNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq -c configuration.txt\r\n\r\n\r\nAnd got a different output:\r\nbash\r\n*** INFO: CHECK DEPENDENCIES ***\r\njava version \"1.8.0_101\"\r\nJava(TM) SE Runtime Environment (build 1.8.0_101-b13)\r\nJava HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)\r\n*** INFO: Dependencies satisfied ***\r\n*** INFO: *** Start RnaEditor with: *** ***\r\n*** INFO: FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_1-0-D3_R1.fastq ***\r\n*** INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***\r\n*** INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***\r\n*** INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***\r\n*** INFO: sourceDir:/usr/bin/ ***\r\n*** INFO: threads:4 ***\r\n*** INFO: maxDiff:0.04 ***\r\n*** INFO: seedDiff:2 ***\r\n*** INFO: paired:False ***\r\n*** INFO: keepTemp:False ***\r\n*** INFO: overwrite:False ***\r\n*** INFO: ***\r\n*** INFO: * * * [Skipping] Mapping result File already exists * * * ***\r\n*** INFO: *** CALL VARIANTS WITH FOLLOWING ATTRIBUTES *** ***\r\n*** INFO: Bam-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noDup.realigned.recalibrated.bam ***\r\n*** INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1 ***\r\n*** INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***\r\n*** INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***\r\n*** INFO: HapMap:/cvri/sb/RNAEditor/GRCH38/HAPMAP.vcf ***\r\n*** INFO: 1000G Omni:/cvri/sb/RNAEditor/GRCH38/1000GenomeProject.vcf ***\r\n*** INFO: Alu-Regions:/cvri/sb/RNAEditor/GRCH38/repeats.bed ***\r\n*** INFO: sourceDir:/usr/bin/ ***\r\n*** INFO: threads:4 ***\r\n*** INFO: StandCall:0 ***\r\n*** INFO: standEmit:0 ***\r\n*** INFO: keepTemp:False ***\r\n*** INFO: intronDistance:5 ***\r\n*** INFO: minPts:5 ***\r\n*** INFO: eps:50 ***\r\n*** INFO: overwrite:False ***\r\n*** INFO: [Wed Oct 19 15:25:30 2016] * * * Call variants * * * ***\r\n*** INFO: [SKIP] File already exist ***\r\n*** INFO: [Wed Oct 19 15:25:30 2016] Parsing Variant Data from /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSNPs.vcf ***\r\n *** [DONE] Duration [0:00:00.153624] ***\r\n*** INFO: [Wed Oct 19 15:25:30 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noReadEdges.vcf ***\r\n*** INFO: [Wed Oct 19 15:25:30 2016] Split Variants by Bed File /cvri/sb/RNAEditor/GRCH38/repeats.bed ***\r\n*** STATUS: 100000 Bed Feautes parsed ***\r\n*** STATUS: 200000 Bed Feautes parsed ***\r\n*** STATUS: 300000 Bed Feautes parsed ***\r\n*** STATUS: 400000 Bed Feautes parsed ***\r\n*** STATUS: 500000 Bed Feautes parsed ***\r\n*** STATUS: 600000 Bed Feautes parsed ***\r\n*** STATUS: 700000 Bed Feautes parsed ***\r\n*** STATUS: 800000 Bed Feautes parsed ***\r\n*** STATUS: 900000 Bed Feautes parsed ***\r\n*** STATUS: 1000000 Bed Feautes parsed ***\r\n*** STATUS: 1100000 Bed Feautes parsed ***\r\n*** STATUS: 1200000 Bed Feautes parsed ***\r\n*** STATUS: 1300000 Bed Feautes parsed ***\r\n*** STATUS: 1400000 Bed Feautes parsed ***\r\n*** STATUS: 1500000 Bed Feautes parsed ***\r\n*** STATUS: 1600000 Bed Feautes parsed ***\r\n*** STATUS: 1700000 Bed Feautes parsed ***\r\n*** STATUS: 1800000 Bed Feautes parsed ***\r\n*** STATUS: 1900000 Bed Feautes parsed ***\r\n*** STATUS: 2000000 Bed Feautes parsed ***\r\n*** STATUS: 2100000 Bed Feautes parsed ***\r\n*** STATUS: 2200000 Bed Feautes parsed ***\r\n*** STATUS: 2300000 Bed Feautes parsed ***\r\n*** STATUS: 2400000 Bed Feautes parsed ***\r\n*** STATUS: 2500000 Bed Feautes parsed ***\r\n*** STATUS: 2600000 Bed Feautes parsed ***\r\n*** STATUS: 2700000 Bed Feautes parsed ***\r\n*** STATUS: 2800000 Bed Feautes parsed ***\r\n*** STATUS: 2900000 Bed Feautes parsed ***\r\n*** STATUS: 3000000 Bed Feautes parsed ***\r\n*** STATUS: 3100000 Bed Feautes parsed ***\r\n*** STATUS: 3200000 Bed Feautes parsed ***\r\n*** STATUS: 3300000 Bed Feautes parsed ***\r\n*** STATUS: 3400000 Bed Feautes parsed ***\r\n*** STATUS: 3500000 Bed Feautes parsed ***\r\n*** STATUS: 3600000 Bed Feautes parsed ***\r\n*** STATUS: 3700000 Bed Feautes parsed ***\r\n*** STATUS: 3800000 Bed Feautes parsed ***\r\n*** STATUS: 3900000 Bed Feautes parsed ***\r\n*** STATUS: 4000000 Bed Feautes parsed ***\r\n*** STATUS: 4100000 Bed Feautes parsed ***\r\n*** STATUS: 4200000 Bed Feautes parsed ***\r\n*** STATUS: 4300000 Bed Feautes parsed ***\r\n*** STATUS: 4400000 Bed Feautes parsed ***\r\n*** STATUS: 4500000 Bed Feautes parsed ***\r\n*** STATUS: 4600000 Bed Feautes parsed ***\r\n*** STATUS: 4700000 Bed Feautes parsed ***\r\n*** STATUS: 4800000 Bed Feautes parsed ***\r\n*** STATUS: 4900000 Bed Feautes parsed ***\r\n*** STATUS: 5000000 Bed Feautes parsed ***\r\n*** STATUS: 5100000 Bed Feautes parsed ***\r\n*** STATUS: 5200000 Bed Feautes parsed ***\r\n*** STATUS: 5300000 Bed Feautes parsed ***\r\n*** STATUS: 5400000 Bed Feautes parsed ***\r\n*** STATUS: 5500000 Bed Feautes parsed ***\r\n*** INFO: finished parsing Bed file ***\r\n *** [DONE] Duration [0:01:10.825262] ***\r\n*** INFO: finished creating overlaps ***\r\n *** [DONE] Duration [0:01:10.826497] ***\r\n *** [DONE] Duration [0:01:10.828455] ***\r\n*** INFO: [Wed Oct 19 15:26:41 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.alu.vcf ***\r\n*** INFO: [Wed Oct 19 15:26:41 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.nonAlu.vcf ***\r\n*** INFO: [Wed Oct 19 15:26:41 2016] Assembling Genome from /cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.83.gtf ***\r\n *** [DONE] Duration [0:02:22.236015] ***\r\n*** INFO: [Wed Oct 19 15:29:03 2016] remove Missmatches from the intronic splice junctions ***\r\n *** [DONE] Duration [0:00:01.598600] ***\r\n*** INFO: [Wed Oct 19 15:29:05 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noSpliceJunction.vcf ***\r\n*** INFO: [Wed Oct 19 15:29:05 2016] remove Missmatches from homopolymers ***\r\n*** INFO: 2973 out of 3169 passed the Homopolymer-Filter ***\r\n *** [DONE] Duration [0:00:22.079934] ***\r\n*** INFO: [Wed Oct 19 15:29:27 2016] Print Variants to /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_1-0-D3_R1/clt_1-0-D3_R1.noHomo.vcf ***\r\n*** INFO: [Wed Oct 19 15:29:27 2016] Search non uniquely mapped reads ***\r\n*** INFO: [Wed Oct 19 15:29:27 2016] Create fasta file for blat ***\r\nTraceback (most recent call last):\r\n File \"./RNAEditor.py\", line 75, in run\r\n self.startAnalysis()\r\n File \"./RNAEditor.py\", line 103, in startAnalysis\r\n result = self.callEditSites.startAnalysis()\r\n File \"/cvri/sb/RNAEditor/CallEditingSites.py\", line 453, in startAnalysis\r\n self.blatSearch(nonAluVariants, blatOutfile, 25, 2)\r\n File \"/cvri/sb/RNAEditor/CallEditingSites.py\", line 153, in blatSearch\r\n if not pileupread.is_del and not pileupread.is_refskip:\r\nAttributeError: 'pysam.csamtools.PileupRead' object has no attribute 'is_refskip'\r\n\r\nTraceback (most recent call last):\r\n File \"./RNAEditor.py\", line 77, in run\r\n Helper.error(\"RnaEditor Failed\",self.logFile,self.textField)\r\n File \"/cvri/sb/RNAEditor/Helper.py\", line 749, in error\r\n raise Exception(\"\\n\\n\" + Helper.prefix + \"ERROR: \" + message + Helper.praefix + \"\\n\\n\")\r\nException:\r\n\r\n*** ERROR: RnaEditor Failed ***\r\n\r\n\r\n\r\nNot sure how helpful this is. I will say I very much enjoy that the pipeline is able to pick up from where it left off! This is a very thoughtful feature.\r\nOn another note, obviously the paper is practically published, but it might be more useful for this tool to be in the Java programming language. I know that is counter-intuitive to most Bioinformaticians to use anything but Python, but it would alleviate many of these issues including the dependencies issues I've also mentioned in another post. It would allow you to work directly with the GATK library as oppose to calling it's functionality in a more complicated way through: first Python, then Bash, then ultimately through Java anyways..."}],"action":{"name":"View Issue","url":"https://github.com/djhn75/RNAEditor/issues/2#issuecomment-255123169"}}}

David John Institute of Cardiovascular Regeneration Theodor-Stern-Kai 7 D-60590 Frankfurt am Main +49 69 6301 87952 John@med.uni-frankfurt.de

aaiezza commented 8 years ago

Certainly.

alabaster==0.7.9
argh==0.26.2
Babel==2.3.4
backports-abc==0.4
biopython==1.67
cachetools==1.1.6
certifi==2016.9.26
click==6.6
colorama==0.3.7
CommonMark==0.5.4
ConfigArgParse==0.10.0
contextlib2==0.5.4
CRISPResso==0.9.8
cycler==0.10.0
Cython==0.23.4
decorator==4.0.10
demjson==2.2.4
discord-simple==0.0.1.15
docutils==0.12
enum34==1.1.6
eventlet==0.19.0
Flask==0.11.1
Flask-Cache==0.13.1
Flask-CacheBust==1.0.0
Flask-Compress==1.3.0
Flask-Cors==2.1.2
funcsigs==1.0.2
future==0.15.2
geographiclib==1.46.3
Geohash==1.0
geopy==1.11.0
gevent==1.1.2
googlemaps==2.4.4
gpsoauth==0.4.0
gpxpy==1.1.1
greenlet==0.4.9
gyp==0.1
gzip-reader==0.1
haversine==0.4.5
imagesize==0.7.1
iniherit==0.3.4
itsdangerous==0.24
Jinja2==2.8
LatLon==1.0.1
livereload==2.4.1
MarkupSafe==0.23
matplotlib==1.5.1
mock==2.0.0
networkx==1.11
numpy==1.11.0
paho-mqtt==1.2
pandas==0.18.0
pathtools==0.1.2
pbr==1.10.0
peewee==2.8.1
-e git+https://github.com/pogodevorg/pgoapi.git/@3a02e7416f6924b1bbcbcdde60c10bd247ba8e11#egg=pgoapi
polyline==1.3.1
port-for==0.3.1
protobuf==3.1.0.post1
protobuf-to-dict==0.1.0
pycrypto==2.6.1
pycryptodomex==3.4.2
Pygments==2.1.3
PyMySQL==0.7.5
pyparsing==2.1.1
pyproj==1.9.5.1
Pyrex==0.9.8.5

pysam==0.7.7

PySocks==1.5.6
Pyste==0.9.10
python-dateutil==2.5.3
python-engineio==1.0.3
python-slugify==1.2.1
python-socketio==1.4.2
python-telegram-bot==5.0.0
pytz==2016.7
PyYAML==3.12
raven==5.23.0
recommonmark==0.4.0
requests==2.10.0
requests-mock==1.0.0
s2sphere==0.2.4
scour==0.32
singledispatch==3.4.0.3
six==1.10.0
snowballstemmer==1.2.1
socketIO-client==0.7.0
Sphinx==1.4.5
sphinx-autobuild==0.6.0
sphinx-rtd-theme==0.1.9
timeout-decorator==0.3.2
tornado==4.4.2
Unidecode==0.4.19
urllib3==1.18
virtualenv==15.0.3
watchdog==0.8.3
websocket-client==0.37.0
Werkzeug==0.11.11
xxhash==0.6.1
yoyo-migrations==5.0.3

clt_1-0-D3_R1.noSNPs.vcf.zip

aaiezza commented 8 years ago

David,

A mass upgrade to my pip and python packages seems to have RNAEditor running very differently with no errors. At least from the point I was last at. I'll update this thread and close it pending the results of the current run. Thanks for you help, Alex

djhn75 commented 8 years ago

Ok, thanks. Let me know if it worked.

aaiezza commented 8 years ago

It actually didn't work initially when I ran it from where I left off while I had older versions of things. It's funny you pinged this thread just now though because I kicked it off this morning fresh with a brand new file.

aaiezza commented 8 years ago

Sadly we still get an error. Here is the contents of the output directory:

total 5.8G
drwxrwxr-x 2 aiezza adm    0 Oct 25 09:25 html/
-rwxrwxr-x 1 aiezza adm    0 Oct 25 11:22 clt_2-0-D3_R1.bam*
-rwxrwxr-x 1 aiezza adm 256K Oct 25 09:25 clt_2-0-D3_R1.log*
-rwxrwxr-x 1 aiezza adm 337M Oct 25 09:25 clt_2-0-D3_R1.sai*
-rwxrwxr-x 1 aiezza adm 5.5G Oct 25 09:41 clt_2-0-D3_R1.sam*

I've attached the whole log file. Here is the standard output:

$ RNAEditor.py -i /cvri/cameron/myo_infar_exp/re
[clt_2-0-D3_R1.log.txt](https://github.com/djhn75/RNAEditor/files/551102/clt_2-0-D3_R1.log.txt)
sources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq -c configuration.txt

*** INFO:    CHECK DEPENDENCIES ***
java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
*** INFO:    Dependencies satisfied ***
*** INFO:    *** Start RnaEditor with: *** ***
*** INFO:        FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq ***
*** INFO:        outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_2-0-D3_R1/clt_2-0-D3_R1 ***
*** INFO:        refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO:        dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
*** INFO:        sourceDir:/usr/bin/ ***
*** INFO:        threads:4 ***
*** INFO:        maxDiff:0.04 ***
*** INFO:        seedDiff:2 ***
*** INFO:        paired:False ***
*** INFO:        keepTemp:False ***
*** INFO:        overwrite:False ***
*** INFO:     ***
*** INFO:    [Tue Oct 25 09:25:25 2016] * * * Align Reads with BWA * * * ***
        *** [DONE] Duration [0:15:42.097073] ***
*** INFO:    [Tue Oct 25 09:41:07 2016] * * * convert sai to sam * * * ***
        *** [DONE] Duration [1:41:39.930876] ***
*** INFO:    [Tue Oct 25 11:22:47 2016] * * * Sort Bam File * * * ***
None

Traceback (most recent call last):
  File "./RNAEditor.py", line 75, in run
    self.startAnalysis()
  File "./RNAEditor.py", line 97, in startAnalysis
    mapResultFile=self.mapFastQ.startAnalysis()
  File "/cvri/sb/RNAEditor/MapFastq.py", line 132, in startAnalysis
    Helper.proceedCommand("Sort Bam File", cmd, samFile, bamFile, self.rnaEdit)
  File "/cvri/sb/RNAEditor/Helper.py", line 286, in proceedCommand
    Helper.error(description+ " failed!!!",logFile,textField)
  File "/cvri/sb/RNAEditor/Helper.py", line 749, in error
    raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
Exception:

*** ERROR:    Sort Bam File failed!!! ***

Traceback (most recent call last):
  File "./RNAEditor.py", line 77, in run
    Helper.error("RnaEditor Failed",self.logFile,self.textField)
  File "/cvri/sb/RNAEditor/Helper.py", line 749, in error
    raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
Exception:

*** ERROR:    RnaEditor Failed ***

djhn75 commented 8 years ago

it seems like you samtools installation is not working properly. Could you try to run:

$ samtools sort clt_2-0-D3_R1.sam -o clt_2-0-D3_R1.bam

To see if you get the same result.

Otherwise it would be helpfult to see the header of the sam file by running:

$ head -n 200 clt_2-0-D3_R1.sam

Sorry for all the trouble...

Am 25.10.2016 um 18:07 schrieb Alex Aiezza:

Sadly we still get an error. Here is the contents of the output directory:

total 5.8G drwxrwxr-x 2 aiezza adm 0 Oct 25 09:25 html/ -rwxrwxr-x 1 aiezza adm 0 Oct 25 11:22 clt_2-0-D3_R1.bam -rwxrwxr-x 1 aiezza adm 256K Oct 25 09:25 clt_2-0-D3_R1.log -rwxrwxr-x 1 aiezza adm 337M Oct 25 09:25 clt_2-0-D3_R1.sai -rwxrwxr-x 1 aiezza adm 5.5G Oct 25 09:41 clt_2-0-D3_R1.sam

Here is the log file:

* INFO: CHECK DEPENDENCIES \ INFO: Dependencies satisfied \ INFO: * Start RnaEditor with: * * * INFO: FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq \ INFO: outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_2-0-D3_R1/clt_2-0-D3_R1 \ INFO: refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa \ INFO: dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf \ INFO: sourceDir:/usr/bin/ \ INFO: threads:4 \ INFO: maxDiff:0.04 \ INFO: seedDiff:2 \ INFO: paired:False \ INFO: keepTemp:False \ INFO: overwrite:False \ INFO: * INFO: [Tue Oct 25 09:25:25 2016] * * * Align Reads with BWA * * * [bwa_aln] 17bp reads:max_diff = 2 [bwa_aln] 38bp reads:max_diff = 3 [bwa_aln] 64bp reads:max_diff = 4 [bwa_aln] 93bp reads:max_diff = 5 [bwa_aln] 124bp reads:max_diff = 6 [bwa_aln] 157bp reads:max_diff = 7 [bwa_aln] 190bp reads:max_diff = 8 [bwa_aln] 225bp reads:max_diff = 9 [bwa_aln_core] calculate SA coordinate... 38.28 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.03 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.31 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.39 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.09 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.00 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.13 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.22 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.21 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.14 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.60 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.83 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.42 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.29 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.30 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.98 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.17 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.24 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.87 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.79 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.08 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.70 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.40 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.85 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.26 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.20 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.47 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.57 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.62 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.40 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.27 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.76 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.40 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.63 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.48 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.38 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.65 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.53 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.26 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.51 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.89 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.11 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.80 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.53 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.74 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.93 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.68 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.76 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.24 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.30 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.48 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.21 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.39 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.96 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.16 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.96 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.62 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 36.91 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.63 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.27 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.43 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.21 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.41 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.12 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 39.65 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.86 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.93 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.00 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.11 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.09 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.64 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.60 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 36.76 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.28 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.35 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.28 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 36.96 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.67 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.55 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 37.91 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.43 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.30 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.03 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 38.32 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 2.97 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 22302068 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: /usr/bin/bwa aln -t 4 -n 0.04 -k 2 /cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq [main] Real time: 941.980 sec; CPU: 3276.512 sec * [DONE] Duration [0:15:42.097073] * ** INFO: [Tue Oct 25 09:41:07 2016] * * * convert sai to sam * * * [bwa_aln_core] convert to sequence coordinate... 4.03 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.94 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.26 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.27 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.23 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.87 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.22 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.26 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.34 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.31 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.96 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.97 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.99 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.87 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.79 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.18 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.96 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.89 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.28 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.17 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.88 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.11 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.28 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.23 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.21 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.90 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.92 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.84 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.96 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.82 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.80 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.98 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.09 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.17 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.19 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.00 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.22 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.12 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.07 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.15 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.92 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.83 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.15 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.20 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.15 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.90 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.28 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.08 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.03 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.24 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.12 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.10 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.06 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.11 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.70 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.69 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.91 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.03 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.04 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.15 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.12 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.20 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.09 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.06 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.17 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.14 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.07 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.25 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.25 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.90 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.15 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.19 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.24 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.78 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.77 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.79 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.73 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.53 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.49 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.03 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.98 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.94 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.99 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.87 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.88 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 4.22 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.02 sec [bwa_aln_core] 22302068 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: /usr/bin/bwa samse -r @RG ID:bwa SM:A PL:ILLUMINA PU:HiSEQ2000 /cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_2-0-D3_R1/clt_2-0-D3_R1.sai /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq [main] Real time: 6099.803 sec; CPU: 433.464 sec * [DONE] Duration [1:41:39.930876] * ** INFO: [Tue Oct 25 11:22:47 2016] * * * Sort Bam File * * * [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). * ERROR: Sort Bam File failed!!! * * ERROR: RnaEditor Failed *

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{"api_version":"1.0","publisher":{"api_key":"05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity":{"external_key":"github/djhn75/RNAEditor","title":"djhn75/RNAEditor","subtitle":"GitHub repository","main_image_url":"https://cloud.githubusercontent.com/assets/143418/17495839/a5054eac-5d88-11e6-95fc-7290892c7bb5.png","avatar_image_url":"https://cloud.githubusercontent.com/assets/143418/15842166/7c72db34-2c0b-11e6-9aed-b52498112777.png","action":{"name":"Open in GitHub","url":"https://github.com/djhn75/RNAEditor"}},"updates":{"snippets":[{"icon":"PERSON","message":"@aaiezza in #2: Sadly we still get an error.\r\nHere is the contents of the output directory:\r\nbash\r\ntotal 5.8G\r\ndrwxrwxr-x 2 aiezza adm 0 Oct 25 09:25 html/\r\n-rwxrwxr-x 1 aiezza adm 0 Oct 25 11:22 clt_2-0-D3_R1.bam*\r\n-rwxrwxr-x 1 aiezza adm 256K Oct 25 09:25 clt_2-0-D3_R1.log*\r\n-rwxrwxr-x 1 aiezza adm 337M Oct 25 09:25 clt_2-0-D3_R1.sai*\r\n-rwxrwxr-x 1 aiezza adm 5.5G Oct 25 09:41 clt_2-0-D3_R1.sam*\r\n\r\n\r\nHere is the log file:\r\n```ini\r\n* INFO: CHECK DEPENDENCIES \r\n** INFO: Dependencies satisfied _\r\n INFO: * Start RnaEditor with: * **\r\n_ INFO: \t FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq \r\n** INFO: \t outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_2-0-D3_R1/clt_2-0-D3R1 **\r\n_ INFO: \t refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa \r\n** INFO: \t dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf _\r\n INFO: \t sourceDir:/usr/bin/ **\r\n_ INFO: \t threads:4 \r\n** INFO: \t maxDiff:0.04 _\r\n INFO: \t seedDiff:2 **\r\n_ INFO: \t paired:False \r\n** INFO: \t keepTemp:False _\r\n INFO: \t overwrite:False **\r\n_ INFO: \r\n** INFO: [Tue Oct 25 09:25:25 2016] * * * Align Reads with BWA * * * **_\r\n[bwa_aln] 17bp reads: max_diff = 2\r\n[bwa_aln] 38bp reads: max_diff = 3\r\n[bwa_aln] 64bp reads: max_diff = 4\r\n[bwa_aln] 93bp reads: max_diff = 5\r\n[bwa_aln] 124bp reads: max_diff = 6\r\n[bwa_aln] 157bp reads: max_diff = 7\r\n[bwa_aln] 190bp reads: max_diff = 8\r\n[bwa_aln] 225bp reads: max_diff = 9\r\n[bwa_aln_core] calculate SA coordinate... 38.28 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 262144 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.03 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 524288 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.31 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 786432 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.39 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 1048576 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.09 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 1310720 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.00 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 1572864 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.13 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 1835008 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.22 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 2097152 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.21 sec\r\n[bwa_aln_core] write to the disk... 0.02 sec\r\n[bwa_aln_core] 2359296 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.14 sec\r\n[bwa_aln_core] write to the disk... 0.02 sec\r\n[bwa_aln_core] 2621440 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.60 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 2883584 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.83 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 3145728 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.42 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 3407872 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.29 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 3670016 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.30 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 3932160 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.98 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 4194304 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.17 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 4456448 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.24 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 4718592 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.87 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 4980736 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.79 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 5242880 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.08 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 5505024 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.70 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 5767168 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.40 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 6029312 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.85 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 6291456 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.26 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 6553600 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.20 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 6815744 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.47 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 7077888 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.87 sec\r\n[bwa_aln_core] write to the disk... 0.02 sec\r\n[bwa_aln_core] 7340032 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.57 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 7602176 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.62 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 7864320 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.40 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 8126464 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.27 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 8388608 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.76 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 8650752 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.40 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 8912896 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.63 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 9175040 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.48 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 9437184 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.38 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 9699328 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.65 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 9961472 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.53 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 10223616 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.26 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 10485760 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.51 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 10747904 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.89 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 11010048 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.11 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 11272192 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.80 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 11534336 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.53 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 11796480 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.74 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 12058624 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.93 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 12320768 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.68 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 12582912 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.76 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 12845056 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.24 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 13107200 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.30 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 13369344 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.48 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 13631488 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.21 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 13893632 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.39 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 14155776 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.96 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 14417920 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.16 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 14680064 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.96 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 14942208 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.62 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 15204352 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 36.91 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 15466496 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.63 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 15728640 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.27 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 15990784 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.43 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 16252928 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.21 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 16515072 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.41 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 16777216 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.12 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 17039360 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 39.65 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 17301504 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.86 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 17563648 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.93 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 17825792 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.00 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 18087936 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.11 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 18350080 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.09 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 18612224 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.64 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 18874368 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.60 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 19136512 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 36.76 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 19398656 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.28 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 19660800 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.35 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 19922944 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.28 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 20185088 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 36.96 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 20447232 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.67 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 20709376 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.55 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 20971520 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 37.91 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 21233664 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.43 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 21495808 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.30 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 21757952 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.03 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 22020096 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 38.32 sec\r\n[bwa_aln_core] write to the disk... 0.01 sec\r\n[bwa_aln_core] 22282240 sequences have been processed.\r\n[bwa_aln_core] calculate SA coordinate... 2.97 sec\r\n[bwa_aln_core] write to the disk... 0.00 sec\r\n[bwa_aln_core] 22302068 sequences have been processed.\r\n[main] Version: 0.7.12-r1039\r\n[main] CMD: /usr/bin/bwa aln -t 4 -n 0.04 -k 2 /cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3R1.fastq\r\n[main] Real time: 941.980 sec; CPU: 3276.512 sec\r\n\t** [DONE] Duration [0:15:42.097073] _\r\n_ INFO: [Tue Oct 25 09:41:07 2016] * * * convert sai to sam * * * ***\r\n[bwa_aln_core] convert to sequence coordinate... 4.03 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 262144 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.94 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 524288 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.26 sec\r\n[bwa_aln_core] refine gapped alignments... 0.51 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 786432 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.27 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 1048576 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.23 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 1310720 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.87 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 1572864 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.22 sec\r\n[bwa_aln_core] refine gapped alignments... 0.47 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 1835008 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.26 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 2097152 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.34 sec\r\n[bwa_aln_core] refine gapped alignments... 0.51 sec\r\n[bwa_aln_core] print alignments... 0.21 sec\r\n[bwa_aln_core] 2359296 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.31 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 2621440 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.96 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 2883584 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.97 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 3145728 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.99 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 3407872 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.87 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 3670016 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.79 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 3932160 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.18 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 4194304 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.96 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 4456448 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.89 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 4718592 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.28 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 4980736 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.17 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 5242880 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.88 sec\r\n[bwa_aln_core] refine gapped alignments... 0.47 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 5505024 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.11 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.21 sec\r\n[bwa_aln_core] 5767168 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.28 sec\r\n[bwa_aln_core] refine gapped alignments... 0.51 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 6029312 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.23 sec\r\n[bwa_aln_core] refine gapped alignments... 0.45 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 6291456 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.21 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 6553600 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.90 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 6815744 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.92 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 7077888 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.84 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 7340032 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.96 sec\r\n[bwa_aln_core] refine gapped alignments... 0.50 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 7602176 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.82 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 7864320 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.80 sec\r\n[bwa_aln_core] refine gapped alignments... 0.43 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 8126464 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.98 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 8388608 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.09 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 8650752 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.17 sec\r\n[bwa_aln_core] refine gapped alignments... 0.47 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 8912896 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.19 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 9175040 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.00 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 9437184 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.22 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 9699328 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.12 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 9961472 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.07 sec\r\n[bwa_aln_core] refine gapped alignments... 0.46 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 10223616 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.15 sec\r\n[bwa_aln_core] refine gapped alignments... 0.50 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 10485760 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.92 sec\r\n[bwa_aln_core] refine gapped alignments... 0.44 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 10747904 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.83 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 11010048 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.15 sec\r\n[bwa_aln_core] refine gapped alignments... 0.49 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 11272192 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.20 sec\r\n[bwa_aln_core] refine gapped alignments... 0.47 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 11534336 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.15 sec\r\n[bwa_aln_core] refine gapped alignments... 0.47 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 11796480 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 3.90 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 12058624 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.28 sec\r\n[bwa_aln_core] refine gapped alignments... 0.52 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 12320768 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.08 sec\r\n[bwa_aln_core] refine gapped alignments... 0.47 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 12582912 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.03 sec\r\n[bwa_aln_core] refine gapped alignments... 0.50 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 12845056 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.24 sec\r\n[bwa_aln_core] refine gapped alignments... 0.51 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 13107200 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.12 sec\r\n[bwa_aln_core] refine gapped alignments... 0.48 sec\r\n[bwa_aln_core] print alignments... 0.20 sec\r\n[bwa_aln_core] 13369344 sequences have been processed.\r\n[bwa_aln_core] convert to sequence coordinate... 4.1

aaiezza commented 8 years ago

Not at all. I'm happy to troubleshoot it. headOf_clt_2-0-D3_R1.sam samtools ran fine on its own.

aaiezza commented 8 years ago

Again I'm getting errors in the next steps:

 $ RNAEditor.py -i /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq -c configuration.txt

*** INFO:    CHECK DEPENDENCIES ***
java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
*** INFO:    Dependencies satisfied ***
*** INFO:    *** Start RnaEditor with: *** ***
*** INFO:        FastQ-File: /cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/clt_2-0-D3_R1.fastq ***
*** INFO:        outfilePrefix:/cvri/cameron/myo_infar_exp/resources/deliv_Cameron072516_data/cleaned_fastq/rnaEditor/clt_2-0-D3_R1/clt_2-0-D3_R1 ***
*** INFO:        refGenome:/cvri/sb/RNAEditor/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ***
*** INFO:        dbsnp:/cvri/sb/RNAEditor/GRCH38/dbSNP.vcf ***
*** INFO:        sourceDir:/usr/bin/ ***
*** INFO:        threads:4 ***
*** INFO:        maxDiff:0.04 ***
*** INFO:        seedDiff:2 ***
*** INFO:        paired:False ***
*** INFO:        keepTemp:False ***
*** INFO:        overwrite:False ***
*** INFO:     ***
*** INFO:    [Thu Oct 27 10:26:57 2016] * * * Align Reads with BWA * * * ***
*** INFO:        [SKIP] File already exist ***
*** INFO:    [Thu Oct 27 10:26:57 2016] * * * convert sai to sam * * * ***
*** INFO:        [SKIP] File already exist ***
*** INFO:    [Thu Oct 27 10:26:57 2016] * * * Sort Bam File * * * ***
*** INFO:        [SKIP] File already exist ***
*** INFO:    [Thu Oct 27 10:26:57 2016] * * * Index Bam File * * * ***
        *** [DONE] Duration [0:00:00.044432] ***
*** INFO:    [Thu Oct 27 10:26:57 2016] * * * Remove PCR duplicates * * * ***
None

Traceback (most recent call last):
  File "./RNAEditor.py", line 75, in run
    self.startAnalysis()
  File "./RNAEditor.py", line 97, in startAnalysis
    mapResultFile=self.mapFastQ.startAnalysis()
  File "/cvri/sb/RNAEditor/MapFastq.py", line 143, in startAnalysis
    Helper.proceedCommand("Remove PCR duplicates", cmd, bamFile, markedFile, self.rnaEdit)
  File "/cvri/sb/RNAEditor/Helper.py", line 286, in proceedCommand
    Helper.error(description+ " failed!!!",logFile,textField)
  File "/cvri/sb/RNAEditor/Helper.py", line 749, in error
    raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
Exception:

*** ERROR:    Remove PCR duplicates failed!!! ***

Traceback (most recent call last):
  File "./RNAEditor.py", line 77, in run
    Helper.error("RnaEditor Failed",self.logFile,self.textField)
  File "/cvri/sb/RNAEditor/Helper.py", line 749, in error
    raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
Exception:

*** ERROR:    RnaEditor Failed ***

djhn75 commented 8 years ago

thats pretty weird... You could try to run it again.

Would it be ok for you to send me one of your fastQ files? So that i can try it one my local machine?

I could sent you a link to our FTP-Server.

aaiezza commented 8 years ago

Sure. We could give it a go. alessandro_aiezza[at]urmc[dot]rochester[dot]edu

aaiezza commented 8 years ago

It is uploaded. Thanks for your help on this!

djhn75 commented 8 years ago

Ok, i will give it a try.

djhn75 / RNAEditor

Malformed Output files #2

Done. There were no warn messages.