Error "Can't open NA.2bit to read" #75
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Hi Sejjbia,
Sorry for the trouble with the software.
This is an older software project and we are currently working to make a
more general and exportable version.
First, I am assuming that you are using the deployment branch from GitHub
repository, have successfully built
the Conda environment, and are executing from within it.
The presence of hg18.2bit proves that BS genome libraries are functioning.
The refGenome value is typically taken from the sampleInfo file not the
processing parameter file.
Please add a column to your sampleInfo file 'refGenome' and set this value
to 'hg18' and let me know
if this resolves the issue.
Best,
John
…On Mon, Nov 4, 2019 at 4:42 PM sejjbia ***@***.***> wrote:
Hi
I am trying to run the test on the fastq files contained in the
validationDataSet/Data folder following your instructions but I get the
following error after processing of clone1-4
(...)
sample clone1-4
barcoded 104
LTRed 92
linkered 102
ltredlinkered 90
[1] TRUE
*mustOpen: Can't open NA.2bit to read: No such file or directory*
[1] TRUE
*Error in strsplit(alignFile, "/")[[1]] : subscript out of bounds Calls:
alignSeqs Execution halted*
processingParams.tsv are as follows
qualityThreshold badQualityBases qualitySlidingWindow mingDNA minPctIdent
maxAlignStart maxFragLength refGenome
? 5 10 30 95 5 2500 hg18
Genome hg18 is installed properly and hg18.2bit is generated as well
(tried also changing to hg19. Same error)
Can you help?
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First, I am assuming that you are using the deployment branch from GitHub YES This is the content of the sampleInfo.tsv file This is the whole script call and output I get |
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Hi Sejjbia,
Sorry for the trouble.
Based on your path, I suspect you are working with Luca Biasco.
Please set up a means for me to retrieve your analysis directory including
sequencing data and I will take a look on my side.
John
…On Mon, Nov 11, 2019 at 5:17 PM sejjbia ***@***.***> wrote:
First, I am assuming that you are using the deployment branch from GitHub
*YES*
have successfully built the Conda environment, and are executing from
within it. *YES*
Please add a column to your sampleInfo file 'refGenome' and set this value
to 'hg18' and let me know *I tried your fix but unfortunately it's not
working. I still get the same error.*
*This is the content of the sampleInfo.tsv file*
alias linkerSequence bcSeq gender primer ltrBit largeLTRFrag vectorSeq
refGenome clone1-1 CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT
AATCCGTACAGC f GAAAATC TCTAGCA TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT
p746vector.fasta hg18 clone1-2
CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT ACACCTGGTGAT f GAAAATC
TCTAGCA TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT p746vector.fasta hg18 clone1-3
CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT TATCGTTGACCA f GAAAATC
TCTAGCA TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT p746vector.fasta hg18 clone1-4
CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT TTACTGTGCGAT f GAAAATC
TCTAGCA TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT p746vector.fasta hg18
This is the whole script call and output I get
~/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet$ Rscript ~/INSPIIRED-INSPIIRED-deployment/components/intSiteCaller/intSiteCaller.R
AATCCGTACAGC Data/demultiplexedReps/clone1-1_R1.fastq.gz
ACACCTGGTGAT Data/demultiplexedReps/clone1-2_R1.fastq.gz
TATCGTTGACCA Data/demultiplexedReps/clone1-3_R1.fastq.gz
TTACTGTGCGAT Data/demultiplexedReps/clone1-4_R1.fastq.gz
AATCCGTACAGC Data/demultiplexedReps/clone1-1_R2.fastq.gz
ACACCTGGTGAT Data/demultiplexedReps/clone1-2_R2.fastq.gz
TATCGTTGACCA Data/demultiplexedReps/clone1-3_R2.fastq.gz
TTACTGTGCGAT Data/demultiplexedReps/clone1-4_R2.fastq.gz
[1] TRUE
1
alias clone1-1
linkerSequence CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT
bcSeq AATCCGTACAGC
gender f
primer GAAAATC
ltrBit TCTAGCA
largeLTRFrag TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT
vectorSeq p746vector.fasta
refGenome hg18
linkerCommon AGTCCCTTAAGCGGAG
qualityThreshold ?
badQualityBases 5
qualitySlidingWindow 10
mingDNA 30
minPctIdent 95
maxAlignStart 5
maxFragLength 2500
refGenome hg18
read1 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-1_R1.fastq.gz
read2 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-1_R2.fastq.gz
[,1]
sample clone1-1
barcoded 87
[,1]
sample clone1-1
barcoded 87
LTRed 80
linkered 85
ltredlinkered 78
[1] TRUE
2
alias clone1-2
linkerSequence CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT
bcSeq ACACCTGGTGAT
gender f
primer GAAAATC
ltrBit TCTAGCA
largeLTRFrag TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT
vectorSeq p746vector.fasta
refGenome hg18
linkerCommon AGTCCCTTAAGCGGAG
qualityThreshold ?
badQualityBases 5
qualitySlidingWindow 10
mingDNA 30
minPctIdent 95
maxAlignStart 5
maxFragLength 2500
refGenome hg18
read1 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-2_R1.fastq.gz
read2 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-2_R2.fastq.gz
[,1]
sample clone1-2
barcoded 73
[,1]
sample clone1-2
barcoded 73
LTRed 66
linkered 72
ltredlinkered 65
[1] TRUE
3
alias clone1-3
linkerSequence CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT
bcSeq TATCGTTGACCA
gender f
primer GAAAATC
ltrBit TCTAGCA
largeLTRFrag TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT
vectorSeq p746vector.fasta
refGenome hg18
linkerCommon AGTCCCTTAAGCGGAG
qualityThreshold ?
badQualityBases 5
qualitySlidingWindow 10
mingDNA 30
minPctIdent 95
maxAlignStart 5
maxFragLength 2500
refGenome hg18
read1 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-3_R1.fastq.gz
read2 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-3_R2.fastq.gz
[,1]
sample clone1-3
barcoded 101
[,1]
sample clone1-3
barcoded 101
LTRed 95
linkered 101
ltredlinkered 95
[1] TRUE
4
alias clone1-4
linkerSequence CGCAGACATCCCGTCCCATNNNNNNNNNNNNCTCCGCTTAAGGGACT
bcSeq TTACTGTGCGAT
gender f
primer GAAAATC
ltrBit TCTAGCA
largeLTRFrag TGCTAGAGATTTTCCACACTGACTAAAAGGGTCT
vectorSeq p746vector.fasta
refGenome hg18
linkerCommon AGTCCCTTAAGCGGAG
qualityThreshold ?
badQualityBases 5
qualitySlidingWindow 10
mingDNA 30
minPctIdent 95
maxAlignStart 5
maxFragLength 2500
refGenome hg18
read1 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-4_R1.fastq.gz
read2 /home/sejjbia/INSPIIRED-INSPIIRED-deployment/inputs/validationDataSet/Data/demultiplexedReps/clone1-4_R2.fastq.gz
[,1]
sample clone1-4
barcoded 104
[,1]
sample clone1-4
barcoded 104
LTRed 92
linkered 102
ltredlinkered 90
[1] TRUE
mustOpen: Can't open NA.2bit to read: No such file or directory
[1] TRUE
Error in strsplit(alignFile, "/")[[1]] : subscript out of bounds
Calls: alignSeqs
Execution halted
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Hi
I am trying to run the test on the fastq files contained in the validationDataSet/Data folder following your instructions but I get the following error after processing of clone1-4
(...)
sample clone1-4
barcoded 104
LTRed 92
linkered 102
ltredlinkered 90
[1] TRUE
mustOpen: Can't open NA.2bit to read: No such file or directory
[1] TRUE
Error in strsplit(alignFile, "/")[[1]] : subscript out of bounds
Calls: alignSeqs
Execution halted
processingParams.tsv are as follows
qualityThreshold badQualityBases qualitySlidingWindow mingDNA minPctIdent maxAlignStart maxFragLength refGenome
? 5 10 30 95 5 2500 hg18
Genome hg18 is installed properly and hg18.2bit is generated as well
(tried also changing to hg19. Same error)
Can you help?
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