Hi,
I have been trying to run the following bwa mem command:
bwa mem -M -t 16 w_ind.fa SRR412532_1.fastq.gz SRR412532_2.fastq.gz | samtools view -Sb - | samtools sort - SRR412532.sorted && samtools index SRR412532.sorted.bam
And for each iteration get the following:
[M:rocess] read 1777778 sequences (160000020 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 2, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1777778 reads in 75.678 CPU sec, 22.324 real sec
This shoud be a paired read dataset and when I check the FASTQ files I see:
gzcat SRR412532_1.fastq.gz | head
@SRR412532.1 FCC02L0ACXX:3:1101:1130:1956/1
NGAGCTTCAGGCCCAGGCCAAGGCTTACTTTGAGAAGACGCAGGAGCAGCTAACACCCCTGGTCAAGAAGGCCGGAACTGACCTGATCAA
+
#1=DDDDEHHHGGIGHI=FHGGGIG>BAFGHC>=BCGG>:?DG?CB;FECE>CC@G1=5,,;?;@ACA;>;2=;'820>@>>>C<>@@A>
@SRR412532.2 FCC02L0ACXX:3:1101:1035:1967/1
NACAAAAAGCAAAATGAATCTAGCTGTCCCTGTCCTGGCCGGTATTCCATCTTCTAGAACCTGTTTCCGTGTTTTTCCTGGAGTGTCTGC
+
#1:BDFFFF?FHHIGEHIB@AHIGICFDEGGIHGEEHIIGEG?FFEDHIGGGIIIG;CGGGEGGHGA3;.;.?B@=@AC>>55(5>5;A#
@SRR412532.3 FCC02L0ACXX:3:1101:1464:1954/1
NTGCTTTTCTGCCCTGGAAGTTGATGAGGCATATGTTCCCAAAGAGTTTAACGCTGAAACATTCACCTTCCATGCAGACTTATGCACACT
gzcat SRR412532_2.fastq.gz | head
@SRR412532.1 FCC02L0ACXX:3:1101:1130:1956/2
GTTGGGAGAGGGCTCCAGACCTGGCCAGTGGGGGTTCTAGGGGCCAGCAGGGGAGGGAAGACAATGGTCTGGACGCCTCACTGGGTGGCA
+
@B@?DDDDAHFHHIFHIJIGIGCHHIGI3?FGII7;FE@GHIBHAEB?@E;>>8?@2'588ACCCDC(44?9@AB><B9(8@A#######
@SRR412532.2 FCC02L0ACXX:3:1101:1035:1967/2
GGGTTTAGGGACCTCCCTGGGTGGAACAATCTACACGGTTGAAGCACTAGCAGGGAGGTTCTAGTGGGATCACACGTTTATTAACATGCT
+
?@@=BDFFGHDFFGGHIGIHCFEHHGGHGHGGGGGHIDBFHIJCFHCAGIFGHGIHEB?;BBC>;AC6A>?=CDCB?A<BDDCDDCA@CC
@SRR412532.3 FCC02L0ACXX:3:1101:1464:1954/2
GGCTTGTGTTTCACCAGCTCAGCAAGTGCAGATTGTTTCTTGACTTGTTTCTCAGCCTCAGGAAGTGTGCATAAGACTGCATGGAAGGTG
I am not sure why there are not enough FR pairs as the reads seem to be in the same order with matching headings... Am probably missing something obvious!!! Any ideas??
All help much appreciated!!
Thanks in advance
I have been trying to run the following bwa mem command:
bwa mem -M -t 16 w_ind.fa SRR412532_1.fastq.gz SRR412532_2.fastq.gz | samtools view -Sb - | samtools sort - SRR412532.sorted && samtools index SRR412532.sorted.bam
And for each iteration get the following:
[M:rocess] read 1777778 sequences (160000020 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 2, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1777778 reads in 75.678 CPU sec, 22.324 real sec
This shoud be a paired read dataset and when I check the FASTQ files I see:
gzcat SRR412532_1.fastq.gz | head
@SRR412532.1 FCC02L0ACXX:3:1101:1130:1956/1
NGAGCTTCAGGCCCAGGCCAAGGCTTACTTTGAGAAGACGCAGGAGCAGCTAACACCCCTGGTCAAGAAGGCCGGAACTGACCTGATCAA
+
#1=DDDDEHHHGGIGHI=FHGGGIG>BAFGHC>=BCGG>:?DG?CB;FECE>CC@G1=5,,;?;@ACA;>;2=;'820>@>>>C<>@@A>
@SRR412532.2 FCC02L0ACXX:3:1101:1035:1967/1
NACAAAAAGCAAAATGAATCTAGCTGTCCCTGTCCTGGCCGGTATTCCATCTTCTAGAACCTGTTTCCGTGTTTTTCCTGGAGTGTCTGC
+
#1:BDFFFF?FHHIGEHIB@AHIGICFDEGGIHGEEHIIGEG?FFEDHIGGGIIIG;CGGGEGGHGA3;.;.?B@=@AC>>55(5>5;A#
@SRR412532.3 FCC02L0ACXX:3:1101:1464:1954/1
NTGCTTTTCTGCCCTGGAAGTTGATGAGGCATATGTTCCCAAAGAGTTTAACGCTGAAACATTCACCTTCCATGCAGACTTATGCACACT
gzcat SRR412532_2.fastq.gz | head
@SRR412532.1 FCC02L0ACXX:3:1101:1130:1956/2
GTTGGGAGAGGGCTCCAGACCTGGCCAGTGGGGGTTCTAGGGGCCAGCAGGGGAGGGAAGACAATGGTCTGGACGCCTCACTGGGTGGCA
+
@B@?DDDDAHFHHIFHIJIGIGCHHIGI3?FGII7;FE@GHIBHAEB?@E;>>8?@2'588ACCCDC(44?9@AB><B9(8@A#######
@SRR412532.2 FCC02L0ACXX:3:1101:1035:1967/2
GGGTTTAGGGACCTCCCTGGGTGGAACAATCTACACGGTTGAAGCACTAGCAGGGAGGTTCTAGTGGGATCACACGTTTATTAACATGCT
+
?@@=BDFFGHDFFGGHIGIHCFEHHGGHGHGGGGGHIDBFHIJCFHCAGIFGHGIHEB?;BBC>;AC6A>?=CDCB?A<BDDCDDCA@CC
@SRR412532.3 FCC02L0ACXX:3:1101:1464:1954/2
GGCTTGTGTTTCACCAGCTCAGCAAGTGCAGATTGTTTCTTGACTTGTTTCTCAGCCTCAGGAAGTGTGCATAAGACTGCATGGAAGGTG
I am not sure why there are not enough FR pairs as the reads seem to be in the same order with matching headings... Am probably missing something obvious!!! Any ideas??
All help much appreciated!!
Thanks in advance
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