I'm running bowtie2 on a windows 7, 64 bit machine. My reads are prokaryotic paired end reads derived from an Illumina HiSeq instrument
below are the outputs for 2 alignments:
Result1:
C:\bowtie2>perl bowtie2 --very-fast-local -t -p2 -x genomeindex -1 R:\OperonNGSdata\run_data\A-1_GGACCC_L008_R1_001.fastq -2 R:\OperonNGSdata\run_data\A-1_GGACCC_L008_R2_001.fastq -S A1_Alignment.sam
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Multiseed full-index search: 02:06:00
24462238 reads; of these:
24462238 (100.00%) were paired; of these:
1566890 (6.41%) aligned concordantly 0 times
5594011 (22.87%) aligned concordantly exactly 1 time
17301337 (70.73%) aligned concordantly >1 times
----
1566890 pairs aligned concordantly 0 times; of these:
156916 (10.01%) aligned discordantly 1 time
----
1409974 pairs aligned 0 times concordantly or discordantly; of these:
2819948 mates make up the pairs; of these:
2064379 (73.21%) aligned 0 times
45713 (1.62%) aligned exactly 1 time
709856 (25.17%) aligned >1 times
95.78% overall alignment rate
Time searching: 02:06:00
Overall time: 02:06:00
Result2 :
C:\bowtie2>perl bowtie2 --very-fast-local -t -p2 -x genomeindex -1 R:\OperonNGSdata\run_data\A-2_TTCAGC_L008_R1_001.fastq -2 R:\OperonNGSdata\run_data\A-2_TTCAG
C_L008_R2_001.fastq -S A2_Alignment.sam
Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:00
Saw ASCII character 7 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
bowtie2-align exited with value 255
As can be seen, the first run completes successfully, while the second one quits unexpectedly after throwing an error. This is confusing since the samples are replicates processed in exactly the same way on the same instrument and (presumably) identically processed according to the latest version of the Illumina pipeline (version ??).
below are the outputs for 2 alignments:
Result1:
C:\bowtie2>perl bowtie2 --very-fast-local -t -p2 -x genomeindex -1 R:\OperonNGSdata\run_data\A-1_GGACCC_L008_R1_001.fastq -2 R:\OperonNGSdata\run_data\A-1_GGACCC_L008_R2_001.fastq -S A1_Alignment.sam
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Multiseed full-index search: 02:06:00
24462238 reads; of these:
24462238 (100.00%) were paired; of these:
1566890 (6.41%) aligned concordantly 0 times
5594011 (22.87%) aligned concordantly exactly 1 time
17301337 (70.73%) aligned concordantly >1 times
----
1566890 pairs aligned concordantly 0 times; of these:
156916 (10.01%) aligned discordantly 1 time
----
1409974 pairs aligned 0 times concordantly or discordantly; of these:
2819948 mates make up the pairs; of these:
2064379 (73.21%) aligned 0 times
45713 (1.62%) aligned exactly 1 time
709856 (25.17%) aligned >1 times
95.78% overall alignment rate
Time searching: 02:06:00
Overall time: 02:06:00
Result2 :
C:\bowtie2>perl bowtie2 --very-fast-local -t -p2 -x genomeindex -1 R:\OperonNGSdata\run_data\A-2_TTCAGC_L008_R1_001.fastq -2 R:\OperonNGSdata\run_data\A-2_TTCAG
C_L008_R2_001.fastq -S A2_Alignment.sam
Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:00
Saw ASCII character 7 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
bowtie2-align exited with value 255
As can be seen, the first run completes successfully, while the second one quits unexpectedly after throwing an error. This is confusing since the samples are replicates processed in exactly the same way on the same instrument and (presumably) identically processed according to the latest version of the Illumina pipeline (version ??).
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