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I am having hassle building in index file from a fasta record… IAs you could see under calculus tutor, I am getting a warning: "Encountered empty reference series" and an mistakes:
I'm using this software in my device and blog and it's working perfectly fine.
Were you able to fix this error? Command: bowtie2-build --wrapper basic-0 $/home/Kaleb.gatto/Bowtie2/bowtie2-2.2.8/example/reference/lambda_virus.fa lambda_virus
Let me share the error file, that way you could explain me better. Are you referring genome.txt file to be a reference genome file? I removed all sequences containing Ns from the fasta file. # reads processed: 11120169 # reads with at least one reported alignment: 40701 (0.37%) # reads that failed to align: 11079468 (99.63%) Reported 40701 alignments # reads processed: 11120169 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 11120169 (100.00%) No alignments #...
Let me share me error file, that way you could explain me better. Are you referring genome.txt file to be a reference genome file? I removed all sequences conjtaing Ns from the fasta file. # reads processed: 11120169 # reads with at least one reported alignment: 40701 (0.37%) # reads that failed to align: 11079468 (99.63%) Reported 40701 alignments # reads processed: 11120169 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 11120169 (100.00%) No alignments # reads...
bowtie-build seems to think that your genome.txt file contains long stretches of, or all, Ns and therefore unable to build an index.
Hi, did you figured out the above error message? if yes, Could you help me out. Thank you
I ran bowtie 2 against a reference genome and it worked perfectly. After saving the data to external, I deleted the paired-end reads from my hpc directory. Later, we decided to align reads against the mito-genome, so I uploaded the same exact files to my directory, and running the exact same command on the exact same files (but with different reference), I got the error " Error, fewer reads in file specified with -2 than in file specified with -1" I know the files have the same number of reads because...
Please close this ticket The command issued should have been: bowtie2 \ -t \ -p 20 \ -x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \ -q \ -U /data/fastq_file.fq \ --very-sensitive \ --un /data/requested_unaligned_fastq_file.fq -S /data/requested_sam_file.sam; This is "--un" and not "-un" Small typo caused a lot of self-induced pain Apologies for the disturbance...and cheers...
(ERR): bowtie2-align died with signal 7 (BUS) (core dumped)
Apologies, the second command should read: bowtie2 \ -t \ -p 20 \ -x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \ -q \ -U /data/fastq_file.fq \ --very-sensitive \ -S /data/requested_sam_file.sam;
Unaligned File Request Triggers Bowtie2 to Fail