Thanks for the quick reply,
but as i tried to execute the command as you suggested, it seems fastq_screen tries to obtain bowtie's index file, and not with bowtie2 as specified with the --aligner flag.
this is the command i executed:
and this is the error message i get :
any other suggestions?
it doesn't really matter to me which bowtie to use, whether it is bowtie or bowtie2.
Cheers.
Chen
but as i tried to execute the command as you suggested, it seems fastq_screen tries to obtain bowtie's index file, and not with bowtie2 as specified with the --aligner flag.
this is the command i executed:
Code:
fastq_screen --subset 1000000 --illumina1_3 --threads 22 --outdir /someOutDirPath --aligner bowtie2 --paired /pathTo/raw_data/SomeFastq_L008_R1_001.fastq /pathTo/raw_data/SomeRealtedFastq_R2_001.fastq
Code:
Reading configuration from '/PathTo/fastq_screen_v0.4.1/fastq_screen.conf' Using '/PathTo/bowtie2' as bowtie2 path Using 8 threads for searches Skipping DATABASE 'Human' since no bowtie index was found at '/PathTo/GRCh37/Sequence/Bowtie2Index' Skipping DATABASE 'Mouse' since no bowtie index was found at '/PathTo/GRCm38/Sequence/Bowtie2Index' Skipping DATABASE 'Rat' since no bowtie index was found at '/PathTo/RGSC3.4/Sequence/Bowtie2Index' Skipping DATABASE 'Ecoli' since no bowtie index was found at '/PathTo/EB1/Sequence/Bowtie2Index' Skipping DATABASE 'Yeast' since no bowtie index was found at '/PathTo/Ensembl/EF4/Sequence/Bowtie2Index' Skipping DATABASE 'PhiX' since no bowtie index was found at '/PathTo/1993-04-28/Sequence/Bowtie2Index' Skipping DATABASE 'Adapters' since no bowtie index was found at '/PathTo/Contaminants' No search libraries were configured at /PathTo/fastq_screen_v0.4.1//fastq_screen line 119.
it doesn't really matter to me which bowtie to use, whether it is bowtie or bowtie2.
Cheers.
Chen
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