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StevenWingett / FastQ-Screen

Detecting contamination in NGS data and multi-species analysis
https://stevenwingett.github.io/FastQ-Screen/
GNU General Public License v3.0
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Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 #72

Open Ayush09-cmd opened 6 days ago

Ayush09-cmd commented 6 days ago

hello, i am screening the minion generated sequences of bacterial genome and getting these results. even after geeting killed the sequences are showing hits on these genomes. is it running properly? ![Uploading Screenshot from 2024-09-12 10-09-26.png…]() /fastq_screen combined.fastq --conf /media/ham/General/AYUSH/whole_genome_analysis/fastqscreen/FastQ-Screen-0.15.3/FastQ_Screen_Genomes/fastq_screen.conf --aligner bowtie2 --subset 50000 Using fastq_screen v0.15.3 Reading configuration from '/media/ham/General/AYUSH/whole_genome_analysis/fastqscreen/FastQ-Screen-0.15.3/FastQ_Screen_Genomes/fastq_screen.conf' Using '/home/ham/miniconda3/envs/fastq-screen/bin/bowtie2' as Bowtie 2 path Skipping DATABASE 'Bacillushaynessi' since no Bowtie 2 index was found at '/media/ham/General/AYUSH/whole_genome_analysis/fastqscreen/FastQ-Screen-0.15.3/FastQ_Screen_Genomes/bacillus_haynessi' Adding database Human Adding database Mouse Adding database Rat Adding database Drosophila Adding database Worm Adding database Yeast Adding database Arabidopsis Adding database Ecoli Adding database rRNA Adding database MT Adding database PhiX Adding database Lambda Adding database Vectors Adding database Adapters Using 4 threads for searches Option --subset set to 50000 reads Processing combined.fastq Counting sequences in combined.fastq Making reduced sequence file with ratio 2:1 Searching combined.fastq_temp_subset.fastq against Human Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against Mouse Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against Rat

Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against Drosophila Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against Worm Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against Yeast Searching combined.fastq_temp_subset.fastq against Arabidopsis Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against Ecoli Aligner warning: Killed Aligner warning: (ERR): bowtie2-align exited with value 137 Searching combined.fastq_temp_subset.fastq against rRNA Searching combined.fastq_temp_subset.fastq against MT Searching combined.fastq_temp_subset.fastq against PhiX Searching combined.fastq_temp_subset.fastq against Lambda Searching combined.fastq_temp_subset.fastq against Vectors Searching combined.fastq_temp_subset.fastq against Adapters Perl module GD::Graph::bars not installed, skipping charts Processing complete

StevenWingett commented 5 days ago

Hi,

Thanks for your message. I believe Bowtie2 error code 137 means you don't have enough RAM. Could you allocate more RAM (e.g. 50GB)?

Also, how long are your read? Bowtie2 is a short read aligner - although I am looking into adding long-read capability next week.

Many thanks,

Steven

Ayush09-cmd commented 5 days ago

Actually I had fastq sequences from minion which are long reads would it be an issue