User: mutantjoo0

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mutantjoo00
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Posts by mutantjoo0

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Comment: C: bbmap.sh: line 352 /random number/ Killed
... (continued reply) # fastqc results: Measure Value Filename Std_bbmapped.bam File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 66328781 Sequences flagged as poor quality 0 Sequence length 24-150 %GC 47 Measure Value Filename Std2_bbmapped.bam File type Conve ...
written 6 months ago by mutantjoo00
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Comment: C: bbmap.sh: line 352 /random number/ Killed
... Yes, I tried and it did not work. Followings are two trials I did with difference in the order of BBMap flag and their output. As you can see, quality of outputs are not bad although those two have difference in number of **Total Sequences**. # trial 1: $ /mnt/home/leejooy5/Downloads/bbmap/b ...
written 6 months ago by mutantjoo00
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Comment: C: bbmap.sh: line 352 /random number/ Killed
... Sorry for the inconvenience. I made mistakes misleading you. There are no file contains * in its name. I used symbol ** NAME ** to highlight NAME in bold. ...
written 6 months ago by mutantjoo00
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Comment: C: bbmap.sh: line 352 /random number/ Killed
... Here is my resource in hpc: (base) -bash-4.2$ free -mh total used free shared buff/cache available Mem: 377G 35G 289G 4.5G 52G 335G Swap: 0B 0B 0B I tried with higher mem ...
written 6 months ago by mutantjoo00
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Comment: C: bbmap.sh: line 352 /random number/ Killed
... Hi Genomax, Thank you for your comment. Followings are commands I originally used to index and map. # to index: /mnt/home/leejooy5/Downloads/bbmap/bbmap.sh -Xmx20g ref=../megahit_assembly/SAMPLE/SAMPLE.final.contigs.fa nodisk # to map: /mnt/home/leejooy5/Downloads/bbmap/ ...
written 6 months ago by mutantjoo00
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bbmap.sh: line 352 /random number/ Killed
... Hello Jedai Masters of Biostars, I keep facing crash while mapping contig files with BBMap (v.38.76). I am running command "**bbmap.sh in=sample_r1.fastq in2=sample_r2.fastq out=./sample_bbmapped.sam bamscript=bs.sh**" and process stops on "**Started 40 mapping threads**" as highlighted in quote be ...
bbmap metagenome bbmap.sh: line 352 killed written 7 months ago by mutantjoo00 • updated 7 months ago by genomax89k

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