User: freuv

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freuv0
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Posts by freuv

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Comment: C: PICARD ValidateSamFile terminating prematurely, without errors, processes only p
... I am unable to install the latest version, as the cluster I work on has java v-1.7.0_151. Please advise. Thanks! F ...
written 3 days ago by freuv0
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Comment: C: PICARD ValidateSamFile terminating prematurely, without errors, processes only p
... Picard 1.67 Command Line: java -Xmx12G -Xms12G -jar ValidateSamFile.jar I=input.bam MODE=VERBOSE O=results.txt MAX_OUTPUT=10000000 TMP_DIR=/local2/tmp ...
written 3 days ago by freuv0
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Comment: C: Using SSPACE: how to calculate 'expected/observed insert size between paired rea
... If you don't mind, can you please explain what these two values mean? - expected/observed insert size between paired reads - minimum allowed error My raw reads are 150bp -- what value of 'k' would I use? Thanks for your help! ...
written 3 days ago by freuv0
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Using SSPACE: how to calculate 'expected/observed insert size between paired reads and the minimum allowed error?'
... Hi, I am using SSPACE for scaffolding of AbySS contigs -- the tool requires a text library file with some info re: the reads. It is unclear what and how the following required numbers for this text library file are calculated. - expected/observed insert size between paired reads - minimum allow ...
genome assembly alignment sequencing written 4 days ago by freuv0
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PICARD ValidateSamFile terminating prematurely, without errors, processes only portion of total reads
... Hi, I am processing ~200 million WGS aligned reads with Picard's ValidateSamFile, with the following options: **MODE=VERBOSE MAX_OUTPUT=10000000** TMP_DIR=[/local2/tmp] IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VAL ...
genome assembly sequencing written 6 days ago by freuv0
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Answer: A: Can't find ABYSS-P after compiling
... Hi everyone, Thank you for your help. I re-compiled AbySS using the same version of MPI I was trying to run AbySS with, and it pulled up the correct libmpi. Resolved! ...
written 6 days ago by freuv0
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Answer: A: ERROR 127: ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot o
... Hi everyone, Thank you for your help. I re-compiled AbySS using the same version of MPI I was trying to run AbySS with, and it pulled up the correct libmpi. Resolved! ...
written 6 days ago by freuv0
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Comment: C: Can't find ABYSS-P after compiling
... Hi @Medhat, Thank you for your message. I re-compiled --with-openmpi and ABYSS-P was subsequently created. However, I am running into an issue with ABYSS-P when multithreading as follows: 'ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or ...
written 17 days ago by freuv0
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ERROR 127: ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory
... Hi, I am running ABYSS but seem to be running into issues when multithreading -- please see error message below: ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory ABYSS-P: error while loading shared libraries: libmpi.so.40: canno ...
assembly abyss written 17 days ago by freuv0
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Can't find ABYSS-P after compiling
... Hi, I am unable to find ABYSS-P after compiling both ABYSS and OpenMPI. Please advise. Thank you! ...
assembly abyss written 17 days ago by freuv0

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