crossbow

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hadoop map failure

1

I'm using Crossbow with Hadoop 2.4 on a cluster of 3, and get this error: ## Crossbow job Hadoop streaming commands in: /tmp/crossbow-9ZzYhbmcKc/invoke.scripts/cb.7742.hadoop.sh # Running... # Stage 1 of 4....

soaphee

Hello, I'm getting the following error when run **soapsnp**: ``` ... Processing TRINITY_DN154966_c175_g1_i1 Processing TRINITY_DN268204_c0_g1_i1 Processing TRINITY_DN171129_c3_g1_i1 Processing TRINITY_DN167603_c3052_g26_i1 Processing TRINITY_DN172399_c1264_g1_i2 Processing TRINITY_DN154966_c440_g2_i1 Processing TRINITY_DN143030_c98_g1_i1 Processing TRINITY_DN170398_c2_g3_i1 Processing TRINITY_DN166585_c2299_g1_i2 Errors...

patrick-douglas

EMR seems to fail always at the last step

4

I am getting results similar to http://www.biostars.org/p/83060/

vlad-belogrudov

referenced sra are not found on FTP server

2

Sample invocation of the tool with e.coli does not work because sra files mentioned in manifest don't exist any longer

vlad-belogrudov

make cannot proceed due to problems with downloaded archives - wget gets them in form archive.tar.gz.download but the script tries to unpack archive.tar.gz The makefile also needs some cleanup to...

vlad-belogrudov

One of the ways to use cb_\* scripts can be putting symbolic links to them in /usr/local/bin or similar paths (instead of polluting ever growing PATH). Unfortunately the Perl scripts...

vlad-belogrudov