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March 19, 2011 21:40
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Error message when run crossbow1.1.1 on E.coli (small) example on single machine
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| Hi crossbow1.1.1 users, | |
| I got error message when I ran crossbow on e.coli (small) sample on single computer via the command line on mac desktop running OSX 10.6.6. I hope someone can give me suggestions on what I should try so that I can successfully run crossbow on e.coli example mentioned in crossbow manual at http://bowtie-bio.sourceforge.net/crossbow/manual.shtml#single-computer | |
| I had installed the most recent crossbow 1.1.1 and sratoolkit.2.0rc5-mac64 on my mac desktop with OSX 10.6.6. Following are the steps I had performed: | |
| ---------------------------------------------------------- | |
| (1) Set up environment variables in my .profile file: | |
| ---------------------------------------------------------- | |
| # Set CROSSBOW_HOME environment variable to point to crossbow directory | |
| export CROSSBOW_HOME=/Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1 | |
| # Set CROSSBOW_REFS environment variable to point to CROSSBOW_REFS directory | |
| export CROSSBOW_REFS=/Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS | |
| # Set CROSSBOW_SRATOOLKIT_HOME environment variable to point to SRA toolkit directory | |
| export CROSSBOW_SRATOOLKIT_HOME=/Users/mcmahan/mcmahan/downloadApplications/sraToolkit/sratoolkit.2.0rc5-mac64 | |
| export SRATOOLKIT_HOME=/Users/mcmahan/mcmahan/downloadApplications/sraToolkit/sratoolkit.2.0rc5-mac64 | |
| -------------------------------------------------------------------------- | |
| (2) Test my crossbow installation by running and PASS install test: | |
| -------------------------------------------------------------------------- | |
| :~ mcmahan$ $CROSSBOW_HOME/cb_local --test | |
| . | |
| . | |
| Searching for 'fastq-dump' binary... | |
| Specified via --sra-toolkit?....no | |
| $CROSSBOW_SRATOOLKIT_HOME specified?....YES (/Users/mcmahan/mcmahan/downloadApplications/sraToolkit/sratoolkit.2.0rc5-mac64) | |
| Runnable?....YES | |
| Summary: | |
| bowtie: INSTALLED at /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie | |
| soapsnp: INSTALLED at /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/soapsnp | |
| fastq-dump: INSTALLED at /Users/mcmahan/mcmahan/downloadApplications/sraToolkit/sratoolkit.2.0rc5-mac64/fastq-dump | |
| PASSED install test | |
| ---------------------------------------------------------------------------------------- | |
| (3) Download and unzip e_coli.jar from http://crossbow-refs.s3.amazonaws.com/e_coli.jar: | |
| ---------------------------------------------------------------------------------------- | |
| :~ mcmahan$ cd $CROSSBOW_REFS/e_coli && unzip e_coli.jar | |
| Archive: e_coli.jar | |
| creating: META-INF/ | |
| inflating: META-INF/MANIFEST.MF | |
| creating: sequences/ | |
| inflating: sequences/chr0.fa | |
| creating: snps/ | |
| creating: index/ | |
| inflating: index/index.3.ebwt | |
| inflating: index/index.4.ebwt | |
| inflating: index/index.1.ebwt | |
| inflating: index/index.2.ebwt | |
| inflating: index/index.rev.1.ebwt | |
| inflating: index/index.rev.2.ebwt | |
| inflating: cmap.txt | |
| :~ mcmahan$ ls -F $CROSSBOW_REFS/e_coli | |
| META-INF/ cmap.txt e_coli.jar index/ sequences/ snps/ | |
| --------------------------------------------------------------------- | |
| (4) Run crossbow on e.coli example using small.manifest file: | |
| --------------------------------------------------------------------- | |
| LOCATION WHERE I RUN CROSSBOW: | |
| :e_coli mcmahan$ pwd | |
| /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli | |
| :e_coli mcmahan$ ls | |
| full.manifest small.manifest | |
| RUN CROSSBOW WITH FOLLOWING SPECIFIED OPTIONS (I followed the web crossbow manual): | |
| :e_coli mcmahan$ $CROSSBOW_HOME/cb_local | |
| --input=small.manifest | |
| --preprocess | |
| --reference=$CROSSBOW_REFS/e_coli | |
| --output=output_small | |
| --all-haploids | |
| --cpus=1 | |
| --bowtie=/Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie | |
| --soapsnp=/Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/soapsnp | |
| NOTE: I am not sure whether the options I used to run crossbow are correct for the latest release crossbow1.1.1, because I get error message. | |
| -------------------------------------------------------------------- | |
| (5) Below is the error message I got from running crossbow: | |
| -------------------------------------------------------------------- | |
| Crossbow job | |
| ------------ | |
| Local commands in: /tmp/crossbow-nxf4WcogQf/invoke.scripts/cb.10720.sh | |
| Running... | |
| === Directory checker === | |
| Time: 22:39:29 15-Mar-2011 | |
| Input: /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/small.manifest | |
| Output: /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small | |
| Intermediate: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720 | |
| Counters: /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters | |
| Options: [ --force ] | |
| Removing directory /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small due to --force | |
| Removing directory /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters due to --force | |
| ========================== | |
| Stage 1 of 4. Preprocess | |
| ========================== | |
| Time: 22:39:30 15-Mar-2011 | |
| === Map === | |
| # parallel mappers: 1 | |
| Input: /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/small.manifest | |
| Output: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc | |
| Intermediate: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc.map.pre | |
| Retries / delay: 3 / 5 | |
| Options: [ --line-by-line --force ] | |
| Starting 1 mappers with command: | |
| perl /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc --counters /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt | |
| Pid 10742 processing input ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/litesra/SRR/SRR014/SRR014475/SRR014475.lite.sra 0 [1 of 1]... | |
| All children succeeded | |
| -- Map counters -- | |
| Short read preprocessor Read data fetched 930624152 | |
| Short read preprocessor Read data fetched (un-SRAed) 1431533624 | |
| Short read preprocessor Read data fetched (uncompressed) 1431533624 | |
| Short read preprocessor Read data pushed to local filesystem (compressed) 333795101 | |
| Short read preprocessor Read files pushed to local filesystem 1068039241 | |
| Short read preprocessor Unpaired URLs 1 | |
| Short read preprocessor Unpaired reads 8909572 | |
| Short read preprocessor Warnings 0 | |
| Short read preprocessor Read data fetched 930624152 | |
| Short read preprocessor Read data fetched (un-SRAed) 1431533624 | |
| Short read preprocessor Read data fetched (uncompressed) 1431533624 | |
| Short read preprocessor Read data pushed to local filesystem (compressed) 333795101 | |
| Short read preprocessor Read files pushed to local filesystem 1068039241 | |
| Short read preprocessor Unpaired URLs 1 | |
| Short read preprocessor Unpaired reads 8909572 | |
| Short read preprocessor Warnings 0 | |
| Removing /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc.map.pre (to keep, specify --keep-all) | |
| ========================== | |
| Stage 2 of 4. Align | |
| ========================== | |
| Time: 23:05:50 15-Mar-2011 | |
| === Map === | |
| # parallel mappers: 1 | |
| Input: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc | |
| Output: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align | |
| Intermediate: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align.map.pre | |
| Retries / delay: 3 / 5 | |
| Options: [ --force ] | |
| Starting 1 mappers with command: | |
| perl /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/Align.pl --bowtie /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie --discard-reads=0 --index-local=/Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS/e_coli/index/index --partlen=1000000 --qual=phred33 --counters /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt --truncate=0 -- --partition 1000000 --mm -t --hadoopout --startverbose -M 1 | |
| Pid 11221 processing input /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc/map-10742 [1 of 19]... | |
| Non-zero return (2304) after executing command 'cat /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc/map-10742 | perl /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/Align.pl --bowtie /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie --discard-reads=0 --index-local=/Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS/e_coli/index/index --partlen=1000000 --qual=phred33 --counters /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt --truncate=0 -- --partition 1000000 --mm -t --hadoopout --startverbose -M 1 >/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align/map-11221 2>/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align.map.pre/map.err/map-11221' | |
| Retrying in 5 seconds... | |
| Non-zero return (2304) after executing command 'cat /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc/map-10742 | perl /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/Align.pl --bowtie /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie --discard-reads=0 --index-local=/Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS/e_coli/index/index --partlen=1000000 --qual=phred33 --counters /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt --truncate=0 -- --partition 1000000 --mm -t --hadoopout --startverbose -M 1 >/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align/map-11221 2>/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align.map.pre/map.err/map-11221' | |
| Retrying in 5 seconds... | |
| Non-zero return (2304) after executing command 'cat /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc/map-10742 | perl /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/Align.pl --bowtie /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie --discard-reads=0 --index-local=/Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS/e_coli/index/index --partlen=1000000 --qual=phred33 --counters /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt --truncate=0 -- --partition 1000000 --mm -t --hadoopout --startverbose -M 1 >/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align/map-11221 2>/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align.map.pre/map.err/map-11221' | |
| Retrying in 5 seconds... | |
| Non-zero return (2304) after executing command 'cat /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc/map-10742 | perl /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/Align.pl --bowtie /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie --discard-reads=0 --index-local=/Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS/e_coli/index/index --partlen=1000000 --qual=phred33 --counters /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt --truncate=0 -- --partition 1000000 --mm -t --hadoopout --startverbose -M 1 >/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align/map-11221 2>/private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align.map.pre/map.err/map-11221' | |
| Retrying in 5 seconds... | |
| Fatal error 1.1.1:M130: Out of retries; aborting... | |
| When requesting support, please include the full output printed here. | |
| If a child process was the cause of the error, the output should | |
| include the relevant error message from the child's error log. You may | |
| be asked to provide additional files as well. | |
| ****** | |
| * Aborting master loop because child 11221 failed | |
| * (other children may also have failed) | |
| * Input file or string was: | |
| * /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/preproc/map-10742: | |
| * Error message is in file: /private/tmp/crossbow-nxf4WcogQf/crossbow/intermediate/10720/align.map.pre/map.err/map-11221, also printed below | |
| ****** | |
| * Align.pl: s3cmd: found: , given: | |
| * Align.pl: jar: found: /usr/bin/jar, given: | |
| * Align.pl: hadoop: found: , given: | |
| * Align.pl: wget: found: /usr/local/bin/wget, given: | |
| * Align.pl: s3cfg: | |
| * Align.pl: bowtie: found: , given: /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/bin/mac64/bowtie | |
| * Align.pl: partition len: 1000000 | |
| * Align.pl: ref: | |
| * Align.pl: quality: phred33 | |
| * Align.pl: truncate at: 0 | |
| * Align.pl: discard mate: 0 | |
| * Align.pl: discard reads < truncate len: 0 | |
| * Align.pl: SAM passthrough: 0 | |
| * Align.pl: Straight through: 0 | |
| * Align.pl: local index path: /Users/mcmahan/mcmahan/downloadApplications/crossbow/CROSSBOW_REFS/e_coli/index/index | |
| * Align.pl: counters: /Users/mcmahan/mcmahan/downloadApplications/crossbow/crossbow-1.1.1/example/e_coli/output_small_counters/counters.txt | |
| * Align.pl: dest dir: | |
| * Align.pl: bowtie args: --partition 1000000 --mm -t --hadoopout --startverbose -M 1 | |
| * Align.pl: ls -al | |
| * Align.pl: total 0 | |
| * drwxr-xr-x 5 mcmahan wheel 170 Mar 15 23:06 . | |
| * drwxr-xr-x 3 mcmahan wheel 102 Mar 15 23:05 .. | |
| * -rw-r--r-- 1 mcmahan wheel 0 Mar 15 23:05 .tmp.11224 | |
| * -rw-r--r-- 1 mcmahan wheel 0 Mar 15 23:05 .tmp.11244 | |
| * -rw-r--r-- 1 mcmahan wheel 0 Mar 15 23:06 .tmp.11265 | |
| * Align.pl: Retrived 1 counters from previous stages | |
| * Align.pl: Read first line of stdin: | |
| * Written 8909572 spots | |
| * Bad number of read tokens ; expected 3 or 5: | |
| * Written 8909572 spots | |
| ****** | |
| Aborting master loop because child failed | |
| Fatal error 1.1.1:M140: Aborting because child with PID 11221 exited abnormally | |
| When requesting support, please include the full output printed here. | |
| If a child process was the cause of the error, the output should | |
| include the relevant error message from the child's error log. You may | |
| be asked to provide additional files as well. | |
| Non-zero exitlevel from Align stage | |
| Thanks, | |
| Linda | |
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