help need for running Myrna

[yanzhangusa]

I installed Myrna in our server and passed installation test. But when I try to run the example according to manual explained, I got the following error message for running yeast:
yzhang@shadowfax:~/myrna-1.1.1/example/yeast> $MYRNA_HOME/myrna_local --input=$MYRNA_HOME/example/yeast/small.manifest --preprocess --reference=$MYRNA_REFS/yeast_ensembl_61 --output=output_small --quality solex
a64 --cpus=5

Myrna job
------------
Local commands in: /tmp/myrna-IbVVLek3Z2/invoke.scripts/myrna.4200.sh
Running...
=== Directory checker ===
Time: 16:13:23 31-Mar-2011
Input: /home/yzhang/myrna-1.1.1/example/yeast/small.manifest
Output: /home/yzhang/myrna-1.1.1/example/yeast/output_small
Intermediate: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200
Counters: /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters
Options: [ --force ]
==========================
Stage 1 of 7. Preprocess
==========================
Time: 16:13:23 31-Mar-2011
=== Map ===
# parallel mappers: 5
Input: /home/yzhang/myrna-1.1.1/example/yeast/small.manifest
Output: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc
Intermediate: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre
Retries / delay: 3 / 5
Options: [ --line-by-line --force ]
Starting 5 mappers with command:
perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt
Pid 4286 processing input ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra 0 wild-1 [1 of 2]...
Pid 4287 processing input ftp://ftp-trace.ncbi.nih.gov/sra/sra...14339.lite.sra 0 rrp6_lsm1_pat1-1 [2 of 2]...
Non-zero return (512) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
Retrying in 5 seconds...
Non-zero return (512) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
Retrying in 5 seconds...
Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
Retrying in 5 seconds...
Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
Retrying in 5 seconds...
Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
Retrying in 5 seconds...
Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
Retrying in 5 seconds...
Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
Retrying in 5 seconds...
Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
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.
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 4286 failed
* (other children may also have failed)
* Input file or string was:
* ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra 0 wild-1
:
* Error message is in file: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286, also printed below
******
* Copy.pl: Retrived 0 counters from previous stages
* Copy.pl: Line: ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra 0 wild-1
* Copy.pl: Not a comment line
* Copy.pl: Doing unpaired entry SRR014335.lite.sra
* Copy.pl: Fetching ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra SRR014335.lite.sra 0
* reporter:counter:Short read preprocessor,Read data fetched,510809892
* sh: - : invalid option
* Usage: sh [GNU long option] [option] ...
* sh [GNU long option] [option] script-file ...
* GNU long options:
* --debug
* --debugger
* --dump-po-strings
* --dump-strings
* --help
* --init-file
* --login
* --noediting
* --noprofile
* --norc
* --posix
* --protected
* --rcfile
* --restricted
* --verbose
* --version
* --wordexp
* Shell options:
* -irsD or -c command or -O shopt_option (invocation only)
* -abefhkmnptuvxBCHP or -o option
* fastq-dump could not be found in SRATOOLKIT_HOME or PATH; please specify --sraconv
******
Fatal error 1.1.1:M140: Aborting because child with PID 4286 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 Preprocess stage
yzhang@shadowfax:~/myrna-1.1.1/example/yeast>

[George Wang]

I am having same issue. Did you resolve the issue, and can you shed some lights? Thanks.

[yanzhangusa]

use sratoolkit transfer sra format file to fastq format then run myrna. myran has problem running sratoolkit in its pipeline. I don't have any problem after that. you could download sratoolkit from NCBI. Good luck.

[George Wang]

Great, Thank you very much!

[cutcopy11]

~/Desktop/MYRNA_HOME/example/yeast$ ../../myrna_local --input=small.manifest --preprocess --reference=../../MYRNA_REFS/yeast_ensembl_61 --output=output_small --quality solexa64 --cpus=4

I got the same error.

If I physically download the files and convert them to fastq. How do I change the input option? --input=? Also, I no longer need the --preprocess option, right?

[yanzhangusa]

still the same input just change filename list in small.manifest. don't need preprocess

[9000revs]

Did you install the SRA toolkit and set the env var MYRNA_SRATOOLKIT_HOME?