Provean Sus scrofa - Revision history

Dawes001 at 15:02, 15 July 2019

2019-07-15T15:02:03Z

← Older revision		Revision as of 17:02, 15 July 2019
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	#SBATCH --error=error_output_%j.txt		#SBATCH --error=error_output_%j.txt
	#SBATCH --job-name=Provean		#SBATCH --job-name=Provean
	~~#SBATCH --partition=ABGC_Research~~
	#cat outVEP_*.txt \| awk '$11~/\//' \| sed 's/:/\t/' \| sort -k6 >prot_alt.txt		#cat outVEP_*.txt \| awk '$11~/\//' \| sed 's/:/\t/' \| sort -k6 >prot_alt.txt
	TELLER=100		TELLER=100
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	#SBATCH --error=error_output_%j.txt		#SBATCH --error=error_output_%j.txt
	#SBATCH --job-name=Provean		#SBATCH --job-name=Provean
	~~#SBATCH --partition=ABGC_Research~~
	TRANS=$1		TRANS=$1
	PROT=`cat /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa \| grep $TRANS \| sed 's/ \+/\t/g' \| sed 's/^>//' \| cut -f1`		PROT=`cat /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa \| grep $TRANS \| sed 's/ \+/\t/g' \| sed 's/^>//' \| cut -f1`

Dawes001 at 13:45, 19 March 2019

2019-03-19T13:45:47Z

← Older revision		Revision as of 15:45, 19 March 2019
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	== See also ==		== See also ==
	[[Provean_1.1.3 \| Provean on ~~the B4F Cluster~~]]		[[Provean_1.1.3 \| Provean on Anunna]]

Megen002: /* Master script to control the submission of jobs and cleaning */

2013-12-29T11:23:20Z

Master script to control the submission of jobs and cleaning

← Older revision		Revision as of 13:23, 29 December 2013
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	for i in `seq 10 60`; do ssh node0$i 'rm -rf /tmp/provean*'; done;		for i in `seq 10 60`; do ssh node0$i 'rm -rf /tmp/provean*'; done;
	for i in `seq 1 9`; do ssh node00$i 'rm -rf /tmp/provean*'; done;		for i in `seq 1 9`; do ssh node00$i 'rm -rf /tmp/provean*'; done;
	TRANS=`cat prot_alt.txt ~~\| head -15000~~ \| cut -f6 \| sort \| uniq`;		TRANS=`cat prot_alt.txt \| cut -f6 \| sort \| uniq`;
	TELLER2=0;		TELLER2=0;
	for TRAN in $TRANS; do		for TRAN in $TRANS; do

Megen002: /* Master script to control the submission of jobs and cleaning */

2013-12-27T12:34:10Z

Master script to control the submission of jobs and cleaning

← Older revision		Revision as of 14:34, 27 December 2013
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	echo "$PROT $TRAN already done";		echo "$PROT $TRAN already done";
	else		else
	echo "will do sbatch testProvean_sub.sh $TRAN'";		echo "will do sbatch testProvean_sub.sh $TRAN";
	sbatch runProvean_sub.sh $TRAN;		sbatch runProvean_sub.sh $TRAN;
	let TELLER2+=1;		let TELLER2+=1;

Megen002 at 12:27, 27 December 2013

2013-12-27T12:27:56Z

← Older revision		Revision as of 14:27, 27 December 2013
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			This page describes the procedure for mapping all known variants (batch of first 150 pigs, wild boar re-sequencing) at the ABGC.

			== Pre-requisites ==
	From Variant Effect Predictor output, select only protein altering variants and sort by transcript:		From Variant Effect Predictor output, select only protein altering variants and sort by transcript:
	<source lang='bash'>		<source lang='bash'>
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	/lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa		/lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa

			== Automated procedure for mapping ==
			The Provean analysis is somewhat involved because of an apparent bug in the program that results in conflict in temporary files. This is particularly problematic when farming out thousands of individual searches (i.e. per protein sequence) on the cluster. The cluster nodes need periodic 'cleaning' of those remaining temporary directories.

			=== Master script to control the submission of jobs and cleaning ===
	The following script will add 300 runs every hour. Note that it will kill remaining Provean processes, and, importantly, will clean the <code>/tmp</code> dirs of all nodes of remaining Provean related temporary folders. This to prevent the error message that Provean has problems creating temporary folders.		The following script will add 300 runs every hour. Note that it will kill remaining Provean processes, and, importantly, will clean the <code>/tmp</code> dirs of all nodes of remaining Provean related temporary folders. This to prevent the error message that Provean has problems creating temporary folders.
	<source lang='bash'>		<source lang='bash'>
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	</source>		</source>

			=== The slave script that does the actual submission ===
	The 'runProvean_sub.sh' script referred to in the above script consists of the following code:		The 'runProvean_sub.sh' script referred to in the above script consists of the following code:
	<source lang='bash'>		<source lang='bash'>
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	</source>		</source>

			== Alternative: submission per transcript - no cleaning ==
	Individual transcripts can also be submitted using the following script:		Individual transcripts can also be submitted using the following script:
	<source lang='bash'>		<source lang='bash'>

Megen002: /* See also */

2013-12-27T12:23:18Z

Megen002 at 12:22, 27 December 2013

2013-12-27T12:22:23Z

← Older revision		Revision as of 14:22, 27 December 2013
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	</source>		</source>

			== See also ==

Megen002 at 11:02, 27 December 2013

2013-12-27T11:02:31Z

← Older revision		Revision as of 13:02, 27 December 2013
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	/lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa		/lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa

			The following script will add 300 runs every hour. Note that it will kill remaining Provean processes, and, importantly, will clean the <code>/tmp</code> dirs of all nodes of remaining Provean related temporary folders. This to prevent the error message that Provean has problems creating temporary folders.
	<source lang='bash'>		<source lang='bash'>
	!/bin/bash		!/bin/bash

Megen002 at 11:00, 27 December 2013

2013-12-27T11:00:06Z

@@ Line 74: / Line 74: @@
 mv $TRANS.var $PROT.var;
 provean.sh -q $PROT.fa -v $PROT.var --save_supporting_set $PROT.sss >$PROT.result.txt 2>$PROT.error;
 </source>

Megen002 at 10:58, 27 December 2013

2013-12-27T10:58:26Z

@@ Line 45: / Line 45: @@
          else
            echo "will do sbatch testProvean_sub.sh $TRAN'";
-           sbatch testProvean_sub.sh $TRAN;
+           sbatch runProvean_sub.sh $TRAN;
            let TELLER2+=1;
            echo "teller onder: $TELLER2";
@@ Line 54: / Line 54: @@
 done
 </source>

← Older revision		Revision as of 14:23, 27 December 2013
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	== See also ==		== See also ==
			[[Provean_1.1.3 \| Provean on the B4F Cluster]]