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CNVer error mmolstad Bioinformatics 0 01-10-2011 02:09 PM

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Old 01-13-2012, 12:11 PM   #1
dmacmillan
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Location: British Columbia

Join Date: Jan 2012
Posts: 49
Default CNVer Help

I had a question regarding CNVer if anyone has some experience. I ran the cnver.pl with correct parameters, however, I get a ton of output on the screen and some of it doesn't looks good.

Here is an example:

Code:
Exec at 12:44:30, Fri Jan 13, 2012 awk '{ if ($6 == 3) print $0 }'  /home/dmacmillan/copy_num_ana/CNVer/workdir/mapping_files/chr22.mmap  | sort -k4n,4 -k3n
,3 -k1n,1  | /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/cluster/cluster_matepairs --mean=398 --stdev=58 --colID=-1 --colDist=0 --colChr=1 --colLeft
=2 --colRight=3 --colTemplate=4 --baseLenFactor=1 --mdJoinTolerance=6 --type=3 --concise=1 > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.t3...
No matepairs to cluster.

Exec at 12:44:30, Fri Jan 13, 2012 grep -h EDGE /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.t[0123] | /home/dmacmillan/copy_num_ana/CNVer/cnver
-0.8.1/src/cluster/screen_contig_breaks --mean=398 --stdev=58 --tolerance=572 --breaksFile = /home/dmacmillan/copy_num_ana/CNVer/hg18comp/contig_breaks_fold
er/chr22.cbs | awk '{ if (($5 >= 2) && ($8 < 10000000)) print $0 }' > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.links...

Exec at 12:44:30, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/axt_to_binary /home/dmacmillan/copy_num_ana/CNVer/hg18comp/self_align
ments_folder/chr22.axt 49691432 /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.edges...
Axtbin
Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/make_reference_graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr2
2//chr22.edges /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.graph...
Converged after 1 iterations
num_edges: 0
num_nodes: 0

Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/fill_reference_graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr2
2//chr22.graph 49691432...

Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/make_donor_graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//c
hr22.graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.links /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.scov /home/dmacmillan/cop
y_num_ana/CNVer/workdir/chr22//chr22.masks /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.gc 1> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22/
/chr22.problem 2> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.graphinfo...

Exec at 12:44:31, Fri Jan 13, 2012 perl /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/flow_solve/make_cs2_graph.pl on coverage: 10 chr22.problem 2 0 2
0 1 0 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/cs2-4.6/...
Starting cs2 graph builder...
0 read_arrival= nodecnt=1 totalarccnt=0
Arc Count 0
Starting cs2...

line 1 of input - bad value of a parameter in the problem line
Done with cs2.
Done with cs2 graph builder...
Running perl /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/flow_solve//affiner.pl 2  1 10 0 20 < outfile.txt > nf
Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/report_cnvs /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.graphinfo /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.problem.out 100 0 2> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.raw 1> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.used_dgs...

Exec at 12:44:31, Fri Jan 13, 2012 cat /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.raw | /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/intRemove2  /home/dmacmillan/copy_num_ana/CNVer/hg18comp/contig_breaks_folder/chr22.cbs > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.raw.screened...
Read in 12 forbidden intervals.

Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/smoother.sh 5 1000 chr22.cnvs.raw.screened > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.smoothed...

Exec at 12:44:31, Fri Jan 13, 2012 cat /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.smoothed | awk -v OFS="\t" '{ if ($4 > 0) print $1, $2, $3, "gain"; else print $1, $2, $3, "loss" }' | /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/post_analysis/doc_walker /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.scov /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.gc | awk -v OFS="\t" '{ print $1, $2, $3, $4, $6 }' > /home/dmacmillan/copy_num_ana/CNVer/workdir/calls//chr22.cnvs...
Here are the steps that I took to achieve this:
Code:
Steps:
1. Untar the CNVer tar.gz source file
2. cd into the directory
3. type "./configure" (no quotations) and hit enter
4. type "make" hit enter
5. cd .. into folder containing cnver-0.8.1, hg18comp
6. Created file "bam_files_to_use.txt" by doing
	i. echo -e "file1.bam\nfile2.bam" > bam_files_to_use.txt
7. type "export CNVER_FOLDER=/home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1" or wherever your cnver-0.8.1 folder is.
8. ran the following command:
./cnver.pl --map_list /home/dmacmillan/copy_num_ana/CNVer/bams_to_use.txt --ref_folder /home/dmacmillan/copy_num_ana/CNVer/hg18comp --work_dir /home/dmacmillan/copy_num_ana/CNVer/workdir  --read_len 150 --mean_insert 398 --stdev_insert 58 --min_mps 2
I do not receive a workdir/results folder in the end, and most, if not all the files in the chr[1-22]/x/y folders are 0 bytes. Any suggestions would be appreciated
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Old 01-29-2012, 05:28 AM   #2
CNVboy
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Location: boston

Join Date: Jun 2011
Posts: 27
Default

Have you solved your problem?
thx

Quote:
Originally Posted by dmacmillan View Post
I had a question regarding CNVer if anyone has some experience. I ran the cnver.pl with correct parameters, however, I get a ton of output on the screen and some of it doesn't looks good.

Here is an example:

Code:
Exec at 12:44:30, Fri Jan 13, 2012 awk '{ if ($6 == 3) print $0 }'  /home/dmacmillan/copy_num_ana/CNVer/workdir/mapping_files/chr22.mmap  | sort -k4n,4 -k3n
,3 -k1n,1  | /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/cluster/cluster_matepairs --mean=398 --stdev=58 --colID=-1 --colDist=0 --colChr=1 --colLeft
=2 --colRight=3 --colTemplate=4 --baseLenFactor=1 --mdJoinTolerance=6 --type=3 --concise=1 > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.t3...
No matepairs to cluster.

Exec at 12:44:30, Fri Jan 13, 2012 grep -h EDGE /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.t[0123] | /home/dmacmillan/copy_num_ana/CNVer/cnver
-0.8.1/src/cluster/screen_contig_breaks --mean=398 --stdev=58 --tolerance=572 --breaksFile = /home/dmacmillan/copy_num_ana/CNVer/hg18comp/contig_breaks_fold
er/chr22.cbs | awk '{ if (($5 >= 2) && ($8 < 10000000)) print $0 }' > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.links...

Exec at 12:44:30, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/axt_to_binary /home/dmacmillan/copy_num_ana/CNVer/hg18comp/self_align
ments_folder/chr22.axt 49691432 /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.edges...
Axtbin
Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/make_reference_graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr2
2//chr22.edges /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.graph...
Converged after 1 iterations
num_edges: 0
num_nodes: 0

Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/fill_reference_graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr2
2//chr22.graph 49691432...

Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/make_donor_graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//c
hr22.graph /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.links /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.scov /home/dmacmillan/cop
y_num_ana/CNVer/workdir/chr22//chr22.masks /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.gc 1> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22/
/chr22.problem 2> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.graphinfo...

Exec at 12:44:31, Fri Jan 13, 2012 perl /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/flow_solve/make_cs2_graph.pl on coverage: 10 chr22.problem 2 0 2
0 1 0 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/cs2-4.6/...
Starting cs2 graph builder...
0 read_arrival= nodecnt=1 totalarccnt=0
Arc Count 0
Starting cs2...

line 1 of input - bad value of a parameter in the problem line
Done with cs2.
Done with cs2 graph builder...
Running perl /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/flow_solve//affiner.pl 2  1 10 0 20 < outfile.txt > nf
Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/report_cnvs /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.graphinfo /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.problem.out 100 0 2> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.raw 1> /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.used_dgs...

Exec at 12:44:31, Fri Jan 13, 2012 cat /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.raw | /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/intRemove2  /home/dmacmillan/copy_num_ana/CNVer/hg18comp/contig_breaks_folder/chr22.cbs > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.raw.screened...
Read in 12 forbidden intervals.

Exec at 12:44:31, Fri Jan 13, 2012 /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/smoother.sh 5 1000 chr22.cnvs.raw.screened > /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.smoothed...

Exec at 12:44:31, Fri Jan 13, 2012 cat /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.cnvs.smoothed | awk -v OFS="\t" '{ if ($4 > 0) print $1, $2, $3, "gain"; else print $1, $2, $3, "loss" }' | /home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1/src/post_analysis/doc_walker /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.scov /home/dmacmillan/copy_num_ana/CNVer/workdir/chr22//chr22.gc | awk -v OFS="\t" '{ print $1, $2, $3, $4, $6 }' > /home/dmacmillan/copy_num_ana/CNVer/workdir/calls//chr22.cnvs...
Here are the steps that I took to achieve this:
Code:
Steps:
1. Untar the CNVer tar.gz source file
2. cd into the directory
3. type "./configure" (no quotations) and hit enter
4. type "make" hit enter
5. cd .. into folder containing cnver-0.8.1, hg18comp
6. Created file "bam_files_to_use.txt" by doing
	i. echo -e "file1.bam\nfile2.bam" > bam_files_to_use.txt
7. type "export CNVER_FOLDER=/home/dmacmillan/copy_num_ana/CNVer/cnver-0.8.1" or wherever your cnver-0.8.1 folder is.
8. ran the following command:
./cnver.pl --map_list /home/dmacmillan/copy_num_ana/CNVer/bams_to_use.txt --ref_folder /home/dmacmillan/copy_num_ana/CNVer/hg18comp --work_dir /home/dmacmillan/copy_num_ana/CNVer/workdir  --read_len 150 --mean_insert 398 --stdev_insert 58 --min_mps 2
I do not receive a workdir/results folder in the end, and most, if not all the files in the chr[1-22]/x/y folders are 0 bytes. Any suggestions would be appreciated
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Old 01-30-2012, 08:59 AM   #3
dmacmillan
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Unfortunately not
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Old 03-28-2012, 04:44 PM   #4
pashadag
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You probably need to use an absolute filename inside of bam_files_to_use.txt
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Old 07-25-2014, 03:48 PM   #5
arcolombo698
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Posts: 142
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can CNVer be used on RNAseq (NGS short mated reads) ?
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Old 07-28-2014, 06:19 AM   #6
pashadag
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CNVer was not designed to work with RNA seq data
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Old 07-28-2014, 08:46 AM   #7
arcolombo698
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Yes thank you... it is true that CNV analysis must have WGS or WES. thank you very much.
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