bjtrost / tcag-wgs-cnv-workflow Goto Github PK

hello @bjtrost please i am new to some of these softwares, i tried calling CNV with some set of data i have following the ERDS pipeline but it keeps on with these errors, please could you let me know what the problem is?
these are my inputs :
perl erds_pipeline.pl -b /mnt/e/SNV_GATK_NVG/pass_snv/Quartet_DNA_ILM_NVG_LCL5_1_20170329_sorted_RG_RmDup.bam -v /mnt/e/SNV_GATK_NVG/Quartet_DNA_ILM_NVG_LCL5_1_20170329_XJT_BWA_HC_SNV_RAW.vcf -o /mnt/e/SNV_GATK_NVG/benue/ -r /mnt/e/ERDS/erds_tcag/src/GRCh38_full_analysis_set_plus_decoy_hla.fa

and i get errors like this:

Error code for chrHLA-DRB1*16:02:01 is 0
[Tue Dec 11 17:49:18 2018] PID 9215 is performing computation for chrchrUn_JTFH01001990v1_decoy
Error code for chrchrUn_JTFH01001993v1_decoy is 0
Error: File /mnt/e/SNV_GATK_NVG/benue//cnv/gcbin/0.gcbin not found
Use of uninitialized value $in in substitution (s///) at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 62.
Use of uninitialized value $in in split at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 63.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Error: File /mnt/e/SNV_GATK_NVG/benue//cnv/gcbin/1.gcbin not found
Use of uninitialized value $in in substitution (s///) at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 62.
Use of uninitialized value $in in split at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 63.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr1.rd
Can't open /mnt/e/SNV_GATK_NVG/benue//cnv/chr1.vit at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 95.
17:51:48 Dec 11 2018 ERDS finished step 2 in RPG...
17:51:48 Dec 11 2018 ERDS stared step 3 in RPG...
[Tue Dec 11 17:51:48 2018] PID 17085 is performing computation for chrchrY
[Tue Dec 11 17:51:48 2018] PID 17086 is performing computation for chrchrX
[Tue Dec 11 17:51:48 2018] PID 17088 is performing computation for chrchr22
[Tue Dec 11 17:51:48 2018] PID 17090 is performing computation for chrchr21
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chrX.rd
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr22.rd
[Tue Dec 11 17:51:48 2018] PID 17086 is performing computation for chrchr19
[Tue Dec 11 17:51:48 2018] PID 17085 is performing computation for chrchr20
[Tue Dec 11 17:51:48 2018] PID 17088 is performing computation for chrchr18
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr21.rd
[Tue Dec 11 17:51:48 2018] PID 17090 is performing computation for chrchr17
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr19.rd
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr20.rd
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr17.rd

i couldn't paste all the errors, so i picked where they all differs. please can you help how i could fix this? thank you

Hi,

I have learned from the article "A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data" that combining ERDs and cnvnator to call CNVs.
However, I couldn't find avaiable ERDs sources. Could you please tell me where can I get ERDs?

Thank you very much.

Best wishes,
SongtaoGui

Dear Dr. Trost,
I found your manuscript about "A comprehensive Workflow for RD based CNV identification from WGS data" very interesting. Since I found this GitHub page with all scripts for reproducing results, I would like to know if raw reads (or BAM files) for some of the samples sequenced in the context of this work are publicly available.
Thank you in advance.

Hi,

I followed the script process_cnvs.erds+.sh, and I get the following error. Could you please help me out with it?

/scratch/SOFTWARE/TCAG-WGS-CNV-workflow/format_cnvnator_results.py /scratch/SOFTWARE/TCAG-WGS-CNV-workflow/format_erds_results.py /scratch/SOFTWARE/TCAG-WGS-CNV-workflow/merge_cnvnator_results.py /scratch/SOFTWARE/TCAG-WGS-CNV-workflow/merge_erds_results.py /scratch/SOFTWARE/TCAG-WGS-CNV-workflow/add_features.py /scratch/SOFTWARE/TCAG-WGS-CNV-workflow/hg19_gap.bed
Set-up..
Found erds/original, creating erds/formatted
Found cnvn/original, creating cnvn/formatted_filtered
Formatting, filtering and merging cnvn output
Warning: Header not found, using default..
Traceback (most recent call last):
File "/scratch/SOFTWARE/TCAG-WGS-CNV-workflow/format_cnvnator_results.py", line 69, in
type = format[words[header_index["CNV_type"]]]
KeyError: '1'
Traceback (most recent call last):
File "/scratch/SOFTWARE/TCAG-WGS-CNV-workflow/merge_cnvnator_results.py", line 181, in
gaps[chrm]=[[int(words[1]),int(words[2]),words[3]]]
IndexError: list index out of range
Formatting and merging erds output
Traceback (most recent call last):
File "/scratch/SOFTWARE/TCAG-WGS-CNV-workflow/merge_erds_results.py", line 180, in
gaps[chrm]=[[int(words[1]),int(words[2]),words[3]]]
IndexError: list index out of range
genearting sample ids..
merging erds and cnvn calls
Merged erds output not found ...
check log files._**

Thanks!

Dear bjtrost,
I tried out the CNV discovery pipeline on NA12878 data.
Since I noted that erds+/NA12878.erds+.txt file contains the same variants reported in erds/merged/ NA12878.erds.vcf.cluster.txt, I had a look at the code, and I noticed that in process_cnvs_erds+.sh there is command:
$python_path "$erds_plus" -i $erds_dir/merged/$f".erds.vcf.cluster.txt" -a $cnvn_dir/merged/$f".calls.txt.cluster.txt" -o $merge_dir/$f.erds+.txt -s $f -c 0 -p reciprocal
with -c parameter set to 0.
When trying to set it to 50, to reproduce the 50% reciprocal overlap reported in the article, I noticed that the produced output file was the same as when I set -c to 0.
Do you know if there is something that I am missing?
Thanks

Hi Brett,

In your paper you mention that you identified 71 genic CNVs in 959 MSSNG probands. I'm wondering if you performed any filtering steps to derive this number beyond intersecting de novo CNVs with a bed file of genic regions.

Dear bjtrost,
after changing the line:
gap_file="$root"/hg19_gap.bed
to
gap_file="$root"/hg38_gap.bed
in process_cnvs.erds+.sh (and saving the appropriate gap table), I noticed that the file cnvn/merged/NA12878.calls.txt.cluster.txt also contains some lines where the second column (the chromosome ID) is missing 'chr'.
I think this may be due to some commands in merge_cnvnator_results.py script (probably something like the following):
chrm = words[1].replace("chr","")
How do you think this could be solved?
Thank you

Hi Brett,

I'm trying to run your CNV_read_depth_checker.sh script and came across the error below. It's calling on get_normalized_depth.py, which is calling on CNVworkflowlib.py at this point.

I'm having trouble resolving it because "parse_region" isn't part of the CNVworkflowlib.py script and I'm afraid the problem affects lines 22, 25-26, 28-29, and 31. Am I missing something?

$ ./CNV_read_depth_checker.sh proband_sorted.bam chr9:72777841-72778868
Traceback (most recent call last):
File "get_normalized_depth.py", line 21, in <module>
chr, start, end = CNVworkflowlib.parse_region(args.region.replace(",", ""))
AttributeError: 'module' object has no attribute 'parse_region'

Hi,
In MANTA.py or LUMPY.py, a module named VCF was used. I wonder how to get this module? Cause I cannot find a VCF.py that matched , and pip also failed to get this module.

Thanks!

I am trying to use the code provided with this workflow to merge the CNV results from CNVnator and ERDS. More specifically, using the process_cnvs.erds+.sh file.
However, it comes with an error on line 81. I find the error comes from the echo $f" "$g. It seems like something missing then this cannot be interpreted correctly. I run one by one for line 81 as:

[jyang32@cnode337 filtered]$ echo for f in ls $cnvn_dir/formatted_filtered/filtered/
for f in TCGA-05-5429-01A-01D-1625-08.calls.filtered.txt
[jyang32@cnode337 filtered]$ echo do g=echo $f| sed 's/.calls.filtered.txt//g'
do g=TCGA-05-5429-01A-01D-1625-08
[jyang32@cnode337 filtered]$ echo $f"TCGA-05-5429-01A-01D-1625-08.calls.filtered.txt" "$g

Can you please let me know what is this used for? Maybe then I can figure out where is the problem.

Hi,

While running erds_tcag, I find that the run seems successfully but the resulting VCF is empty. Below are the details of the run. What could be causing this problem? I would appreciate anyway you can be of help @bjtrost .

`############################ERDS1.1############################
Your input command line is
perl /mnt/data/ike/software/ERDS-master/erds_tcag/src/erds_pipeline.pl -b Data_Files/BAM_old/sample1_sorted.bam -v Data_Files/VCF/sample1.vcf -o ERDS_TCAG_indVCF_sample1 -r /mnt/data/reference/hs37d5.fa
13:39:55 Jan 8 2020 ERDS stared step 0 in sample1...
[Wed Jan 8 13:39:55 2020] PID 20759 is performing computation for hs37d5
[Wed Jan 8 13:39:55 2020] PID 20760 is performing computation for NC_007605
[Wed Jan 8 13:39:55 2020] PID 20761 is performing computation for GL000192.1
[Wed Jan 8 13:39:55 2020] PID 20762 is performing computation for GL000225.1
[Wed Jan 8 13:39:56 2020] PID 20760 is performing computation for GL000193.1
[Wed Jan 8 13:39:56 2020] PID 20759 is performing computation for GL000194.1
[Wed Jan 8 13:39:56 2020] PID 20762 is performing computation for GL000222.1
[Wed Jan 8 13:39:56 2020] PID 20761 is performing computation for GL000200.1
[Wed Jan 8 13:39:57 2020] PID 20760 is performing computation for GL000195.1
[Wed Jan 8 13:39:57 2020] PID 20759 is performing computation for GL000212.1
[Wed Jan 8 13:39:57 2020] PID 20762 is performing computation for GL000224.1
[Wed Jan 8 13:39:57 2020] PID 20761 is performing computation for GL000223.1
[Wed Jan 8 13:39:58 2020] PID 20760 is performing computation for GL000205.1
[Wed Jan 8 13:39:58 2020] PID 20759 is performing computation for GL000219.1
[Wed Jan 8 13:39:58 2020] PID 20762 is performing computation for GL000216.1
[Wed Jan 8 13:39:58 2020] PID 20761 is performing computation for GL000215.1
[Wed Jan 8 13:40:02 2020] PID 20760 is performing computation for GL000199.1
[Wed Jan 8 13:40:02 2020] PID 20759 is performing computation for GL000217.1
[Wed Jan 8 13:40:02 2020] PID 20761 is performing computation for GL000211.1
[Wed Jan 8 13:40:02 2020] PID 20762 is performing computation for GL000213.1
[Wed Jan 8 13:40:02 2020] PID 20760 is performing computation for GL000218.1
[Wed Jan 8 13:40:02 2020] PID 20759 is performing computation for GL000220.1
[Wed Jan 8 13:40:02 2020] PID 20761 is performing computation for GL000209.1
[Wed Jan 8 13:40:03 2020] PID 20762 is performing computation for GL000221.1
[Wed Jan 8 13:40:03 2020] PID 20759 is performing computation for GL000214.1
[Wed Jan 8 13:40:03 2020] PID 20760 is performing computation for GL000228.1
[Wed Jan 8 13:40:03 2020] PID 20761 is performing computation for GL000227.1
[Wed Jan 8 13:40:04 2020] PID 20762 is performing computation for GL000191.1
[Wed Jan 8 13:40:04 2020] PID 20759 is performing computation for GL000208.1
[Wed Jan 8 13:40:04 2020] PID 20760 is performing computation for GL000198.1
[Wed Jan 8 13:40:04 2020] PID 20761 is performing computation for GL000204.1
[Wed Jan 8 13:40:05 2020] PID 20762 is performing computation for GL000233.1
[Wed Jan 8 13:40:05 2020] PID 20759 is performing computation for GL000237.1
[Wed Jan 8 13:40:05 2020] PID 20760 is performing computation for GL000230.1
[Wed Jan 8 13:40:05 2020] PID 20761 is performing computation for GL000242.1
[Wed Jan 8 13:40:10 2020] PID 20762 is performing computation for GL000243.1
[Wed Jan 8 13:40:11 2020] PID 20759 is performing computation for GL000241.1
[Wed Jan 8 13:40:15 2020] PID 20760 is performing computation for GL000236.1
[Wed Jan 8 13:40:15 2020] PID 20761 is performing computation for GL000240.1
[Wed Jan 8 13:40:17 2020] PID 20762 is performing computation for GL000206.1
[Wed Jan 8 13:40:17 2020] PID 20759 is performing computation for GL000232.1
[Wed Jan 8 13:40:17 2020] PID 20760 is performing computation for GL000234.1
[Wed Jan 8 13:40:17 2020] PID 20761 is performing computation for GL000202.1
[Wed Jan 8 13:40:18 2020] PID 20762 is performing computation for GL000238.1
[Wed Jan 8 13:40:18 2020] PID 20759 is performing computation for GL000244.1
[Wed Jan 8 13:40:18 2020] PID 20760 is performing computation for GL000248.1
[Wed Jan 8 13:40:18 2020] PID 20761 is performing computation for GL000196.1
[Wed Jan 8 13:40:18 2020] PID 20762 is performing computation for GL000249.1
[Wed Jan 8 13:40:18 2020] PID 20759 is performing computation for GL000246.1
[Wed Jan 8 13:40:18 2020] PID 20760 is performing computation for GL000203.1
[Wed Jan 8 13:40:19 2020] PID 20761 is performing computation for GL000197.1
[Wed Jan 8 13:40:19 2020] PID 20762 is performing computation for GL000245.1
[Wed Jan 8 13:40:19 2020] PID 20759 is performing computation for GL000247.1
[Wed Jan 8 13:40:19 2020] PID 20760 is performing computation for GL000201.1
[Wed Jan 8 13:40:19 2020] PID 20761 is performing computation for GL000235.1
[Wed Jan 8 13:40:19 2020] PID 20762 is performing computation for GL000239.1
[Wed Jan 8 13:40:20 2020] PID 20759 is performing computation for GL000210.1
[Wed Jan 8 13:40:21 2020] PID 20760 is performing computation for GL000231.1
[Wed Jan 8 13:40:25 2020] PID 20761 is performing computation for GL000229.1
[Wed Jan 8 13:40:25 2020] PID 20762 is performing computation for GL000226.1
[Wed Jan 8 13:40:28 2020] PID 20759 is performing computation for GL000207.1
[Wed Jan 8 13:40:29 2020] PID 20760 is performing computation for MT
[Wed Jan 8 13:40:29 2020] PID 20761 is performing computation for Y
[Wed Jan 8 13:40:29 2020] PID 20762 is performing computation for X
[Wed Jan 8 13:40:30 2020] PID 20759 is performing computation for 22
[Wed Jan 8 13:40:30 2020] PID 20761 is performing computation for 20
[Wed Jan 8 13:40:31 2020] PID 20762 is performing computation for 19
[Wed Jan 8 13:40:31 2020] PID 20759 is performing computation for 18
[Wed Jan 8 13:40:35 2020] PID 20761 is performing computation for 16
[Wed Jan 8 13:40:35 2020] PID 20762 is performing computation for 15
[Wed Jan 8 13:40:35 2020] PID 20759 is performing computation for 14
[Wed Jan 8 13:40:36 2020] PID 20761 is performing computation for 12
[Wed Jan 8 13:40:36 2020] PID 20762 is performing computation for 11
[Wed Jan 8 13:40:36 2020] PID 20759 is performing computation for 10
[Wed Jan 8 13:40:36 2020] PID 20761 is performing computation for 8
[Wed Jan 8 13:40:36 2020] PID 20762 is performing computation for 7
[Wed Jan 8 13:40:37 2020] PID 20759 is performing computation for 6
[Wed Jan 8 13:40:37 2020] PID 20761 is performing computation for 4
[Wed Jan 8 13:40:37 2020] PID 20762 is performing computation for 3
[Wed Jan 8 13:40:37 2020] PID 20759 is performing computation for 2
[Wed Jan 8 13:40:39 2020] PID 20760 is performing computation for 21
[Wed Jan 8 13:40:45 2020] PID 20760 is performing computation for 17
[Wed Jan 8 13:40:45 2020] PID 20760 is performing computation for 13
[Wed Jan 8 13:40:46 2020] PID 20760 is performing computation for 9
[Wed Jan 8 13:40:46 2020] PID 20760 is performing computation for 5
[Wed Jan 8 13:40:47 2020] PID 20760 is performing computation for 1
13:40:48 Jan 8 2020 ERDS finished step 0 in sample1...
13:40:48 Jan 8 2020 ERDS stared step 1 in sample1...
13:41:11 Jan 8 2020 ERDS finished step 1 in sample1...
13:41:11 Jan 8 2020 ERDS stared step 2 in sample1...
no chromosome ERDS_TCAG_indVCF_sample1/cnv/1.rd
Can't open ERDS_TCAG_indVCF_sample1/cnv/1.vit at ERDS_TCAG_indVCF_sample1/script/em.pl line 95.
13:41:12 Jan 8 2020 ERDS finished step 2 in sample1...
13:41:12 Jan 8 2020 ERDS stared step 3 in sample1...
[Wed Jan 8 13:41:12 2020] PID 21882 is performing computation for Y
[Wed Jan 8 13:41:12 2020] PID 21883 is performing computation for X
[Wed Jan 8 13:41:12 2020] PID 21884 is performing computation for 22
[Wed Jan 8 13:41:12 2020] PID 21885 is performing computation for 21
no chromosome ERDS_TCAG_indVCF_sample1/cnv/X.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/21.rd
[Wed Jan 8 13:41:12 2020] PID 21883 is performing computation for 19
[Wed Jan 8 13:41:12 2020] PID 21885 is performing computation for 17
no chromosome ERDS_TCAG_indVCF_sample1/cnv/22.rd
[Wed Jan 8 13:41:12 2020] PID 21882 is performing computation for 20
[Wed Jan 8 13:41:12 2020] PID 21884 is performing computation for 18
no chromosome ERDS_TCAG_indVCF_sample1/cnv/19.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/17.rd
[Wed Jan 8 13:41:12 2020] PID 21883 is performing computation for 15
[Wed Jan 8 13:41:12 2020] PID 21885 is performing computation for 13
no chromosome ERDS_TCAG_indVCF_sample1/cnv/20.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/18.rd
[Wed Jan 8 13:41:12 2020] PID 21882 is performing computation for 16
[Wed Jan 8 13:41:12 2020] PID 21884 is performing computation for 14
no chromosome ERDS_TCAG_indVCF_sample1/cnv/13.rd
[Wed Jan 8 13:41:12 2020] PID 21885 is performing computation for 9
no chromosome ERDS_TCAG_indVCF_sample1/cnv/15.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/14.rd
[Wed Jan 8 13:41:12 2020] PID 21883 is performing computation for 11
no chromosome ERDS_TCAG_indVCF_sample1/cnv/16.rd
[Wed Jan 8 13:41:12 2020] PID 21884 is performing computation for 10
[Wed Jan 8 13:41:12 2020] PID 21882 is performing computation for 12
no chromosome ERDS_TCAG_indVCF_sample1/cnv/9.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/10.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/11.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/12.rd
[Wed Jan 8 13:41:12 2020] PID 21884 is performing computation for 6
[Wed Jan 8 13:41:12 2020] PID 21883 is performing computation for 7
[Wed Jan 8 13:41:12 2020] PID 21885 is performing computation for 5
[Wed Jan 8 13:41:12 2020] PID 21882 is performing computation for 8
no chromosome ERDS_TCAG_indVCF_sample1/cnv/7.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/5.rd
[Wed Jan 8 13:41:12 2020] PID 21883 is performing computation for 3
[Wed Jan 8 13:41:12 2020] PID 21885 is performing computation for 1
no chromosome ERDS_TCAG_indVCF_sample1/cnv/8.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/6.rd
[Wed Jan 8 13:41:12 2020] PID 21882 is performing computation for 4
[Wed Jan 8 13:41:12 2020] PID 21884 is performing computation for 2
no chromosome ERDS_TCAG_indVCF_sample1/cnv/1.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/3.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/2.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv/4.rd
13:41:12 Jan 8 2020 ERDS finished step 3 in sample1...
13:41:12 Jan 8 2020 ERDS stared step 4 in sample1...
[Wed Jan 8 13:41:12 2020] PID 21911 is performing computation for Y
[Wed Jan 8 13:41:12 2020] PID 21912 is performing computation for X
[Wed Jan 8 13:41:12 2020] PID 21913 is performing computation for 22
[Wed Jan 8 13:41:12 2020] PID 21914 is performing computation for 21
no chromosome ERDS_TCAG_indVCF_sample1/cnv/21.vit
[Wed Jan 8 13:41:12 2020] PID 21914 is performing computation for 17
no chromosome ERDS_TCAG_indVCF_sample1/cnv/22.vit
[Wed Jan 8 13:41:12 2020] PID 21913 is performing computation for 18
[Wed Jan 8 13:41:12 2020] PID 21911 is performing computation for 20
no chromosome ERDS_TCAG_indVCF_sample1/cnv/X.vit
[Wed Jan 8 13:41:12 2020] PID 21912 is performing computation for 19
no chromosome ERDS_TCAG_indVCF_sample1/cnv/17.vit
[Wed Jan 8 13:41:12 2020] PID 21914 is performing computation for 13
no chromosome ERDS_TCAG_indVCF_sample1/cnv/18.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/19.vit
[Wed Jan 8 13:41:12 2020] PID 21913 is performing computation for 14
no chromosome ERDS_TCAG_indVCF_sample1/cnv/20.vit
[Wed Jan 8 13:41:12 2020] PID 21912 is performing computation for 15
[Wed Jan 8 13:41:12 2020] PID 21911 is performing computation for 16
no chromosome ERDS_TCAG_indVCF_sample1/cnv/13.vit
[Wed Jan 8 13:41:12 2020] PID 21914 is performing computation for 9
no chromosome ERDS_TCAG_indVCF_sample1/cnv/14.vit
[Wed Jan 8 13:41:12 2020] PID 21913 is performing computation for 10
no chromosome ERDS_TCAG_indVCF_sample1/cnv/16.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/15.vit
[Wed Jan 8 13:41:12 2020] PID 21911 is performing computation for 12
[Wed Jan 8 13:41:12 2020] PID 21912 is performing computation for 11
no chromosome ERDS_TCAG_indVCF_sample1/cnv/9.vit
[Wed Jan 8 13:41:12 2020] PID 21914 is performing computation for 5
no chromosome ERDS_TCAG_indVCF_sample1/cnv/10.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/12.vit
[Wed Jan 8 13:41:12 2020] PID 21913 is performing computation for 6
no chromosome ERDS_TCAG_indVCF_sample1/cnv/11.vit
[Wed Jan 8 13:41:12 2020] PID 21911 is performing computation for 8
[Wed Jan 8 13:41:12 2020] PID 21912 is performing computation for 7
no chromosome ERDS_TCAG_indVCF_sample1/cnv/5.vit
[Wed Jan 8 13:41:12 2020] PID 21914 is performing computation for 1
no chromosome ERDS_TCAG_indVCF_sample1/cnv/6.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/8.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/7.vit
[Wed Jan 8 13:41:12 2020] PID 21913 is performing computation for 2
[Wed Jan 8 13:41:12 2020] PID 21911 is performing computation for 4
[Wed Jan 8 13:41:12 2020] PID 21912 is performing computation for 3
no chromosome ERDS_TCAG_indVCF_sample1/cnv/1.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/2.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/4.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv/3.vit
13:41:12 Jan 8 2020 ERDS finished step 4 in sample1...
13:41:12 Jan 8 2020 ERDS stared step 5 in sample1...
13:41:12 Jan 8 2020 ERDS finished step 5 in sample1...
13:41:12 Jan 8 2020 ERDS stared step 6 in sample1...
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/1.rd
Can't open ERDS_TCAG_indVCF_sample1/cnv_1000/1.vit at ERDS_TCAG_indVCF_sample1/script/pre_hmm_dup.pl line 206.
13:41:36 Jan 8 2020 ERDS finished step 6 in sample1...
13:41:36 Jan 8 2020 ERDS stared step 7 in sample1...
[Wed Jan 8 13:41:36 2020] PID 21975 is performing computation for Y
[Wed Jan 8 13:41:36 2020] PID 21976 is performing computation for X
[Wed Jan 8 13:41:36 2020] PID 21977 is performing computation for 22
[Wed Jan 8 13:41:36 2020] PID 21978 is performing computation for 21
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/22.rd
[Wed Jan 8 13:41:36 2020] PID 21977 is performing computation for 18
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/21.rd
[Wed Jan 8 13:41:36 2020] PID 21975 is performing computation for 20
[Wed Jan 8 13:41:36 2020] PID 21978 is performing computation for 17
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/X.rd
[Wed Jan 8 13:41:36 2020] PID 21976 is performing computation for 19
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/18.rd
[Wed Jan 8 13:41:36 2020] PID 21977 is performing computation for 14
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/20.rd
[Wed Jan 8 13:41:36 2020] PID 21975 is performing computation for 16
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/17.rd
[Wed Jan 8 13:41:36 2020] PID 21978 is performing computation for 13
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/19.rd
[Wed Jan 8 13:41:36 2020] PID 21976 is performing computation for 15
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/14.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/16.rd
[Wed Jan 8 13:41:36 2020] PID 21977 is performing computation for 10
[Wed Jan 8 13:41:36 2020] PID 21975 is performing computation for 12
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/13.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/15.rd
[Wed Jan 8 13:41:36 2020] PID 21978 is performing computation for 9
[Wed Jan 8 13:41:36 2020] PID 21976 is performing computation for 11
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/12.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/9.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/11.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/10.rd
[Wed Jan 8 13:41:36 2020] PID 21978 is performing computation for 5
[Wed Jan 8 13:41:36 2020] PID 21975 is performing computation for 8
[Wed Jan 8 13:41:36 2020] PID 21976 is performing computation for 7
[Wed Jan 8 13:41:36 2020] PID 21977 is performing computation for 6
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/5.rd
[Wed Jan 8 13:41:36 2020] PID 21978 is performing computation for 1
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/7.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/6.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/8.rd
[Wed Jan 8 13:41:36 2020] PID 21976 is performing computation for 3
[Wed Jan 8 13:41:36 2020] PID 21977 is performing computation for 2
[Wed Jan 8 13:41:36 2020] PID 21975 is performing computation for 4
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/2.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/1.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/4.rd
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/3.rd
13:41:36 Jan 8 2020 ERDS finished step 7 in sample1...
13:41:36 Jan 8 2020 ERDS stared step 8 in sample1...
[Wed Jan 8 13:41:36 2020] PID 22004 is performing computation for Y
[Wed Jan 8 13:41:36 2020] PID 22005 is performing computation for X
[Wed Jan 8 13:41:36 2020] PID 22006 is performing computation for 22
[Wed Jan 8 13:41:36 2020] PID 22007 is performing computation for 21
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/21.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/22.vit
[Wed Jan 8 13:41:36 2020] PID 22007 is performing computation for 17
[Wed Jan 8 13:41:36 2020] PID 22006 is performing computation for 18
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/X.vit
[Wed Jan 8 13:41:36 2020] PID 22004 is performing computation for 20
[Wed Jan 8 13:41:36 2020] PID 22005 is performing computation for 19
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/18.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/17.vit
[Wed Jan 8 13:41:36 2020] PID 22006 is performing computation for 14
[Wed Jan 8 13:41:36 2020] PID 22007 is performing computation for 13
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/19.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/20.vit
[Wed Jan 8 13:41:36 2020] PID 22005 is performing computation for 15
[Wed Jan 8 13:41:36 2020] PID 22004 is performing computation for 16
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/13.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/14.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/15.vit
[Wed Jan 8 13:41:36 2020] PID 22006 is performing computation for 10
[Wed Jan 8 13:41:36 2020] PID 22007 is performing computation for 9
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/16.vit
[Wed Jan 8 13:41:36 2020] PID 22005 is performing computation for 11
[Wed Jan 8 13:41:36 2020] PID 22004 is performing computation for 12
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/10.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/9.vit
[Wed Jan 8 13:41:36 2020] PID 22006 is performing computation for 6
[Wed Jan 8 13:41:36 2020] PID 22007 is performing computation for 5
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/11.vit
[Wed Jan 8 13:41:36 2020] PID 22005 is performing computation for 7
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/12.vit
[Wed Jan 8 13:41:36 2020] PID 22004 is performing computation for 8
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/7.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/5.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/6.vit
[Wed Jan 8 13:41:36 2020] PID 22005 is performing computation for 3
[Wed Jan 8 13:41:36 2020] PID 22007 is performing computation for 1
[Wed Jan 8 13:41:36 2020] PID 22006 is performing computation for 2
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/8.vit
[Wed Jan 8 13:41:36 2020] PID 22004 is performing computation for 4
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/3.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/1.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/2.vit
no chromosome ERDS_TCAG_indVCF_sample1/cnv_1000/4.vit
13:41:36 Jan 8 2020 ERDS finished step 8 in sample1...
13:41:36 Jan 8 2020 ERDS stared step 9 in sample1...
13:41:36 Jan 8 2020 ERDS finished step 9 in sample1...
13:41:36 Jan 8 2020 ERDS stared step 10 in sample1...
13:41:36 Jan 8 2020 ERDS finished all steps in sample1. The results are at ERDS_TCAG_indVCF_sample1.

############################ERDS1.1############################

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