erro during running ipattern

[Taylor95]

Hi,
I got stuck when running ipttern. I followed the scripts in run_ensembleCNV_template.sh but got the erro when running the command:

{IPNBASE}/preprocess/ilmn/ilmn_run.py --data-file-list ${WKDIR}/01_initial_call/run_iPattern/data_aux/${PROJECT_NAME}_data_file.txt --gender-file ${WKDIR}/01_initial_call/run_iPattern/data_au
x/${PROJECT_NAME}_gender_file.txt --bad-sample-file ${WKDIR}/01_initial_call/run_iPattern/data_aux/${PROJECT_NAME}_bad_samples.txt --experiment $PROJECT_NAME --output-directory ${WKDIR}/01_initial_call/run_iPattern/results/ --do-log --do-cleanup --noqsub

The erro is:

SPLIT ALL DATA FAILED.
============================================
Message from stderr:
Splitting files ........
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
------------->>> COLLECTING sample names.
Traceback (most recent call last):
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_all_data_files.py", line 201, in
split_all_data_files (options)
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_all_data_files.py", line 96, in split_all_data_files
f = open (sample_file)
IOError: [Errno 2] No such file or directory: 'test_dir/201715370233_R01C01.txt.sample.txt'
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode

My data as following after step 'Prepare data for individual CNV callers' :

[Header]
[Data]
GSGT Version 2.0.3
Processing Date 12/18/2019 7:26 PM
Content GSAMD-24v1-0_20011747_A1.bpm
Num SNPs 700078
Total SNPs 700078
Num Samples 8959
Total Samples 11074
File 1 of 896
Sample ID SNP Name Chr Position Allele1 - Forward Allele2 - Forward X Y B Allele Freq Log R Ratio
201715370233_R01C01 1:100292476 1 100292476 A A 0.807 0.269 0.0000 0.0727
201715370233_R01C01 1:101064936 1 101064936 A A 3.759 0.832 0.0136 0.5915
201715370233_R01C01 1:103380393 1 103380393 G G 0.112 0.708 0.9230 -0.1378
201715370233_R01C01 1:104303716 1 104303716 G G 0.021 0.836 1.0000 0.0444
201715370233_R01C01 1:104864464 1 104864464 G G 0.472 1.383 0.9962 0.1592
201715370233_R01C01 1:106737318 1 106737318 A A 0.484 0.039 0.0000 -0.0584
201715370233_R01C01 1:109439680 1 109439680 A A 0.530 0.027 0.0000 -0.0187
201715370233_R01C01 1:111119214 1 111119214 G G 0.101 0.911 0.9739 -0.2268
201715370233_R01C01 1:114483147 1 114483147 A A 1.579 0.025 0.0000 0.3099

Would you help me solve this?
Thank you

[Taylor95]

I also find the splitted ipattern, penncnv and quantisnp signal intensity file of the same sample have different lines. For one sample, iPattern has 700079 after removing [Header] section, Penncnv has 690494 lines and Quantisnp has 690394 lines. Shouldn't they be identical?
Moreover, different samples have different lines in Quantisnp. Shouldn't every sample has the same number of markers?

[Roger1116L]

Hi, I got stuck when running ipttern. I followed the scripts in run_ensembleCNV_template.sh but got the erro when running the command:

{IPNBASE}/preprocess/ilmn/ilmn_run.py --data-file-list ${WKDIR}/01_initial_call/run_iPattern/data_aux/${PROJECT_NAME}_data_file.txt --gender-file ${WKDIR}/01_initial_call/run_iPattern/data_au
x/${PROJECT_NAME}_gender_file.txt --bad-sample-file ${WKDIR}/01_initial_call/run_iPattern/data_aux/${PROJECT_NAME}_bad_samples.txt --experiment
P
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{WKDIR}/01_initial_call/run_iPattern/results/ --do-log --do-cleanup --noqsub

The erro is:

SPLIT ALL DATA FAILED.

Message from stderr:
Splitting files ........
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_sample_probe.py", line 36
if ipn.all_probes.has_key (E[ipn.snp_name]):
^
TabError: inconsistent use of tabs and spaces in indentation
------------->>> COLLECTING sample names.
Traceback (most recent call last):
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_all_data_files.py", line 201, in
split_all_data_files (options)
File "/dt3/lyq/CNV/ipattern_CNV/ipn_0.581/preprocess/ilmn/split_all_data_files.py", line 96, in split_all_data_files
f = open (sample_file)
IOError: [Errno 2] No such file or directory: 'test_dir/201715370233_R01C01.txt.sample.txt'
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode
xkpnode

My data as following after step 'Prepare data for individual CNV callers' :

[Header]
[Data]
GSGT Version 2.0.3
Processing Date 12/18/2019 7:26 PM
Content GSAMD-24v1-0_20011747_A1.bpm
Num SNPs 700078
Total SNPs 700078
Num Samples 8959
Total Samples 11074
File 1 of 896
Sample ID SNP Name Chr Position Allele1 - Forward Allele2 - Forward X Y B Allele Freq Log R Ratio
201715370233_R01C01 1:100292476 1 100292476 A A 0.807 0.269 0.0000 0.0727
201715370233_R01C01 1:101064936 1 101064936 A A 3.759 0.832 0.0136 0.5915
201715370233_R01C01 1:103380393 1 103380393 G G 0.112 0.708 0.9230 -0.1378
201715370233_R01C01 1:104303716 1 104303716 G G 0.021 0.836 1.0000 0.0444
201715370233_R01C01 1:104864464 1 104864464 G G 0.472 1.383 0.9962 0.1592
201715370233_R01C01 1:106737318 1 106737318 A A 0.484 0.039 0.0000 -0.0584
201715370233_R01C01 1:109439680 1 109439680 A A 0.530 0.027 0.0000 -0.0187
201715370233_R01C01 1:111119214 1 111119214 G G 0.101 0.911 0.9739 -0.2268
201715370233_R01C01 1:114483147 1 114483147 A A 1.579 0.025 0.0000 0.3099

Would you help me solve this? Thank you

Sir, I've met the same error with you when running iPattern , did you work out for then error"No such file or directory: test_dir/xxxxtxt.sample.txt"? I'll appreciate so much if you can offer some solutions! Thank you