Open Taylor95 opened 4 years ago
Taylor95
commented
4 years ago 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
commented
1 month ago 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 R O J E CT NA M E − − o u t p u t − d i r e c t o r y {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
Hi, I got stuck when running ipttern. I followed the scripts in run_ensembleCNV_template.sh but got the erro when running the command:
The erro is:
My data as following after step 'Prepare data for individual CNV callers' :
Would you help me solve this? Thank you