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Jiaxin Zhao
Jun 18, 2024, 3:36:32 AM6/18/24
to Biociphers
Dear MAJIQ development team and partners using the software:
Hello guys, recently a problem has been bothering me for a long time, please allow me to describe the problem as follows:
Hello guys, recently a problem has been bothering me for a long time, please allow me to describe the problem as follows:
Here are the commands I enter when using voila modulize:
Dir="/cold_data/zhaojiaxin/majiq/"
MAJIQ_LICENSE_FILE="/home/zhaojiaxin/sci_pjt/alt_spl/addon/majiq_license_academic_official.lic" \voila modulize \
-d "$Dir"output_sep/lab8modulize/lab8_AvsB \
"$Dir"splicegraph.sql \
"$Dir"lab8/lab8_MAQC_A-lab8_MAQC_B.deltapsi.voila \
-j8 \
--show-all \
--overwrite
When --show-all parameter is not added, all the lab data have only title, after adding this parameter, some lab results are shown normally, but there are still some labs, the output result file has only title. I have seen this issue discussed in the group, and the possible solutions given by people are to adjust -decomplexify-reads-threshold, -decomplexify-psi-threshold, - decomplexify-deltapsi-threshold, but is that really the case? These parameters are adjusting critical metrics and I don't think you can make changes easily.
Has anyone had a similar problem that has been resolved? Sincerely hope to get professional help from all of you, your help is really important to me!
San Jewell
Jun 18, 2024, 4:56:05 PM6/18/24
to Biociphers
Hello <unknown name>,
When using modulize or tsv modes and providing "deltapsi" or "heterogen" voila files as inputs, by default, the output files will contain only changing events. Using --show-all does not remove all filters such as reads, pri, or dpsi thresholds at all, instead, it just makes sure to include all events, even if they were not considered "changing". If you think that the result without using --show-all should still provide some outputs which are changing, the best way to start would be to check the result using --show-all and see these events which have been filtered out to see why that might be. From there you can likely change the switches --probability-changing-threshold , --changing-between-group-dpsi , and --changing-between-group-dpsi-secondary to loosen up the criteria which are used to call an event as changing. Please check the --help text with modulize to see what each of these switches do and post back here if anything is unclear.
Thanks!
-San
Message has been deleted
Jiaxin Zhao
Jun 18, 2024, 9:37:22 PM6/18/24
to Biociphers
Hello San, sorry to bother you again.
I've read your reply carefully, maybe I didn't express myself very clearly, at the moment my problem is: I've obviously added the parameter --show-all, but I don't get any result only the title.
I understand that you mean that --show-all will show all events, regardless of whether the software (based on a set threshold) determines them to be "changed" or not, they will be shown in the results.
I made sure I added this parameter to my runtime, but I still don't get any results, do you have a clue about this issue?
I've read your reply carefully, maybe I didn't express myself very clearly, at the moment my problem is: I've obviously added the parameter --show-all, but I don't get any result only the title.
I understand that you mean that --show-all will show all events, regardless of whether the software (based on a set threshold) determines them to be "changed" or not, they will be shown in the results.
I made sure I added this parameter to my runtime, but I still don't get any results, do you have a clue about this issue?
Jiaxin Zhao
Jun 19, 2024, 3:35:41 AM6/19/24
to Biociphers
As well, allow me to provide you with detailed information about the voila.log file:
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; license: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; files: [PosixPath('/cold_data/zhaojiaxin/majiq/splicegraph.sql'), PosixPath('/cold_data/zhaojiaxin/majiq/lab8/lab8_M8-lab8_D6.deltapsi.voila')]
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; overwrite: True
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; ignore_inconsistent_group_errors: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; only_binary: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; untrimmed_exons: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; show_all: True
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; heatmap_selection: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; disable_metadata: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; show_read_counts: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; show_per_sample_psi: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; cassettes_constitutive_column: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; junc_gene_dist_column: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; gene_ids: []
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; debug_num_genes: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; include_change_cases: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; output_mpe: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; putative_multi_gene_regions: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; keep_constitutive: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; keep_no_lsvs_modules: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; keep_no_lsvs_junctions: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; decomplexify_psi_threshold: 0.05
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; decomplexify_deltapsi_threshold: 0.0
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; decomplexify_reads_threshold: 1
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; changing_between_group_dpsi: 0.2
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; non_changing_between_group_dpsi: 0.05
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; changing_between_group_dpsi_secondary: 0.1
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; non_changing_median_reads_threshold: 0
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; permissive_event_non_changing_threshold: 1.0
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; non_changing_pvalue_threshold: 0.05
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; non_changing_within_group_IQR: 0.1
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; changing_pvalue_threshold: 0.05
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; probability_changing_threshold: 0.95
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; probability_non_changing_threshold: 0.95
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; directory: /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; nproc: 8
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; debug: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; memory_map_hdf5: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; preserve_handles_hdf5: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; logger: /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6/voila.log
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; silent: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; func: <class 'rna_voila.classify.Classify'>
2024-06-13 16:43:39,189 (PID:1854113) - INFO - Command: /home/zhaojiaxin/anaconda3/envs/majiq/bin/voila modulize -d /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6 /cold_data/zhaojiaxin/majiq/splicegraph.sql /cold_data/zhaojiaxin/majiq/lab8/lab8_M8-lab8_D6.deltapsi.voila -j8 --show-all --overwrite
2024-06-13 16:43:39,189 (PID:1854113) - INFO - Voila v2.5.6.dev1+g8423f68b
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╠╡ ACADEMIC License applied ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ File: majiq_license_academic_official.lic ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ Expiration Date: Never ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-06-13 16:43:39,210 (PID:1854113) - INFO - config file: /tmp/tmpibx65cp9
2024-06-13 16:43:39,211 (PID:1854113) - DEBUG - Generating config object
2024-06-13 16:43:39,213 (PID:1854113) - DEBUG - Generating config object
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| [SETTINGS]
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| cassettes_constitutive_column = False
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| changing_between_group_dpsi = 0.2
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| changing_between_group_dpsi_secondary = 0.1
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| changing_pvalue_threshold = 0.05
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| debug = False
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| decomplexify_deltapsi_threshold = 0.0
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| decomplexify_psi_threshold = 0.05
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| decomplexify_reads_threshold = 1
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| directory = /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| disable_metadata = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| ignore_inconsistent_group_errors = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| include_change_cases = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| junc_gene_dist_column = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| keep_no_lsvs_junctions = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| keep_no_lsvs_modules = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| memory_map_hdf5 = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_between_group_dpsi = 0.05
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_median_reads_threshold = 0
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_pvalue_threshold = 0.05
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_within_group_iqr = 0.1
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| nproc = 8
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| only_binary = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| output_mpe = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| overwrite = True
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| permissive_event_non_changing_threshold = 1.0
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| preserve_handles_hdf5 = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| probability_changing_threshold = 0.95
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| probability_non_changing_threshold = 0.95
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| putative_multi_gene_regions = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| show_all = True
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| show_per_sample_psi = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| show_read_counts = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| silent = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| untrimmed_exons = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| analysis_type = dPSIx1
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG|
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| [FILES]
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| voila = /cold_data/zhaojiaxin/majiq/lab8/lab8_M8-lab8_D6.deltapsi.voila
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| splice_graph = /cold_data/zhaojiaxin/majiq/splicegraph.sql
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG|
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - Generating config object
2024-06-13 16:43:39,216 (PID:1854113) - INFO - dPSIx1 MODULIZE
2024-06-13 16:43:39,288 (PID:1854113) - INFO - Modulizing 62710 gene(s)
2024-06-13 16:43:39,288 (PID:1854113) - INFO - Quantifications based on 1 input file(s)
2024-06-13 16:43:39,288 (PID:1854113) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-06-13 16:43:39,288 (PID:1854113) - INFO - ╠╡ Before Modulization: ║
2024-06-13 16:43:39,288 (PID:1854113) - INFO - ║ Dropping junctions with max(PSI) < 0.050 ║
2024-06-13 16:43:39,289 (PID:1854113) - INFO - ║ Dropping junctions with max(number_of_reads) < 1 ║
2024-06-13 16:43:39,289 (PID:1854113) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-06-13 16:43:39,289 (PID:1854113) - INFO - Writing TSVs to /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6
2024-06-13 16:44:09,426 (PID:1854113) - INFO - Concatenating Results
2024-06-13 16:44:09,485 (PID:1854113) - INFO - Modulization Complete
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; files: [PosixPath('/cold_data/zhaojiaxin/majiq/splicegraph.sql'), PosixPath('/cold_data/zhaojiaxin/majiq/lab8/lab8_M8-lab8_D6.deltapsi.voila')]
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; overwrite: True
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; ignore_inconsistent_group_errors: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; only_binary: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; untrimmed_exons: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; show_all: True
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; heatmap_selection: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; disable_metadata: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; show_read_counts: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; show_per_sample_psi: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; cassettes_constitutive_column: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; junc_gene_dist_column: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; gene_ids: []
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; debug_num_genes: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; include_change_cases: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; output_mpe: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; putative_multi_gene_regions: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; keep_constitutive: None
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; keep_no_lsvs_modules: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; keep_no_lsvs_junctions: False
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; decomplexify_psi_threshold: 0.05
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; decomplexify_deltapsi_threshold: 0.0
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; decomplexify_reads_threshold: 1
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; changing_between_group_dpsi: 0.2
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; non_changing_between_group_dpsi: 0.05
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; changing_between_group_dpsi_secondary: 0.1
2024-06-13 16:43:39,188 (PID:1854113) - DEBUG - Argument; non_changing_median_reads_threshold: 0
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; permissive_event_non_changing_threshold: 1.0
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; non_changing_pvalue_threshold: 0.05
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; non_changing_within_group_IQR: 0.1
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; changing_pvalue_threshold: 0.05
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; probability_changing_threshold: 0.95
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; probability_non_changing_threshold: 0.95
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; directory: /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; nproc: 8
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; debug: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; memory_map_hdf5: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; preserve_handles_hdf5: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; logger: /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6/voila.log
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; silent: False
2024-06-13 16:43:39,189 (PID:1854113) - DEBUG - Argument; func: <class 'rna_voila.classify.Classify'>
2024-06-13 16:43:39,189 (PID:1854113) - INFO - Command: /home/zhaojiaxin/anaconda3/envs/majiq/bin/voila modulize -d /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6 /cold_data/zhaojiaxin/majiq/splicegraph.sql /cold_data/zhaojiaxin/majiq/lab8/lab8_M8-lab8_D6.deltapsi.voila -j8 --show-all --overwrite
2024-06-13 16:43:39,189 (PID:1854113) - INFO - Voila v2.5.6.dev1+g8423f68b
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╠╡ ACADEMIC License applied ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ File: majiq_license_academic_official.lic ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ Expiration Date: Never ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ║ ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-06-13 16:43:39,210 (PID:1854113) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-06-13 16:43:39,210 (PID:1854113) - INFO - config file: /tmp/tmpibx65cp9
2024-06-13 16:43:39,211 (PID:1854113) - DEBUG - Generating config object
2024-06-13 16:43:39,213 (PID:1854113) - DEBUG - Generating config object
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| [SETTINGS]
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| cassettes_constitutive_column = False
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| changing_between_group_dpsi = 0.2
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| changing_between_group_dpsi_secondary = 0.1
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| changing_pvalue_threshold = 0.05
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| debug = False
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| decomplexify_deltapsi_threshold = 0.0
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| decomplexify_psi_threshold = 0.05
2024-06-13 16:43:39,214 (PID:1854113) - DEBUG - CFG| decomplexify_reads_threshold = 1
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| directory = /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| disable_metadata = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| ignore_inconsistent_group_errors = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| include_change_cases = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| junc_gene_dist_column = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| keep_no_lsvs_junctions = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| keep_no_lsvs_modules = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| memory_map_hdf5 = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_between_group_dpsi = 0.05
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_median_reads_threshold = 0
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_pvalue_threshold = 0.05
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| non_changing_within_group_iqr = 0.1
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| nproc = 8
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| only_binary = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| output_mpe = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| overwrite = True
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| permissive_event_non_changing_threshold = 1.0
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| preserve_handles_hdf5 = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| probability_changing_threshold = 0.95
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| probability_non_changing_threshold = 0.95
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| putative_multi_gene_regions = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| show_all = True
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| show_per_sample_psi = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| show_read_counts = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| silent = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| untrimmed_exons = False
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| analysis_type = dPSIx1
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG|
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| [FILES]
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| voila = /cold_data/zhaojiaxin/majiq/lab8/lab8_M8-lab8_D6.deltapsi.voila
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG| splice_graph = /cold_data/zhaojiaxin/majiq/splicegraph.sql
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - CFG|
2024-06-13 16:43:39,215 (PID:1854113) - DEBUG - Generating config object
2024-06-13 16:43:39,216 (PID:1854113) - INFO - dPSIx1 MODULIZE
2024-06-13 16:43:39,288 (PID:1854113) - INFO - Modulizing 62710 gene(s)
2024-06-13 16:43:39,288 (PID:1854113) - INFO - Quantifications based on 1 input file(s)
2024-06-13 16:43:39,288 (PID:1854113) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-06-13 16:43:39,288 (PID:1854113) - INFO - ╠╡ Before Modulization: ║
2024-06-13 16:43:39,288 (PID:1854113) - INFO - ║ Dropping junctions with max(PSI) < 0.050 ║
2024-06-13 16:43:39,289 (PID:1854113) - INFO - ║ Dropping junctions with max(number_of_reads) < 1 ║
2024-06-13 16:43:39,289 (PID:1854113) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-06-13 16:43:39,289 (PID:1854113) - INFO - Writing TSVs to /cold_data/zhaojiaxin/majiq/output_sep/lab8modulize/lab8_8vs6
2024-06-13 16:44:09,426 (PID:1854113) - INFO - Concatenating Results
2024-06-13 16:44:09,485 (PID:1854113) - INFO - Modulization Complete
San Jewell
Jun 24, 2024, 5:35:27 PM6/24/24
to Biociphers
Hello,
I've deleted your other topic on the board, let's stick to this thread until the issue is resolved.
This sounds as if there may be something wrong with the build, in that you are not getting any LSVs properly generated. Can you try a few things to narrow it down?
1) please add the flags --keep-constitutive --keep-no-lsvs-modules --keep-no-lsvs-junctions to your run, and let me know if you begin seeing a lot of other data in the tsv output files in that case.
2) would you be able to provide the log for the majiq build and the majiq deltapsi command outputs?
Thank you,
-San
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