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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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CRISPResso command failed (return value 127) on region #0: #52

Closed pankajki closed 5 years ago

pankajki commented 5 years ago

Using Crespresso 2.0.23 CRISPRessoWGS terminated with following error message: Total region analyzed 18227 Similar message for all 18227 regions. Running CRISPResso on region #1/18227: /home/pankum/miniconda3/lib/python2.7/site-packages/CRISPResso.py -r1 /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted/ANALYZED_REGIONS/REGION_R_1.fastq.gz -a catctctctagggcaacgtcggctgcagctgagatggctgctccccggtg -o /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted --name R_1 --needleman_wunsch_gap_extend -2 --max_rows_alleles_around_cut_to_plot 50 --aln_seed_count 5 --needleman_wunsch_aln_matrix_loc EDNAFULL --quantification_window_size 1 --quantification_window_center -3 --trimmomatic_command trimmomatic --conversion_nuc_from C --min_bp_quality_or_N 0 --default_min_aln_score 60 --needleman_wunsch_gap_incentive 1 --plot_window_size 40 --aln_seed_min 2 --needleman_wunsch_gap_open -20 --aln_seed_len 10 --conversion_nuc_to T --min_single_bp_quality 0 --exclude_bp_from_left 15 --min_average_read_quality 0 --min_frequency_alleles_around_cut_to_plot 0.2 --exclude_bp_from_right 15 CRISPResso command failed (return value 127) on region #0: "/home/pankum/miniconda3/lib/python2.7/site-packages/CRISPResso.py -r1 /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted/ANALYZED_REGIONS/REGION_R_1.fastq.gz -a catctctctagggcaacgtcggctgcagctgagatggctgctccccggtg -o /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted --name R_1 --needleman_wunsch_gap_extend -2 --max_rows_alleles_around_cut_to_plot 50 --aln_seed_count 5 --needleman_wunsch_aln_matrix_loc EDNAFULL --quantification_window_size 1 --quantification_window_center -3 --trimmomatic_command trimmomatic --conversion_nuc_from C --min_bp_quality_or_N 0 --default_min_aln_score 60 --needleman_wunsch_gap_incentive 1 --plot_window_size 40 --aln_seed_min 2 --needleman_wunsch_gap_open -20 --aln_seed_len 10 --conversion_nuc_to T --min_single_bp_quality 0 --exclude_bp_from_left 15 --min_average_read_quality 0 --min_frequency_alleles_around_cut_to_plot 0.2 --exclude_bp_from_right 15"

lucapinello commented 5 years ago

You need to open the issue under: https://github.com/pinellolab/crispresso2

On Tue, Apr 9, 2019 at 4:19 PM pankajki notifications@github.com wrote:

Using Crespresso 2.0.23 CRISPRessoWGS terminated with following error message: Total region analyzed 18227 Similar message for all 18227 regions. Running CRISPResso on region #1 https://github.com/lucapinello/CRISPResso/pull/1/18227: /home/pankum/miniconda3/lib/python2.7/site-packages/CRISPResso.py -r1 /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted/ANALYZED_REGIONS/REGION_R_1.fastq.gz -a catctctctagggcaacgtcggctgcagctgagatggctgctccccggtg -o /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted --name R_1 --needleman_wunsch_gap_extend -2 --max_rows_alleles_around_cut_to_plot 50 --aln_seed_count 5 --needleman_wunsch_aln_matrix_loc EDNAFULL --quantification_window_size 1 --quantification_window_center -3 --trimmomatic_command trimmomatic --conversion_nuc_from C --min_bp_quality_or_N 0 --default_min_aln_score 60 --needleman_wunsch_gap_incentive 1 --plot_window_size 40 --aln_seed_min 2 --needleman_wunsch_gap_open -20 --aln_seed_len 10 --conversion_nuc_to T --min_single_bp_quality 0 --exclude_bp_from_left 15 --min_average_read_quality 0 --min_frequency_alleles_around_cut_to_plot 0.2 --exclude_bp_from_right 15 CRISPResso command failed (return value 127) on region #0: "/home/pankum/miniconda3/lib/python2.7/site-packages/CRISPResso.py -r1 /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted/ANALYZED_REGIONS/REGION_R_1.fastq.gz -a catctctctagggcaacgtcggctgcagctgagatggctgctccccggtg -o /san/ongoing/CRISPER_WGS_Data/CRISpresso/B2M-KO_101_predicted/CRISPRessoWGS_on_B2M-KO_101_predicted --name R_1 --needleman_wunsch_gap_extend -2 --max_rows_alleles_around_cut_to_plot 50 --aln_seed_count 5 --needleman_wunsch_aln_matrix_loc EDNAFULL --quantification_window_size 1 --quantification_window_center -3 --trimmomatic_command trimmomatic --conversion_nuc_from C --min_bp_quality_or_N 0 --default_min_aln_score 60 --needleman_wunsch_gap_incentive 1 --plot_window_size 40 --aln_seed_min 2 --needleman_wunsch_gap_open -20 --aln_seed_len 10 --conversion_nuc_to T --min_single_bp_quality 0 --exclude_bp_from_left 15 --min_average_read_quality 0 --min_frequency_alleles_around_cut_to_plot 0.2 --exclude_bp_from_right 15"

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