Hello,
tailseeker (version 3.1.6) delivers the AYB error below.
Provided cores: 96
Rules claiming more threads will be scaled down.
Job counts:
count jobs
20 STAR_alignment
1 all
10 apply_short_polya_filter
10 associate_tags_to_genes
64 basecall_ayb
2 calculate_optimal_parameters
10 contaminant_alignment
10 count_multiple_associations
10 extract_short_polya_tag_alignments
20 filter_approximate_duplicates
1 finalize_measurement_params
10 find_approximate_duplicates
1 generate_accuracy_stats
1 generate_polya_length_distribution_stats_level1
1 generate_polya_length_distribution_stats_level2
10 generate_short_polya_list
20 index_alignments
10 index_sorted_alignments
20 make_filtered_fastq
60 make_gene_level_counts
20 make_gene_level_statistics
10 make_read5_position_dists
128 measure_polya_lengths_from_fluorescence
20 merge_alignments
15 merge_and_deduplicate_taginfo
2 merge_gene_level_stats
1 merge_polya_sites_list
1 merge_read5_position_dists
1 merge_signal_processing_stats
1 plot_global_polya_length_histogram
1 plot_global_polya_length_histogram_level2
1 plot_global_polya_length_virtual_gel
64 process_signals
10 produce_fastq_outputs
10 reevaluate_tails
20 sort_alignments
10 tabix_index_taginfo
10 update_refined_taginfo_for_mapped
616
rule basecall_ayb:
output: scratch/aybcalls/R5_a1215.fastq.gz
wildcards: read=R5, tile=a1215
threads: 32
rule basecall_ayb:
output: scratch/aybcalls/R5_a2207.fastq.gz
wildcards: read=R5, tile=a2207
threads: 32
rule basecall_ayb:
output: scratch/aybcalls/R5_a1113.fastq.gz
wildcards: read=R5, tile=a1113
threads: 32
AYB Message Log; Created by james; 28 February 2017 20:21
AYB Message Log; Created by james; 28 February 2017 20:21
AYB Message Log; Created by james; 28 February 2017 20:21
Information: Information: Log message output level: Warning
Log message output level: Warning
Information: Log message output level: Warning
Information: Input from directory: /location/sample/
Information: Input format selected: cif
Information: Run-folder selected:
Information: Output to directory: /location/sample/scratch/aybcalls/R5_a1215
Information: Information: Input from directory: /location/sample/
Output format selected: fastq.gz
Information: Information: Input format selected: cif
Number of cycles total selected: 100
Information: Information: Information: Number of distinct data blocks selected: 1
Input from directory: /location/sample/
Run-folder selected:
Information: Information: Information: Input format selected: cif
Number of iterations selected: 5
Information: Output to directory: /location/sample/scratch/aybcalls/R5_a1113
Information: Information: Run-folder selected:
Thin factor selected: 1
Information: Information: Output to directory: /location/sample/scratch/aybcalls/R5_a2207
Thin clusters with 3 or more zero data cycles
Information: Information: Output format selected: fastq.gz
Quality calibration by calibration table selected
Information: Output format selected: fastq.gz
Information: Information: Generalised error value selected: 38
Number of cycles total selected: 100
Number of cycles total selected: 100
Information: Information: Information: Number of distinct data blocks selected: 1
Using 32 thread(s) (32 requested)
Information: Number of distinct data blocks selected: 1
Number of iterations selected: 5
Information: Information: Number of iterations selected: 5
Information: Lane tile range selected: lanes: 1, tiles 1215
Thin factor selected: 1
Information: Information: Thin factor selected: 1
Thin clusters with 3 or more zero data cycles
Information: Information: Thin clusters with 3 or more zero data cycles
Quality calibration by calibration table selected
Information: Quality calibration by calibration table selected
Information: Information: Generalised error value selected: 38
Generalised error value selected: 38
Information: Information: Using 32 thread(s) (32 requested)
Using 32 thread(s) (32 requested)
Information: Information: Lane tile range selected: lanes: 1, tiles 1113
Lane tile range selected: lanes: 1, tiles 2207
/bin/bash: line 1: 35320 Segmentation fault (core dumped) /Applications/folder/work/bin/AYB2/bin/AYB -p 32 -o /location/sample/scratch/aybcalls/R5_a1113 -i /location/sample/ -b R100 -f fastq.gz -r L1T1113
Error in job basecall_ayb while creating output file scratch/aybcalls/R5_a1113.fastq.gz.
RuleException:
CalledProcessError in line 156 of /Applications/folder/work/bin/tailseeker_v316_feb2017/tailseeker/main.py:
Command '/Applications/folder/work/bin/AYB2/bin/AYB -p 32 -o /location/sample/scratch/aybcalls/R5_a1113 -i /location/sample/ -b R100 -f fastq.gz -r L1T1113' returned non-zero exit status 139
File "/Applications/folder/work/bin/tailseeker_v316_feb2017/tailseeker/main.py", line 156, in __rule_basecall_ayb
Will exit after finishing currently running jobs.
/bin/bash: line 1: 35319 Segmentation fault (core dumped) /Applications/folder/work/bin/AYB2/bin/AYB -p 32 -o /location/sample/scratch/aybcalls/R5_a1215 -i /location/sample/ -b R100 -f fastq.gz -r L1T1215
Error in job basecall_ayb while creating output file scratch/aybcalls/R5_a1215.fastq.gz.
RuleException:
CalledProcessError in line 156 of /Applications/folder/work/bin/tailseeker_v316_feb2017/tailseeker/main.py:
Command '/Applications/folder/work/bin/AYB2/bin/AYB -p 32 -o /location/sample/scratch/aybcalls/R5_a1215 -i /location/sample/ -b R100 -f fastq.gz -r L1T1215' returned non-zero exit status 139
File "/Applications/folder/work/bin/tailseeker_v316_feb2017/tailseeker/main.py", line 156, in __rule_basecall_ayb
Will exit after finishing currently running jobs.
/bin/bash: line 1: 35321 Segmentation fault (core dumped) /Applications/folder/work/bin/AYB2/bin/AYB -p 32 -o /location/sample/scratch/aybcalls/R5_a2207 -i /location/sample/ -b R100 -f fastq.gz -r L1T2207
Error in job basecall_ayb while creating output file scratch/aybcalls/R5_a2207.fastq.gz.
RuleException:
CalledProcessError in line 156 of /Applications/folder/work/bin/tailseeker_v316_feb2017/tailseeker/main.py:
Command '/Applications/folder/work/bin/AYB2/bin/AYB -p 32 -o /location/sample/scratch/aybcalls/R5_a2207 -i /location/sample/ -b R100 -f fastq.gz -r L1T2207' returned non-zero exit status 139
File "/Applications/folder/work/bin/tailseeker_v316_feb2017/tailseeker/main.py", line 156, in __rule_basecall_ayb
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message