Job ID = 12265076 SRX = SRX2969570 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:16 34279594 reads; of these: 34279594 (100.00%) were unpaired; of these: 2226327 (6.49%) aligned 0 times 29122463 (84.96%) aligned exactly 1 time 2930804 (8.55%) aligned >1 times 93.51% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 24397352 / 32053267 = 0.7612 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 06:21:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:21:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:22:07: 1000000 INFO @ Sat, 03 Apr 2021 06:22:15: 2000000 INFO @ Sat, 03 Apr 2021 06:22:24: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 06:22:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:22:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:22:31: 4000000 INFO @ Sat, 03 Apr 2021 06:22:37: 1000000 INFO @ Sat, 03 Apr 2021 06:22:39: 5000000 INFO @ Sat, 03 Apr 2021 06:22:46: 2000000 INFO @ Sat, 03 Apr 2021 06:22:47: 6000000 INFO @ Sat, 03 Apr 2021 06:22:54: 3000000 INFO @ Sat, 03 Apr 2021 06:22:55: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 06:22:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:22:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:23:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:23:01: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:23:01: #1 total tags in treatment: 7655915 INFO @ Sat, 03 Apr 2021 06:23:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:23:01: #1 tags after filtering in treatment: 7655915 INFO @ Sat, 03 Apr 2021 06:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:23:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:23:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:23:01: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:23:01: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:23:01: start model_add_line... INFO @ Sat, 03 Apr 2021 06:23:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:23:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:23:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:23:02: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 06:23:02: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 03 Apr 2021 06:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.05_model.r WARNING @ Sat, 03 Apr 2021 06:23:02: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:23:02: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 03 Apr 2021 06:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:23:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:23:02: 4000000 INFO @ Sat, 03 Apr 2021 06:23:09: 1000000 INFO @ Sat, 03 Apr 2021 06:23:10: 5000000 INFO @ Sat, 03 Apr 2021 06:23:18: 6000000 INFO @ Sat, 03 Apr 2021 06:23:19: 2000000 INFO @ Sat, 03 Apr 2021 06:23:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:23:25: 7000000 INFO @ Sat, 03 Apr 2021 06:23:28: 3000000 INFO @ Sat, 03 Apr 2021 06:23:31: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:23:31: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:23:31: #1 total tags in treatment: 7655915 INFO @ Sat, 03 Apr 2021 06:23:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:23:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:23:31: #1 tags after filtering in treatment: 7655915 INFO @ Sat, 03 Apr 2021 06:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:23:31: #1 finished! INFO @ Sat, 03 Apr 2021 06:23:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:23:32: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:23:32: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:23:32: start model_add_line... INFO @ Sat, 03 Apr 2021 06:23:32: start X-correlation... INFO @ Sat, 03 Apr 2021 06:23:32: end of X-cor INFO @ Sat, 03 Apr 2021 06:23:32: #2 finished! INFO @ Sat, 03 Apr 2021 06:23:32: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 06:23:32: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 03 Apr 2021 06:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.10_model.r WARNING @ Sat, 03 Apr 2021 06:23:32: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:23:32: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 03 Apr 2021 06:23:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:23:32: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.05_summits.bed INFO @ Sat, 03 Apr 2021 06:23:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6385 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:23:37: 4000000 INFO @ Sat, 03 Apr 2021 06:23:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:23:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:23:54: 6000000 INFO @ Sat, 03 Apr 2021 06:24:03: 7000000 INFO @ Sat, 03 Apr 2021 06:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.10_summits.bed INFO @ Sat, 03 Apr 2021 06:24:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3404 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:24:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:24:09: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:24:09: #1 total tags in treatment: 7655915 INFO @ Sat, 03 Apr 2021 06:24:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:24:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:24:09: #1 tags after filtering in treatment: 7655915 INFO @ Sat, 03 Apr 2021 06:24:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:24:09: #1 finished! INFO @ Sat, 03 Apr 2021 06:24:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:24:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:24:10: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:24:10: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:24:10: start model_add_line... INFO @ Sat, 03 Apr 2021 06:24:10: start X-correlation... INFO @ Sat, 03 Apr 2021 06:24:10: end of X-cor INFO @ Sat, 03 Apr 2021 06:24:10: #2 finished! INFO @ Sat, 03 Apr 2021 06:24:10: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 06:24:10: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 03 Apr 2021 06:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.20_model.r WARNING @ Sat, 03 Apr 2021 06:24:10: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:24:10: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 03 Apr 2021 06:24:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:24:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:24:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:24:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969570/SRX2969570.20_summits.bed INFO @ Sat, 03 Apr 2021 06:24:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1124 records, 4 fields): 5 millis CompletedMACS2peakCalling