Job ID = 14159105 SRX = DRX184552 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: 00:06:08 28391575 reads; of these: 28391575 (100.00%) were unpaired; of these: 3013622 (10.61%) aligned 0 times 20424932 (71.94%) aligned exactly 1 time 4953021 (17.45%) aligned >1 times 89.39% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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 12 files... [bam_rmdupse_core] 5923382 / 25377953 = 0.2334 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.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 @ Wed, 08 Dec 2021 19:36:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:36:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:36:43: 1000000 INFO @ Wed, 08 Dec 2021 19:36:47: 2000000 INFO @ Wed, 08 Dec 2021 19:36:52: 3000000 INFO @ Wed, 08 Dec 2021 19:36:57: 4000000 INFO @ Wed, 08 Dec 2021 19:37:01: 5000000 INFO @ Wed, 08 Dec 2021 19:37:06: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.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 @ Wed, 08 Dec 2021 19:37:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:37:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:37:10: 7000000 INFO @ Wed, 08 Dec 2021 19:37:12: 1000000 INFO @ Wed, 08 Dec 2021 19:37:15: 8000000 INFO @ Wed, 08 Dec 2021 19:37:17: 2000000 INFO @ Wed, 08 Dec 2021 19:37:20: 9000000 INFO @ Wed, 08 Dec 2021 19:37:22: 3000000 INFO @ Wed, 08 Dec 2021 19:37:24: 10000000 INFO @ Wed, 08 Dec 2021 19:37:26: 4000000 INFO @ Wed, 08 Dec 2021 19:37:29: 11000000 INFO @ Wed, 08 Dec 2021 19:37:31: 5000000 INFO @ Wed, 08 Dec 2021 19:37:34: 12000000 INFO @ Wed, 08 Dec 2021 19:37:36: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.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 @ Wed, 08 Dec 2021 19:37:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:37:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:37:38: 13000000 INFO @ Wed, 08 Dec 2021 19:37:40: 7000000 INFO @ Wed, 08 Dec 2021 19:37:43: 1000000 INFO @ Wed, 08 Dec 2021 19:37:43: 14000000 INFO @ Wed, 08 Dec 2021 19:37:45: 8000000 INFO @ Wed, 08 Dec 2021 19:37:47: 2000000 INFO @ Wed, 08 Dec 2021 19:37:48: 15000000 INFO @ Wed, 08 Dec 2021 19:37:50: 9000000 INFO @ Wed, 08 Dec 2021 19:37:52: 3000000 INFO @ Wed, 08 Dec 2021 19:37:53: 16000000 INFO @ Wed, 08 Dec 2021 19:37:54: 10000000 INFO @ Wed, 08 Dec 2021 19:37:57: 4000000 INFO @ Wed, 08 Dec 2021 19:37:57: 17000000 INFO @ Wed, 08 Dec 2021 19:37:59: 11000000 INFO @ Wed, 08 Dec 2021 19:38:01: 5000000 INFO @ Wed, 08 Dec 2021 19:38:02: 18000000 INFO @ Wed, 08 Dec 2021 19:38:03: 12000000 INFO @ Wed, 08 Dec 2021 19:38:06: 6000000 INFO @ Wed, 08 Dec 2021 19:38:07: 19000000 INFO @ Wed, 08 Dec 2021 19:38:08: 13000000 INFO @ Wed, 08 Dec 2021 19:38:09: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 19:38:09: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 19:38:09: #1 total tags in treatment: 19454571 INFO @ Wed, 08 Dec 2021 19:38:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:38:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:38:09: #1 tags after filtering in treatment: 19454571 INFO @ Wed, 08 Dec 2021 19:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 19:38:09: #1 finished! INFO @ Wed, 08 Dec 2021 19:38:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:38:10: #2 number of paired peaks: 174 WARNING @ Wed, 08 Dec 2021 19:38:10: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Wed, 08 Dec 2021 19:38:10: start model_add_line... INFO @ Wed, 08 Dec 2021 19:38:10: start X-correlation... INFO @ Wed, 08 Dec 2021 19:38:11: end of X-cor INFO @ Wed, 08 Dec 2021 19:38:11: #2 finished! INFO @ Wed, 08 Dec 2021 19:38:11: #2 predicted fragment length is 181 bps INFO @ Wed, 08 Dec 2021 19:38:11: #2 alternative fragment length(s) may be 2,48,89,132,151,181,195,239 bps INFO @ Wed, 08 Dec 2021 19:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.05_model.r INFO @ Wed, 08 Dec 2021 19:38:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:38:11: 7000000 INFO @ Wed, 08 Dec 2021 19:38:13: 14000000 INFO @ Wed, 08 Dec 2021 19:38:16: 8000000 INFO @ Wed, 08 Dec 2021 19:38:18: 15000000 INFO @ Wed, 08 Dec 2021 19:38:20: 9000000 INFO @ Wed, 08 Dec 2021 19:38:22: 16000000 INFO @ Wed, 08 Dec 2021 19:38:25: 10000000 INFO @ Wed, 08 Dec 2021 19:38:27: 17000000 INFO @ Wed, 08 Dec 2021 19:38:30: 11000000 INFO @ Wed, 08 Dec 2021 19:38:32: 18000000 INFO @ Wed, 08 Dec 2021 19:38:34: 12000000 INFO @ Wed, 08 Dec 2021 19:38:36: 19000000 INFO @ Wed, 08 Dec 2021 19:38:38: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 19:38:38: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 19:38:38: #1 total tags in treatment: 19454571 INFO @ Wed, 08 Dec 2021 19:38:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:38:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:38:39: #1 tags after filtering in treatment: 19454571 INFO @ Wed, 08 Dec 2021 19:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 19:38:39: #1 finished! INFO @ Wed, 08 Dec 2021 19:38:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:38:39: 13000000 INFO @ Wed, 08 Dec 2021 19:38:40: #2 number of paired peaks: 174 WARNING @ Wed, 08 Dec 2021 19:38:40: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Wed, 08 Dec 2021 19:38:40: start model_add_line... INFO @ Wed, 08 Dec 2021 19:38:40: start X-correlation... INFO @ Wed, 08 Dec 2021 19:38:40: end of X-cor INFO @ Wed, 08 Dec 2021 19:38:40: #2 finished! INFO @ Wed, 08 Dec 2021 19:38:40: #2 predicted fragment length is 181 bps INFO @ Wed, 08 Dec 2021 19:38:40: #2 alternative fragment length(s) may be 2,48,89,132,151,181,195,239 bps INFO @ Wed, 08 Dec 2021 19:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.10_model.r INFO @ Wed, 08 Dec 2021 19:38:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:38:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:38:44: 14000000 INFO @ Wed, 08 Dec 2021 19:38:49: 15000000 INFO @ Wed, 08 Dec 2021 19:38:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:38:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:38:58: 17000000 INFO @ Wed, 08 Dec 2021 19:39:03: 18000000 INFO @ Wed, 08 Dec 2021 19:39:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:39:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:39:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.05_summits.bed INFO @ Wed, 08 Dec 2021 19:39:07: Done! INFO @ Wed, 08 Dec 2021 19:39:07: 19000000 pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11443 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:39:09: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 19:39:09: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 19:39:09: #1 total tags in treatment: 19454571 INFO @ Wed, 08 Dec 2021 19:39:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:39:10: #1 tags after filtering in treatment: 19454571 INFO @ Wed, 08 Dec 2021 19:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 19:39:10: #1 finished! INFO @ Wed, 08 Dec 2021 19:39:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:39:11: #2 number of paired peaks: 174 WARNING @ Wed, 08 Dec 2021 19:39:11: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Wed, 08 Dec 2021 19:39:11: start model_add_line... INFO @ Wed, 08 Dec 2021 19:39:11: start X-correlation... INFO @ Wed, 08 Dec 2021 19:39:11: end of X-cor INFO @ Wed, 08 Dec 2021 19:39:11: #2 finished! INFO @ Wed, 08 Dec 2021 19:39:11: #2 predicted fragment length is 181 bps INFO @ Wed, 08 Dec 2021 19:39:11: #2 alternative fragment length(s) may be 2,48,89,132,151,181,195,239 bps INFO @ Wed, 08 Dec 2021 19:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.20_model.r INFO @ Wed, 08 Dec 2021 19:39:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:39:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:39:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:39:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:39:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.10_summits.bed INFO @ Wed, 08 Dec 2021 19:39:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6885 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:39:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:40:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/DRX184552/DRX184552.20_summits.bed INFO @ Wed, 08 Dec 2021 19:40:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2504 records, 4 fields): 3 millis CompletedMACS2peakCalling