Job ID = 14518874 SRX = ERX5409220 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 40206458 spots for ERR5693766/ERR5693766.sra Written 40206458 spots for ERR5693766/ERR5693766.sra 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:36:06 40206458 reads; of these: 40206458 (100.00%) were unpaired; of these: 1392420 (3.46%) aligned 0 times 28575497 (71.07%) aligned exactly 1 time 10238541 (25.46%) aligned >1 times 96.54% overall alignment rate Time searching: 00:36:09 Overall time: 00:36:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 2227752 / 38814038 = 0.0574 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 @ Sat, 15 Jan 2022 13:26:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Jan 2022 13:26:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 13:26:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 13:26:42: 1000000 INFO @ Sat, 15 Jan 2022 13:26:49: 2000000 INFO @ Sat, 15 Jan 2022 13:26:57: 3000000 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 @ Sat, 15 Jan 2022 13:27:04: 4000000 INFO @ Sat, 15 Jan 2022 13:27:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Jan 2022 13:27:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 13:27:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 13:27:12: 5000000 INFO @ Sat, 15 Jan 2022 13:27:13: 1000000 INFO @ Sat, 15 Jan 2022 13:27:20: 6000000 INFO @ Sat, 15 Jan 2022 13:27:21: 2000000 INFO @ Sat, 15 Jan 2022 13:27:28: 7000000 INFO @ Sat, 15 Jan 2022 13:27:29: 3000000 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 @ Sat, 15 Jan 2022 13:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Jan 2022 13:27:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 13:27:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 13:27:36: 8000000 INFO @ Sat, 15 Jan 2022 13:27:37: 4000000 INFO @ Sat, 15 Jan 2022 13:27:44: 1000000 INFO @ Sat, 15 Jan 2022 13:27:44: 9000000 INFO @ Sat, 15 Jan 2022 13:27:45: 5000000 INFO @ Sat, 15 Jan 2022 13:27:53: 2000000 INFO @ Sat, 15 Jan 2022 13:27:53: 10000000 INFO @ Sat, 15 Jan 2022 13:27:54: 6000000 INFO @ Sat, 15 Jan 2022 13:28:01: 11000000 INFO @ Sat, 15 Jan 2022 13:28:02: 3000000 INFO @ Sat, 15 Jan 2022 13:28:02: 7000000 INFO @ Sat, 15 Jan 2022 13:28:10: 12000000 INFO @ Sat, 15 Jan 2022 13:28:11: 8000000 INFO @ Sat, 15 Jan 2022 13:28:11: 4000000 INFO @ Sat, 15 Jan 2022 13:28:18: 13000000 INFO @ Sat, 15 Jan 2022 13:28:19: 9000000 INFO @ Sat, 15 Jan 2022 13:28:20: 5000000 INFO @ Sat, 15 Jan 2022 13:28:27: 14000000 INFO @ Sat, 15 Jan 2022 13:28:27: 10000000 INFO @ Sat, 15 Jan 2022 13:28:29: 6000000 INFO @ Sat, 15 Jan 2022 13:28:35: 15000000 INFO @ Sat, 15 Jan 2022 13:28:36: 11000000 INFO @ Sat, 15 Jan 2022 13:28:37: 7000000 INFO @ Sat, 15 Jan 2022 13:28:43: 16000000 INFO @ Sat, 15 Jan 2022 13:28:44: 12000000 INFO @ Sat, 15 Jan 2022 13:28:46: 8000000 INFO @ Sat, 15 Jan 2022 13:28:52: 17000000 INFO @ Sat, 15 Jan 2022 13:28:52: 13000000 INFO @ Sat, 15 Jan 2022 13:28:55: 9000000 INFO @ Sat, 15 Jan 2022 13:29:00: 18000000 INFO @ Sat, 15 Jan 2022 13:29:01: 14000000 INFO @ Sat, 15 Jan 2022 13:29:04: 10000000 INFO @ Sat, 15 Jan 2022 13:29:08: 19000000 INFO @ Sat, 15 Jan 2022 13:29:10: 15000000 INFO @ Sat, 15 Jan 2022 13:29:13: 11000000 INFO @ Sat, 15 Jan 2022 13:29:17: 20000000 INFO @ Sat, 15 Jan 2022 13:29:19: 16000000 INFO @ Sat, 15 Jan 2022 13:29:22: 12000000 INFO @ Sat, 15 Jan 2022 13:29:25: 21000000 INFO @ Sat, 15 Jan 2022 13:29:27: 17000000 INFO @ Sat, 15 Jan 2022 13:29:31: 13000000 INFO @ Sat, 15 Jan 2022 13:29:34: 22000000 INFO @ Sat, 15 Jan 2022 13:29:36: 18000000 INFO @ Sat, 15 Jan 2022 13:29:40: 14000000 INFO @ Sat, 15 Jan 2022 13:29:43: 23000000 INFO @ Sat, 15 Jan 2022 13:29:44: 19000000 INFO @ Sat, 15 Jan 2022 13:29:48: 15000000 INFO @ Sat, 15 Jan 2022 13:29:53: 20000000 INFO @ Sat, 15 Jan 2022 13:29:53: 24000000 INFO @ Sat, 15 Jan 2022 13:29:57: 16000000 INFO @ Sat, 15 Jan 2022 13:30:01: 21000000 INFO @ Sat, 15 Jan 2022 13:30:02: 25000000 INFO @ Sat, 15 Jan 2022 13:30:06: 17000000 INFO @ Sat, 15 Jan 2022 13:30:10: 22000000 INFO @ Sat, 15 Jan 2022 13:30:12: 26000000 INFO @ Sat, 15 Jan 2022 13:30:15: 18000000 INFO @ Sat, 15 Jan 2022 13:30:18: 23000000 INFO @ Sat, 15 Jan 2022 13:30:22: 27000000 INFO @ Sat, 15 Jan 2022 13:30:23: 19000000 INFO @ Sat, 15 Jan 2022 13:30:27: 24000000 INFO @ Sat, 15 Jan 2022 13:30:31: 28000000 INFO @ Sat, 15 Jan 2022 13:30:32: 20000000 INFO @ Sat, 15 Jan 2022 13:30:36: 25000000 INFO @ Sat, 15 Jan 2022 13:30:40: 21000000 INFO @ Sat, 15 Jan 2022 13:30:41: 29000000 INFO @ Sat, 15 Jan 2022 13:30:44: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 13:30:49: 22000000 INFO @ Sat, 15 Jan 2022 13:30:49: 30000000 INFO @ Sat, 15 Jan 2022 13:30:53: 27000000 INFO @ Sat, 15 Jan 2022 13:30:58: 23000000 INFO @ Sat, 15 Jan 2022 13:30:58: 31000000 INFO @ Sat, 15 Jan 2022 13:31:02: 28000000 INFO @ Sat, 15 Jan 2022 13:31:06: 32000000 INFO @ Sat, 15 Jan 2022 13:31:06: 24000000 INFO @ Sat, 15 Jan 2022 13:31:10: 29000000 INFO @ Sat, 15 Jan 2022 13:31:14: 33000000 INFO @ Sat, 15 Jan 2022 13:31:15: 25000000 INFO @ Sat, 15 Jan 2022 13:31:19: 30000000 INFO @ Sat, 15 Jan 2022 13:31:22: 34000000 INFO @ Sat, 15 Jan 2022 13:31:24: 26000000 INFO @ Sat, 15 Jan 2022 13:31:28: 31000000 INFO @ Sat, 15 Jan 2022 13:31:31: 35000000 INFO @ Sat, 15 Jan 2022 13:31:33: 27000000 INFO @ Sat, 15 Jan 2022 13:31:36: 32000000 INFO @ Sat, 15 Jan 2022 13:31:39: 36000000 INFO @ Sat, 15 Jan 2022 13:31:41: 28000000 INFO @ Sat, 15 Jan 2022 13:31:44: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 13:31:44: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 13:31:44: #1 total tags in treatment: 36586286 INFO @ Sat, 15 Jan 2022 13:31:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 13:31:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 13:31:45: #1 tags after filtering in treatment: 36586201 INFO @ Sat, 15 Jan 2022 13:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 13:31:45: #1 finished! INFO @ Sat, 15 Jan 2022 13:31:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 13:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 13:31:45: 33000000 INFO @ Sat, 15 Jan 2022 13:31:48: #2 number of paired peaks: 5926 INFO @ Sat, 15 Jan 2022 13:31:48: start model_add_line... INFO @ Sat, 15 Jan 2022 13:31:48: start X-correlation... INFO @ Sat, 15 Jan 2022 13:31:48: end of X-cor INFO @ Sat, 15 Jan 2022 13:31:48: #2 finished! INFO @ Sat, 15 Jan 2022 13:31:48: #2 predicted fragment length is 78 bps INFO @ Sat, 15 Jan 2022 13:31:48: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 15 Jan 2022 13:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.05_model.r WARNING @ Sat, 15 Jan 2022 13:31:49: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 13:31:49: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 15 Jan 2022 13:31:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 13:31:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 13:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 13:31:50: 29000000 INFO @ Sat, 15 Jan 2022 13:31:54: 34000000 INFO @ Sat, 15 Jan 2022 13:31:59: 30000000 INFO @ Sat, 15 Jan 2022 13:32:02: 35000000 INFO @ Sat, 15 Jan 2022 13:32:09: 31000000 INFO @ Sat, 15 Jan 2022 13:32:10: 36000000 INFO @ Sat, 15 Jan 2022 13:32:15: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 13:32:15: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 13:32:15: #1 total tags in treatment: 36586286 INFO @ Sat, 15 Jan 2022 13:32:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 13:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 13:32:16: #1 tags after filtering in treatment: 36586201 INFO @ Sat, 15 Jan 2022 13:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 13:32:16: #1 finished! INFO @ Sat, 15 Jan 2022 13:32:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 13:32:16: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 13:32:18: 32000000 INFO @ Sat, 15 Jan 2022 13:32:19: #2 number of paired peaks: 5926 INFO @ Sat, 15 Jan 2022 13:32:19: start model_add_line... INFO @ Sat, 15 Jan 2022 13:32:19: start X-correlation... INFO @ Sat, 15 Jan 2022 13:32:19: end of X-cor INFO @ Sat, 15 Jan 2022 13:32:19: #2 finished! INFO @ Sat, 15 Jan 2022 13:32:19: #2 predicted fragment length is 78 bps INFO @ Sat, 15 Jan 2022 13:32:19: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 15 Jan 2022 13:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.10_model.r WARNING @ Sat, 15 Jan 2022 13:32:19: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 13:32:19: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 15 Jan 2022 13:32:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 13:32:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 13:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 13:32:27: 33000000 INFO @ Sat, 15 Jan 2022 13:32:36: 34000000 INFO @ Sat, 15 Jan 2022 13:32:45: 35000000 INFO @ Sat, 15 Jan 2022 13:32:53: 36000000 INFO @ Sat, 15 Jan 2022 13:32:59: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 13:32:59: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 13:32:59: #1 total tags in treatment: 36586286 INFO @ Sat, 15 Jan 2022 13:32:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 13:32:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 13:32:59: #1 tags after filtering in treatment: 36586201 INFO @ Sat, 15 Jan 2022 13:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 13:32:59: #1 finished! INFO @ Sat, 15 Jan 2022 13:32:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 13:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 13:33:02: #2 number of paired peaks: 5926 INFO @ Sat, 15 Jan 2022 13:33:02: start model_add_line... INFO @ Sat, 15 Jan 2022 13:33:03: start X-correlation... INFO @ Sat, 15 Jan 2022 13:33:03: end of X-cor INFO @ Sat, 15 Jan 2022 13:33:03: #2 finished! INFO @ Sat, 15 Jan 2022 13:33:03: #2 predicted fragment length is 78 bps INFO @ Sat, 15 Jan 2022 13:33:03: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 15 Jan 2022 13:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.20_model.r WARNING @ Sat, 15 Jan 2022 13:33:03: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 13:33:03: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 15 Jan 2022 13:33:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 13:33:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 13:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 13:33:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 13:33:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 13:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.05_peaks.xls INFO @ Sat, 15 Jan 2022 13:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 13:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.05_summits.bed INFO @ Sat, 15 Jan 2022 13:33:46: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (2936 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 13:34:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.10_peaks.xls INFO @ Sat, 15 Jan 2022 13:34:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 13:34:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.10_summits.bed INFO @ Sat, 15 Jan 2022 13:34:21: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1415 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 13:34:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 13:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.20_peaks.xls INFO @ Sat, 15 Jan 2022 13:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 13:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX5409220/ERX5409220.20_summits.bed INFO @ Sat, 15 Jan 2022 13:35:06: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (649 records, 4 fields): 3 millis CompletedMACS2peakCalling