Job ID = 14518160 SRX = SRX9430829 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 44349667 spots for SRR12978986/SRR12978986.sra Written 44349667 spots for SRR12978986/SRR12978986.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:31:44 44349667 reads; of these: 44349667 (100.00%) were unpaired; of these: 942269 (2.12%) aligned 0 times 31386094 (70.77%) aligned exactly 1 time 12021304 (27.11%) aligned >1 times 97.88% overall alignment rate Time searching: 00:31:49 Overall time: 00:31:49 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 20 files... [bam_rmdupse_core] 1203592 / 43407398 = 0.0277 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 11:06:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.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 11:06:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:06:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:06:57: 1000000 INFO @ Sat, 15 Jan 2022 11:07:02: 2000000 INFO @ Sat, 15 Jan 2022 11:07:08: 3000000 INFO @ Sat, 15 Jan 2022 11:07:13: 4000000 INFO @ Sat, 15 Jan 2022 11:07:18: 5000000 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 11:07:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.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 11:07:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:07:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:07:24: 6000000 INFO @ Sat, 15 Jan 2022 11:07:27: 1000000 INFO @ Sat, 15 Jan 2022 11:07:29: 7000000 INFO @ Sat, 15 Jan 2022 11:07:32: 2000000 INFO @ Sat, 15 Jan 2022 11:07:35: 8000000 INFO @ Sat, 15 Jan 2022 11:07:38: 3000000 INFO @ Sat, 15 Jan 2022 11:07:41: 9000000 INFO @ Sat, 15 Jan 2022 11:07:44: 4000000 INFO @ Sat, 15 Jan 2022 11:07:47: 10000000 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 11:07:50: 5000000 INFO @ Sat, 15 Jan 2022 11:07:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.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 11:07:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:07:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:07:53: 11000000 INFO @ Sat, 15 Jan 2022 11:07:56: 6000000 INFO @ Sat, 15 Jan 2022 11:07:57: 1000000 INFO @ Sat, 15 Jan 2022 11:07:58: 12000000 INFO @ Sat, 15 Jan 2022 11:08:01: 7000000 INFO @ Sat, 15 Jan 2022 11:08:03: 2000000 INFO @ Sat, 15 Jan 2022 11:08:04: 13000000 INFO @ Sat, 15 Jan 2022 11:08:07: 8000000 INFO @ Sat, 15 Jan 2022 11:08:09: 3000000 INFO @ Sat, 15 Jan 2022 11:08:10: 14000000 INFO @ Sat, 15 Jan 2022 11:08:13: 9000000 INFO @ Sat, 15 Jan 2022 11:08:15: 4000000 INFO @ Sat, 15 Jan 2022 11:08:16: 15000000 INFO @ Sat, 15 Jan 2022 11:08:19: 10000000 INFO @ Sat, 15 Jan 2022 11:08:21: 5000000 INFO @ Sat, 15 Jan 2022 11:08:22: 16000000 INFO @ Sat, 15 Jan 2022 11:08:25: 11000000 INFO @ Sat, 15 Jan 2022 11:08:27: 6000000 INFO @ Sat, 15 Jan 2022 11:08:28: 17000000 INFO @ Sat, 15 Jan 2022 11:08:31: 12000000 INFO @ Sat, 15 Jan 2022 11:08:33: 7000000 INFO @ Sat, 15 Jan 2022 11:08:34: 18000000 INFO @ Sat, 15 Jan 2022 11:08:38: 13000000 INFO @ Sat, 15 Jan 2022 11:08:39: 8000000 INFO @ Sat, 15 Jan 2022 11:08:40: 19000000 INFO @ Sat, 15 Jan 2022 11:08:44: 14000000 INFO @ Sat, 15 Jan 2022 11:08:44: 9000000 INFO @ Sat, 15 Jan 2022 11:08:46: 20000000 INFO @ Sat, 15 Jan 2022 11:08:50: 15000000 INFO @ Sat, 15 Jan 2022 11:08:50: 10000000 INFO @ Sat, 15 Jan 2022 11:08:51: 21000000 INFO @ Sat, 15 Jan 2022 11:08:56: 11000000 INFO @ Sat, 15 Jan 2022 11:08:57: 16000000 INFO @ Sat, 15 Jan 2022 11:08:57: 22000000 INFO @ Sat, 15 Jan 2022 11:09:02: 12000000 INFO @ Sat, 15 Jan 2022 11:09:03: 17000000 INFO @ Sat, 15 Jan 2022 11:09:03: 23000000 INFO @ Sat, 15 Jan 2022 11:09:08: 13000000 INFO @ Sat, 15 Jan 2022 11:09:09: 18000000 INFO @ Sat, 15 Jan 2022 11:09:09: 24000000 INFO @ Sat, 15 Jan 2022 11:09:14: 14000000 INFO @ Sat, 15 Jan 2022 11:09:15: 19000000 INFO @ Sat, 15 Jan 2022 11:09:15: 25000000 INFO @ Sat, 15 Jan 2022 11:09:20: 15000000 INFO @ Sat, 15 Jan 2022 11:09:21: 20000000 INFO @ Sat, 15 Jan 2022 11:09:21: 26000000 INFO @ Sat, 15 Jan 2022 11:09:26: 16000000 INFO @ Sat, 15 Jan 2022 11:09:27: 27000000 INFO @ Sat, 15 Jan 2022 11:09:27: 21000000 INFO @ Sat, 15 Jan 2022 11:09:32: 17000000 INFO @ Sat, 15 Jan 2022 11:09:33: 28000000 INFO @ Sat, 15 Jan 2022 11:09:33: 22000000 INFO @ Sat, 15 Jan 2022 11:09:38: 18000000 INFO @ Sat, 15 Jan 2022 11:09:39: 29000000 INFO @ Sat, 15 Jan 2022 11:09:39: 23000000 INFO @ Sat, 15 Jan 2022 11:09:44: 19000000 INFO @ Sat, 15 Jan 2022 11:09:45: 30000000 INFO @ Sat, 15 Jan 2022 11:09:45: 24000000 INFO @ Sat, 15 Jan 2022 11:09:50: 20000000 INFO @ Sat, 15 Jan 2022 11:09:51: 31000000 INFO @ Sat, 15 Jan 2022 11:09:51: 25000000 INFO @ Sat, 15 Jan 2022 11:09:56: 21000000 INFO @ Sat, 15 Jan 2022 11:09:56: 32000000 INFO @ Sat, 15 Jan 2022 11:09:57: 26000000 INFO @ Sat, 15 Jan 2022 11:10:02: 22000000 INFO @ Sat, 15 Jan 2022 11:10:02: 33000000 INFO @ Sat, 15 Jan 2022 11:10:03: 27000000 INFO @ Sat, 15 Jan 2022 11:10:08: 23000000 INFO @ Sat, 15 Jan 2022 11:10:08: 34000000 INFO @ Sat, 15 Jan 2022 11:10:09: 28000000 INFO @ Sat, 15 Jan 2022 11:10:14: 24000000 INFO @ Sat, 15 Jan 2022 11:10:14: 35000000 INFO @ Sat, 15 Jan 2022 11:10:15: 29000000 INFO @ Sat, 15 Jan 2022 11:10:19: 25000000 INFO @ Sat, 15 Jan 2022 11:10:20: 36000000 INFO @ Sat, 15 Jan 2022 11:10:21: 30000000 INFO @ Sat, 15 Jan 2022 11:10:25: 26000000 INFO @ Sat, 15 Jan 2022 11:10:26: 37000000 INFO @ Sat, 15 Jan 2022 11:10:27: 31000000 INFO @ Sat, 15 Jan 2022 11:10:31: 27000000 INFO @ Sat, 15 Jan 2022 11:10:32: 38000000 INFO @ Sat, 15 Jan 2022 11:10:32: 32000000 INFO @ Sat, 15 Jan 2022 11:10:37: 28000000 INFO @ Sat, 15 Jan 2022 11:10:38: 39000000 INFO @ Sat, 15 Jan 2022 11:10:38: 33000000 INFO @ Sat, 15 Jan 2022 11:10:43: 29000000 INFO @ Sat, 15 Jan 2022 11:10:44: 40000000 INFO @ Sat, 15 Jan 2022 11:10:44: 34000000 INFO @ Sat, 15 Jan 2022 11:10:49: 30000000 INFO @ Sat, 15 Jan 2022 11:10:50: 35000000 INFO @ Sat, 15 Jan 2022 11:10:50: 41000000 INFO @ Sat, 15 Jan 2022 11:10:55: 31000000 INFO @ Sat, 15 Jan 2022 11:10:56: 36000000 INFO @ Sat, 15 Jan 2022 11:10:56: 42000000 INFO @ Sat, 15 Jan 2022 11:10:57: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:10:57: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:10:57: #1 total tags in treatment: 42203806 INFO @ Sat, 15 Jan 2022 11:10:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:10:57: #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 11:10:58: #1 tags after filtering in treatment: 42203728 INFO @ Sat, 15 Jan 2022 11:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:10:58: #1 finished! INFO @ Sat, 15 Jan 2022 11:10:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:11:00: 32000000 INFO @ Sat, 15 Jan 2022 11:11:01: #2 number of paired peaks: 4744 INFO @ Sat, 15 Jan 2022 11:11:01: start model_add_line... INFO @ Sat, 15 Jan 2022 11:11:02: 37000000 INFO @ Sat, 15 Jan 2022 11:11:02: start X-correlation... INFO @ Sat, 15 Jan 2022 11:11:02: end of X-cor INFO @ Sat, 15 Jan 2022 11:11:02: #2 finished! INFO @ Sat, 15 Jan 2022 11:11:02: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:11:02: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 15 Jan 2022 11:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.05_model.r WARNING @ Sat, 15 Jan 2022 11:11:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:11:02: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 15 Jan 2022 11:11:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 11:11:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:11:06: 33000000 INFO @ Sat, 15 Jan 2022 11:11:07: 38000000 INFO @ Sat, 15 Jan 2022 11:11:12: 34000000 INFO @ Sat, 15 Jan 2022 11:11:13: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:11:17: 35000000 INFO @ Sat, 15 Jan 2022 11:11:19: 40000000 INFO @ Sat, 15 Jan 2022 11:11:23: 36000000 INFO @ Sat, 15 Jan 2022 11:11:24: 41000000 INFO @ Sat, 15 Jan 2022 11:11:29: 37000000 INFO @ Sat, 15 Jan 2022 11:11:30: 42000000 INFO @ Sat, 15 Jan 2022 11:11:32: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:11:32: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:11:32: #1 total tags in treatment: 42203806 INFO @ Sat, 15 Jan 2022 11:11:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:11:32: #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 11:11:32: #1 tags after filtering in treatment: 42203728 INFO @ Sat, 15 Jan 2022 11:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:11:32: #1 finished! INFO @ Sat, 15 Jan 2022 11:11:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:11:34: 38000000 INFO @ Sat, 15 Jan 2022 11:11:36: #2 number of paired peaks: 4744 INFO @ Sat, 15 Jan 2022 11:11:36: start model_add_line... INFO @ Sat, 15 Jan 2022 11:11:36: start X-correlation... INFO @ Sat, 15 Jan 2022 11:11:36: end of X-cor INFO @ Sat, 15 Jan 2022 11:11:36: #2 finished! INFO @ Sat, 15 Jan 2022 11:11:36: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:11:36: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 15 Jan 2022 11:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.10_model.r WARNING @ Sat, 15 Jan 2022 11:11:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:11:36: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 15 Jan 2022 11:11:36: #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 11:11:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:11:40: 39000000 INFO @ Sat, 15 Jan 2022 11:11:45: 40000000 INFO @ Sat, 15 Jan 2022 11:11:50: 41000000 INFO @ Sat, 15 Jan 2022 11:11:57: 42000000 INFO @ Sat, 15 Jan 2022 11:11:59: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:11:59: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:11:59: #1 total tags in treatment: 42203806 INFO @ Sat, 15 Jan 2022 11:11:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:11:59: #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 11:12:00: #1 tags after filtering in treatment: 42203728 INFO @ Sat, 15 Jan 2022 11:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:12:00: #1 finished! INFO @ Sat, 15 Jan 2022 11:12:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:12:03: #2 number of paired peaks: 4744 INFO @ Sat, 15 Jan 2022 11:12:03: start model_add_line... INFO @ Sat, 15 Jan 2022 11:12:04: start X-correlation... INFO @ Sat, 15 Jan 2022 11:12:04: end of X-cor INFO @ Sat, 15 Jan 2022 11:12:04: #2 finished! INFO @ Sat, 15 Jan 2022 11:12:04: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:12:04: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 15 Jan 2022 11:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.20_model.r WARNING @ Sat, 15 Jan 2022 11:12:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:12:04: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 15 Jan 2022 11:12:04: #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 11:12:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:12:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:13:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.05_summits.bed INFO @ Sat, 15 Jan 2022 11:13:22: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (2026 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:13:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.10_summits.bed INFO @ Sat, 15 Jan 2022 11:13:58: Done! pass1 - making usageList (45 chroms): 0 millis pass2 - checking and writing primary data (1149 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:14:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:14:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:14:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430829/SRX9430829.20_summits.bed INFO @ Sat, 15 Jan 2022 11:14:28: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling