Job ID = 14518169 SRX = SRX9430838 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 40895742 spots for SRR12979003/SRR12979003.sra Written 40895742 spots for SRR12979003/SRR12979003.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:28:45 40895742 reads; of these: 40895742 (100.00%) were unpaired; of these: 833288 (2.04%) aligned 0 times 29009091 (70.93%) aligned exactly 1 time 11053363 (27.03%) aligned >1 times 97.96% overall alignment rate Time searching: 00:28:47 Overall time: 00:28:47 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] 1140369 / 40062454 = 0.0285 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 11:12:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.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 11:12:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:12:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:12:44: 1000000 INFO @ Sat, 15 Jan 2022 11:12:49: 2000000 INFO @ Sat, 15 Jan 2022 11:12:53: 3000000 INFO @ Sat, 15 Jan 2022 11:12:58: 4000000 INFO @ Sat, 15 Jan 2022 11:13:03: 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 11:13:08: 6000000 INFO @ Sat, 15 Jan 2022 11:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.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 11:13:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:13:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:13:13: 7000000 INFO @ Sat, 15 Jan 2022 11:13:14: 1000000 INFO @ Sat, 15 Jan 2022 11:13:18: 8000000 INFO @ Sat, 15 Jan 2022 11:13:19: 2000000 INFO @ Sat, 15 Jan 2022 11:13:23: 9000000 INFO @ Sat, 15 Jan 2022 11:13:24: 3000000 INFO @ Sat, 15 Jan 2022 11:13:28: 10000000 INFO @ Sat, 15 Jan 2022 11:13:29: 4000000 INFO @ Sat, 15 Jan 2022 11:13:33: 11000000 INFO @ Sat, 15 Jan 2022 11:13:34: 5000000 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 11:13:38: 12000000 INFO @ Sat, 15 Jan 2022 11:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.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 11:13:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:13:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:13:39: 6000000 INFO @ Sat, 15 Jan 2022 11:13:43: 13000000 INFO @ Sat, 15 Jan 2022 11:13:45: 7000000 INFO @ Sat, 15 Jan 2022 11:13:45: 1000000 INFO @ Sat, 15 Jan 2022 11:13:49: 14000000 INFO @ Sat, 15 Jan 2022 11:13:50: 8000000 INFO @ Sat, 15 Jan 2022 11:13:51: 2000000 INFO @ Sat, 15 Jan 2022 11:13:54: 15000000 INFO @ Sat, 15 Jan 2022 11:13:55: 9000000 INFO @ Sat, 15 Jan 2022 11:13:56: 3000000 INFO @ Sat, 15 Jan 2022 11:13:59: 16000000 INFO @ Sat, 15 Jan 2022 11:14:00: 10000000 INFO @ Sat, 15 Jan 2022 11:14:02: 4000000 INFO @ Sat, 15 Jan 2022 11:14:04: 17000000 INFO @ Sat, 15 Jan 2022 11:14:06: 11000000 INFO @ Sat, 15 Jan 2022 11:14:08: 5000000 INFO @ Sat, 15 Jan 2022 11:14:10: 18000000 INFO @ Sat, 15 Jan 2022 11:14:11: 12000000 INFO @ Sat, 15 Jan 2022 11:14:14: 6000000 INFO @ Sat, 15 Jan 2022 11:14:15: 19000000 INFO @ Sat, 15 Jan 2022 11:14:16: 13000000 INFO @ Sat, 15 Jan 2022 11:14:20: 7000000 INFO @ Sat, 15 Jan 2022 11:14:20: 20000000 INFO @ Sat, 15 Jan 2022 11:14:21: 14000000 INFO @ Sat, 15 Jan 2022 11:14:26: 21000000 INFO @ Sat, 15 Jan 2022 11:14:26: 8000000 INFO @ Sat, 15 Jan 2022 11:14:27: 15000000 INFO @ Sat, 15 Jan 2022 11:14:31: 22000000 INFO @ Sat, 15 Jan 2022 11:14:32: 16000000 INFO @ Sat, 15 Jan 2022 11:14:32: 9000000 INFO @ Sat, 15 Jan 2022 11:14:36: 23000000 INFO @ Sat, 15 Jan 2022 11:14:37: 17000000 INFO @ Sat, 15 Jan 2022 11:14:38: 10000000 INFO @ Sat, 15 Jan 2022 11:14:42: 24000000 INFO @ Sat, 15 Jan 2022 11:14:43: 18000000 INFO @ Sat, 15 Jan 2022 11:14:44: 11000000 INFO @ Sat, 15 Jan 2022 11:14:47: 25000000 INFO @ Sat, 15 Jan 2022 11:14:48: 19000000 INFO @ Sat, 15 Jan 2022 11:14:51: 12000000 INFO @ Sat, 15 Jan 2022 11:14:52: 26000000 INFO @ Sat, 15 Jan 2022 11:14:53: 20000000 INFO @ Sat, 15 Jan 2022 11:14:56: 13000000 INFO @ Sat, 15 Jan 2022 11:14:57: 27000000 INFO @ Sat, 15 Jan 2022 11:14:58: 21000000 INFO @ Sat, 15 Jan 2022 11:15:02: 14000000 INFO @ Sat, 15 Jan 2022 11:15:03: 28000000 INFO @ Sat, 15 Jan 2022 11:15:04: 22000000 INFO @ Sat, 15 Jan 2022 11:15:08: 29000000 INFO @ Sat, 15 Jan 2022 11:15:08: 15000000 INFO @ Sat, 15 Jan 2022 11:15:09: 23000000 INFO @ Sat, 15 Jan 2022 11:15:13: 30000000 INFO @ Sat, 15 Jan 2022 11:15:14: 24000000 INFO @ Sat, 15 Jan 2022 11:15:14: 16000000 INFO @ Sat, 15 Jan 2022 11:15:19: 31000000 INFO @ Sat, 15 Jan 2022 11:15:19: 25000000 INFO @ Sat, 15 Jan 2022 11:15:20: 17000000 INFO @ Sat, 15 Jan 2022 11:15:24: 32000000 INFO @ Sat, 15 Jan 2022 11:15:25: 26000000 INFO @ Sat, 15 Jan 2022 11:15:26: 18000000 INFO @ Sat, 15 Jan 2022 11:15:29: 33000000 INFO @ Sat, 15 Jan 2022 11:15:30: 27000000 INFO @ Sat, 15 Jan 2022 11:15:32: 19000000 INFO @ Sat, 15 Jan 2022 11:15:34: 34000000 INFO @ Sat, 15 Jan 2022 11:15:35: 28000000 INFO @ Sat, 15 Jan 2022 11:15:38: 20000000 INFO @ Sat, 15 Jan 2022 11:15:40: 35000000 INFO @ Sat, 15 Jan 2022 11:15:41: 29000000 INFO @ Sat, 15 Jan 2022 11:15:44: 21000000 INFO @ Sat, 15 Jan 2022 11:15:45: 36000000 INFO @ Sat, 15 Jan 2022 11:15:46: 30000000 INFO @ Sat, 15 Jan 2022 11:15:49: 22000000 INFO @ Sat, 15 Jan 2022 11:15:50: 37000000 INFO @ Sat, 15 Jan 2022 11:15:51: 31000000 INFO @ Sat, 15 Jan 2022 11:15:55: 23000000 INFO @ Sat, 15 Jan 2022 11:15:56: 38000000 INFO @ Sat, 15 Jan 2022 11:15:56: 32000000 INFO @ Sat, 15 Jan 2022 11:16:01: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:16:01: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:16:01: #1 total tags in treatment: 38922085 INFO @ Sat, 15 Jan 2022 11:16:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:16:01: #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 11:16:01: 24000000 INFO @ Sat, 15 Jan 2022 11:16:02: #1 tags after filtering in treatment: 38922016 INFO @ Sat, 15 Jan 2022 11:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:16:02: #1 finished! INFO @ Sat, 15 Jan 2022 11:16:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:16:02: 33000000 INFO @ Sat, 15 Jan 2022 11:16:05: #2 number of paired peaks: 4568 INFO @ Sat, 15 Jan 2022 11:16:05: start model_add_line... INFO @ Sat, 15 Jan 2022 11:16:05: start X-correlation... INFO @ Sat, 15 Jan 2022 11:16:05: end of X-cor INFO @ Sat, 15 Jan 2022 11:16:05: #2 finished! INFO @ Sat, 15 Jan 2022 11:16:05: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:16:05: #2 alternative fragment length(s) may be 50,511 bps INFO @ Sat, 15 Jan 2022 11:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.05_model.r WARNING @ Sat, 15 Jan 2022 11:16:05: #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 11:16:05: #2 You may need to consider one of the other alternative d(s): 50,511 WARNING @ Sat, 15 Jan 2022 11:16:05: #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 11:16:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:16:07: 34000000 INFO @ Sat, 15 Jan 2022 11:16:07: 25000000 INFO @ Sat, 15 Jan 2022 11:16:12: 35000000 INFO @ Sat, 15 Jan 2022 11:16:13: 26000000 INFO @ Sat, 15 Jan 2022 11:16:17: 36000000 INFO @ Sat, 15 Jan 2022 11:16:18: 27000000 INFO @ Sat, 15 Jan 2022 11:16:22: 37000000 INFO @ Sat, 15 Jan 2022 11:16:24: 28000000 INFO @ Sat, 15 Jan 2022 11:16:28: 38000000 INFO @ Sat, 15 Jan 2022 11:16:30: 29000000 INFO @ Sat, 15 Jan 2022 11:16:33: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:16:33: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:16:33: #1 total tags in treatment: 38922085 INFO @ Sat, 15 Jan 2022 11:16:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:16:33: #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 11:16:34: #1 tags after filtering in treatment: 38922016 INFO @ Sat, 15 Jan 2022 11:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:16:34: #1 finished! INFO @ Sat, 15 Jan 2022 11:16:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:16:36: 30000000 INFO @ Sat, 15 Jan 2022 11:16:37: #2 number of paired peaks: 4568 INFO @ Sat, 15 Jan 2022 11:16:37: start model_add_line... INFO @ Sat, 15 Jan 2022 11:16:37: start X-correlation... INFO @ Sat, 15 Jan 2022 11:16:37: end of X-cor INFO @ Sat, 15 Jan 2022 11:16:37: #2 finished! INFO @ Sat, 15 Jan 2022 11:16:37: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:16:37: #2 alternative fragment length(s) may be 50,511 bps INFO @ Sat, 15 Jan 2022 11:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.10_model.r WARNING @ Sat, 15 Jan 2022 11:16:37: #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 11:16:37: #2 You may need to consider one of the other alternative d(s): 50,511 WARNING @ Sat, 15 Jan 2022 11:16:37: #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 11:16:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:16:41: 31000000 INFO @ Sat, 15 Jan 2022 11:16:47: 32000000 INFO @ Sat, 15 Jan 2022 11:16:53: 33000000 INFO @ Sat, 15 Jan 2022 11:16:58: 34000000 INFO @ Sat, 15 Jan 2022 11:17:04: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:17:10: 36000000 INFO @ Sat, 15 Jan 2022 11:17:15: 37000000 INFO @ Sat, 15 Jan 2022 11:17:21: 38000000 INFO @ Sat, 15 Jan 2022 11:17:26: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:17:26: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:17:26: #1 total tags in treatment: 38922085 INFO @ Sat, 15 Jan 2022 11:17:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:17:26: #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 11:17:27: #1 tags after filtering in treatment: 38922016 INFO @ Sat, 15 Jan 2022 11:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:17:27: #1 finished! INFO @ Sat, 15 Jan 2022 11:17:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:17:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:17:30: #2 number of paired peaks: 4568 INFO @ Sat, 15 Jan 2022 11:17:30: start model_add_line... INFO @ Sat, 15 Jan 2022 11:17:30: start X-correlation... INFO @ Sat, 15 Jan 2022 11:17:30: end of X-cor INFO @ Sat, 15 Jan 2022 11:17:30: #2 finished! INFO @ Sat, 15 Jan 2022 11:17:30: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:17:30: #2 alternative fragment length(s) may be 50,511 bps INFO @ Sat, 15 Jan 2022 11:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.20_model.r WARNING @ Sat, 15 Jan 2022 11:17:30: #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 11:17:30: #2 You may need to consider one of the other alternative d(s): 50,511 WARNING @ Sat, 15 Jan 2022 11:17:30: #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 11:17:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:18:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:18:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.05_summits.bed INFO @ Sat, 15 Jan 2022 11:18:09: Done! pass1 - making usageList (55 chroms): 0 millis pass2 - checking and writing primary data (1923 records, 4 fields): 31 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.10_summits.bed INFO @ Sat, 15 Jan 2022 11:18:41: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1088 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:18:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430838/SRX9430838.20_summits.bed INFO @ Sat, 15 Jan 2022 11:19:37: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 6 millis CompletedMACS2peakCalling