Job ID = 14519610 SRX = SRX6581722 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 35885766 spots for SRR9825055/SRR9825055.sra Written 35885766 spots for SRR9825055/SRR9825055.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: 00:00:01 Multiseed full-index search: 00:46:55 35885766 reads; of these: 35885766 (100.00%) were unpaired; of these: 944393 (2.63%) aligned 0 times 25377627 (70.72%) aligned exactly 1 time 9563746 (26.65%) aligned >1 times 97.37% overall alignment rate Time searching: 00:46:57 Overall time: 00:46:57 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] 3269930 / 34941373 = 0.0936 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 17:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.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 17:39:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:39:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:39:44: 1000000 INFO @ Sat, 15 Jan 2022 17:39:50: 2000000 INFO @ Sat, 15 Jan 2022 17:39:56: 3000000 INFO @ Sat, 15 Jan 2022 17:40:02: 4000000 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 17:40:08: 5000000 INFO @ Sat, 15 Jan 2022 17:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.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 17:40:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:40:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:40:15: 6000000 INFO @ Sat, 15 Jan 2022 17:40:16: 1000000 INFO @ Sat, 15 Jan 2022 17:40:22: 7000000 INFO @ Sat, 15 Jan 2022 17:40:23: 2000000 INFO @ Sat, 15 Jan 2022 17:40:29: 8000000 INFO @ Sat, 15 Jan 2022 17:40:31: 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 17:40:36: 9000000 INFO @ Sat, 15 Jan 2022 17:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.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 17:40:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:40:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:40:39: 4000000 INFO @ Sat, 15 Jan 2022 17:40:44: 10000000 INFO @ Sat, 15 Jan 2022 17:40:46: 1000000 INFO @ Sat, 15 Jan 2022 17:40:46: 5000000 INFO @ Sat, 15 Jan 2022 17:40:51: 11000000 INFO @ Sat, 15 Jan 2022 17:40:53: 2000000 INFO @ Sat, 15 Jan 2022 17:40:54: 6000000 INFO @ Sat, 15 Jan 2022 17:40:58: 12000000 INFO @ Sat, 15 Jan 2022 17:41:01: 3000000 INFO @ Sat, 15 Jan 2022 17:41:02: 7000000 INFO @ Sat, 15 Jan 2022 17:41:06: 13000000 INFO @ Sat, 15 Jan 2022 17:41:09: 4000000 INFO @ Sat, 15 Jan 2022 17:41:10: 8000000 INFO @ Sat, 15 Jan 2022 17:41:13: 14000000 INFO @ Sat, 15 Jan 2022 17:41:17: 5000000 INFO @ Sat, 15 Jan 2022 17:41:17: 9000000 INFO @ Sat, 15 Jan 2022 17:41:21: 15000000 INFO @ Sat, 15 Jan 2022 17:41:24: 6000000 INFO @ Sat, 15 Jan 2022 17:41:25: 10000000 INFO @ Sat, 15 Jan 2022 17:41:28: 16000000 INFO @ Sat, 15 Jan 2022 17:41:32: 7000000 INFO @ Sat, 15 Jan 2022 17:41:33: 11000000 INFO @ Sat, 15 Jan 2022 17:41:35: 17000000 INFO @ Sat, 15 Jan 2022 17:41:40: 8000000 INFO @ Sat, 15 Jan 2022 17:41:41: 12000000 INFO @ Sat, 15 Jan 2022 17:41:42: 18000000 INFO @ Sat, 15 Jan 2022 17:41:48: 9000000 INFO @ Sat, 15 Jan 2022 17:41:48: 13000000 INFO @ Sat, 15 Jan 2022 17:41:50: 19000000 INFO @ Sat, 15 Jan 2022 17:41:55: 10000000 INFO @ Sat, 15 Jan 2022 17:41:56: 14000000 INFO @ Sat, 15 Jan 2022 17:41:57: 20000000 INFO @ Sat, 15 Jan 2022 17:42:03: 11000000 INFO @ Sat, 15 Jan 2022 17:42:04: 15000000 INFO @ Sat, 15 Jan 2022 17:42:04: 21000000 INFO @ Sat, 15 Jan 2022 17:42:11: 12000000 INFO @ Sat, 15 Jan 2022 17:42:11: 22000000 INFO @ Sat, 15 Jan 2022 17:42:12: 16000000 INFO @ Sat, 15 Jan 2022 17:42:18: 13000000 INFO @ Sat, 15 Jan 2022 17:42:19: 23000000 INFO @ Sat, 15 Jan 2022 17:42:19: 17000000 INFO @ Sat, 15 Jan 2022 17:42:26: 24000000 INFO @ Sat, 15 Jan 2022 17:42:26: 14000000 INFO @ Sat, 15 Jan 2022 17:42:27: 18000000 INFO @ Sat, 15 Jan 2022 17:42:33: 25000000 INFO @ Sat, 15 Jan 2022 17:42:34: 15000000 INFO @ Sat, 15 Jan 2022 17:42:35: 19000000 INFO @ Sat, 15 Jan 2022 17:42:40: 26000000 INFO @ Sat, 15 Jan 2022 17:42:41: 16000000 INFO @ Sat, 15 Jan 2022 17:42:43: 20000000 INFO @ Sat, 15 Jan 2022 17:42:48: 27000000 INFO @ Sat, 15 Jan 2022 17:42:49: 17000000 INFO @ Sat, 15 Jan 2022 17:42:50: 21000000 INFO @ Sat, 15 Jan 2022 17:42:55: 28000000 INFO @ Sat, 15 Jan 2022 17:42:57: 18000000 INFO @ Sat, 15 Jan 2022 17:42:58: 22000000 INFO @ Sat, 15 Jan 2022 17:43:02: 29000000 INFO @ Sat, 15 Jan 2022 17:43:05: 19000000 INFO @ Sat, 15 Jan 2022 17:43:06: 23000000 INFO @ Sat, 15 Jan 2022 17:43:10: 30000000 INFO @ Sat, 15 Jan 2022 17:43:12: 20000000 INFO @ Sat, 15 Jan 2022 17:43:13: 24000000 INFO @ Sat, 15 Jan 2022 17:43:17: 31000000 INFO @ Sat, 15 Jan 2022 17:43:20: 21000000 INFO @ Sat, 15 Jan 2022 17:43:21: 25000000 INFO @ Sat, 15 Jan 2022 17:43:22: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:43:22: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:43:22: #1 total tags in treatment: 31671443 INFO @ Sat, 15 Jan 2022 17:43:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:43:22: #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 17:43:23: #1 tags after filtering in treatment: 31671355 INFO @ Sat, 15 Jan 2022 17:43:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:43:23: #1 finished! INFO @ Sat, 15 Jan 2022 17:43:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:43:25: #2 number of paired peaks: 4947 INFO @ Sat, 15 Jan 2022 17:43:25: start model_add_line... INFO @ Sat, 15 Jan 2022 17:43:26: start X-correlation... INFO @ Sat, 15 Jan 2022 17:43:26: end of X-cor INFO @ Sat, 15 Jan 2022 17:43:26: #2 finished! INFO @ Sat, 15 Jan 2022 17:43:26: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:43:26: #2 alternative fragment length(s) may be 75,553 bps INFO @ Sat, 15 Jan 2022 17:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.05_model.r WARNING @ Sat, 15 Jan 2022 17:43:26: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:43:26: #2 You may need to consider one of the other alternative d(s): 75,553 WARNING @ Sat, 15 Jan 2022 17:43:26: #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 17:43:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:43:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:43:28: 22000000 INFO @ Sat, 15 Jan 2022 17:43:29: 26000000 INFO @ Sat, 15 Jan 2022 17:43:35: 23000000 INFO @ Sat, 15 Jan 2022 17:43:36: 27000000 INFO @ Sat, 15 Jan 2022 17:43:43: 24000000 INFO @ Sat, 15 Jan 2022 17:43:44: 28000000 INFO @ Sat, 15 Jan 2022 17:43:51: 25000000 INFO @ Sat, 15 Jan 2022 17:43:52: 29000000 INFO @ Sat, 15 Jan 2022 17:43:58: 26000000 INFO @ Sat, 15 Jan 2022 17:44:00: 30000000 INFO @ Sat, 15 Jan 2022 17:44:06: 27000000 INFO @ Sat, 15 Jan 2022 17:44:08: 31000000 INFO @ Sat, 15 Jan 2022 17:44:13: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:44:13: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:44:13: #1 total tags in treatment: 31671443 INFO @ Sat, 15 Jan 2022 17:44:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:44:13: #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 17:44:14: #1 tags after filtering in treatment: 31671355 INFO @ Sat, 15 Jan 2022 17:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:44:14: #1 finished! INFO @ Sat, 15 Jan 2022 17:44:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:44:14: 28000000 INFO @ Sat, 15 Jan 2022 17:44:16: #2 number of paired peaks: 4947 INFO @ Sat, 15 Jan 2022 17:44:16: start model_add_line... INFO @ Sat, 15 Jan 2022 17:44:16: start X-correlation... INFO @ Sat, 15 Jan 2022 17:44:16: end of X-cor INFO @ Sat, 15 Jan 2022 17:44:16: #2 finished! INFO @ Sat, 15 Jan 2022 17:44:16: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:44:16: #2 alternative fragment length(s) may be 75,553 bps INFO @ Sat, 15 Jan 2022 17:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.10_model.r WARNING @ Sat, 15 Jan 2022 17:44:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:44:16: #2 You may need to consider one of the other alternative d(s): 75,553 WARNING @ Sat, 15 Jan 2022 17:44:16: #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 17:44:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:44:21: 29000000 INFO @ Sat, 15 Jan 2022 17:44:28: 30000000 INFO @ Sat, 15 Jan 2022 17:44:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:44:35: 31000000 INFO @ Sat, 15 Jan 2022 17:44:40: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:44:40: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:44:40: #1 total tags in treatment: 31671443 INFO @ Sat, 15 Jan 2022 17:44:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:44:40: #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 17:44:40: #1 tags after filtering in treatment: 31671355 INFO @ Sat, 15 Jan 2022 17:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:44:40: #1 finished! INFO @ Sat, 15 Jan 2022 17:44:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:44:40: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:44:43: #2 number of paired peaks: 4947 INFO @ Sat, 15 Jan 2022 17:44:43: start model_add_line... INFO @ Sat, 15 Jan 2022 17:44:43: start X-correlation... INFO @ Sat, 15 Jan 2022 17:44:43: end of X-cor INFO @ Sat, 15 Jan 2022 17:44:43: #2 finished! INFO @ Sat, 15 Jan 2022 17:44:43: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:44:43: #2 alternative fragment length(s) may be 75,553 bps INFO @ Sat, 15 Jan 2022 17:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.20_model.r WARNING @ Sat, 15 Jan 2022 17:44:43: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:44:43: #2 You may need to consider one of the other alternative d(s): 75,553 WARNING @ Sat, 15 Jan 2022 17:44:43: #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 17:44:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.05_summits.bed INFO @ Sat, 15 Jan 2022 17:45:07: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (1715 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:45:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:45:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.10_summits.bed INFO @ Sat, 15 Jan 2022 17:45:57: Done! pass1 - making usageList (44 chroms): 0 millis pass2 - checking and writing primary data (992 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581722/SRX6581722.20_summits.bed INFO @ Sat, 15 Jan 2022 17:46:25: Done! pass1 - making usageList (34 chroms): 0 millis pass2 - checking and writing primary data (543 records, 4 fields): 17 millis CompletedMACS2peakCalling