Job ID = 14519565 SRX = SRX9963487 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 35675636 spots for SRR13565203/SRR13565203.sra Written 35675636 spots for SRR13565203/SRR13565203.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: 00:00:00 Multiseed full-index search: 00:30:39 35675636 reads; of these: 35675636 (100.00%) were unpaired; of these: 3941621 (11.05%) aligned 0 times 28841942 (80.84%) aligned exactly 1 time 2892073 (8.11%) aligned >1 times 88.95% overall alignment rate Time searching: 00:30:41 Overall time: 00:30:41 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] 12761188 / 31734015 = 0.4021 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 16:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.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 16:55:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:55:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:56:03: 1000000 INFO @ Sat, 15 Jan 2022 16:56:09: 2000000 INFO @ Sat, 15 Jan 2022 16:56:15: 3000000 INFO @ Sat, 15 Jan 2022 16:56:21: 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 16:56:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.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 16:56:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:56:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:56:28: 5000000 INFO @ Sat, 15 Jan 2022 16:56:33: 1000000 INFO @ Sat, 15 Jan 2022 16:56:35: 6000000 INFO @ Sat, 15 Jan 2022 16:56:40: 2000000 INFO @ Sat, 15 Jan 2022 16:56:41: 7000000 INFO @ Sat, 15 Jan 2022 16:56:47: 3000000 INFO @ Sat, 15 Jan 2022 16:56:48: 8000000 INFO @ Sat, 15 Jan 2022 16:56:54: 4000000 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 16:56:55: 9000000 INFO @ Sat, 15 Jan 2022 16:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.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 16:56:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:56:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:57:01: 5000000 INFO @ Sat, 15 Jan 2022 16:57:02: 10000000 INFO @ Sat, 15 Jan 2022 16:57:04: 1000000 INFO @ Sat, 15 Jan 2022 16:57:09: 11000000 INFO @ Sat, 15 Jan 2022 16:57:10: 6000000 INFO @ Sat, 15 Jan 2022 16:57:11: 2000000 INFO @ Sat, 15 Jan 2022 16:57:17: 12000000 INFO @ Sat, 15 Jan 2022 16:57:17: 7000000 INFO @ Sat, 15 Jan 2022 16:57:18: 3000000 INFO @ Sat, 15 Jan 2022 16:57:24: 13000000 INFO @ Sat, 15 Jan 2022 16:57:25: 8000000 INFO @ Sat, 15 Jan 2022 16:57:26: 4000000 INFO @ Sat, 15 Jan 2022 16:57:31: 14000000 INFO @ Sat, 15 Jan 2022 16:57:32: 9000000 INFO @ Sat, 15 Jan 2022 16:57:34: 5000000 INFO @ Sat, 15 Jan 2022 16:57:38: 15000000 INFO @ Sat, 15 Jan 2022 16:57:39: 10000000 INFO @ Sat, 15 Jan 2022 16:57:41: 6000000 INFO @ Sat, 15 Jan 2022 16:57:46: 16000000 INFO @ Sat, 15 Jan 2022 16:57:47: 11000000 INFO @ Sat, 15 Jan 2022 16:57:48: 7000000 INFO @ Sat, 15 Jan 2022 16:57:53: 17000000 INFO @ Sat, 15 Jan 2022 16:57:54: 12000000 INFO @ Sat, 15 Jan 2022 16:57:56: 8000000 INFO @ Sat, 15 Jan 2022 16:58:01: 18000000 INFO @ Sat, 15 Jan 2022 16:58:02: 13000000 INFO @ Sat, 15 Jan 2022 16:58:03: 9000000 INFO @ Sat, 15 Jan 2022 16:58:08: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:58:08: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:58:08: #1 total tags in treatment: 18972827 INFO @ Sat, 15 Jan 2022 16:58:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:58:08: #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 16:58:09: #1 tags after filtering in treatment: 18972570 INFO @ Sat, 15 Jan 2022 16:58:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:58:09: #1 finished! INFO @ Sat, 15 Jan 2022 16:58:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:58:09: 14000000 INFO @ Sat, 15 Jan 2022 16:58:10: 10000000 INFO @ Sat, 15 Jan 2022 16:58:12: #2 number of paired peaks: 37398 INFO @ Sat, 15 Jan 2022 16:58:12: start model_add_line... INFO @ Sat, 15 Jan 2022 16:58:12: start X-correlation... INFO @ Sat, 15 Jan 2022 16:58:12: end of X-cor INFO @ Sat, 15 Jan 2022 16:58:12: #2 finished! INFO @ Sat, 15 Jan 2022 16:58:12: #2 predicted fragment length is 184 bps INFO @ Sat, 15 Jan 2022 16:58:12: #2 alternative fragment length(s) may be 3,184 bps INFO @ Sat, 15 Jan 2022 16:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.05_model.r INFO @ Sat, 15 Jan 2022 16:58:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:58:16: 15000000 INFO @ Sat, 15 Jan 2022 16:58:17: 11000000 INFO @ Sat, 15 Jan 2022 16:58:23: 16000000 INFO @ Sat, 15 Jan 2022 16:58:24: 12000000 INFO @ Sat, 15 Jan 2022 16:58:29: 17000000 INFO @ Sat, 15 Jan 2022 16:58:31: 13000000 INFO @ Sat, 15 Jan 2022 16:58:36: 18000000 INFO @ Sat, 15 Jan 2022 16:58:38: 14000000 INFO @ Sat, 15 Jan 2022 16:58:43: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:58:43: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:58:43: #1 total tags in treatment: 18972827 INFO @ Sat, 15 Jan 2022 16:58:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:58:43: #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 16:58:43: #1 tags after filtering in treatment: 18972570 INFO @ Sat, 15 Jan 2022 16:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:58:43: #1 finished! INFO @ Sat, 15 Jan 2022 16:58:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:58:44: 15000000 INFO @ Sat, 15 Jan 2022 16:58:46: #2 number of paired peaks: 37398 INFO @ Sat, 15 Jan 2022 16:58:46: start model_add_line... INFO @ Sat, 15 Jan 2022 16:58:47: start X-correlation... INFO @ Sat, 15 Jan 2022 16:58:47: end of X-cor INFO @ Sat, 15 Jan 2022 16:58:47: #2 finished! INFO @ Sat, 15 Jan 2022 16:58:47: #2 predicted fragment length is 184 bps INFO @ Sat, 15 Jan 2022 16:58:47: #2 alternative fragment length(s) may be 3,184 bps INFO @ Sat, 15 Jan 2022 16:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.10_model.r INFO @ Sat, 15 Jan 2022 16:58:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:58:50: 16000000 INFO @ Sat, 15 Jan 2022 16:58:56: 17000000 INFO @ Sat, 15 Jan 2022 16:58:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 16:59:03: 18000000 INFO @ Sat, 15 Jan 2022 16:59:09: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:59:09: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:59:09: #1 total tags in treatment: 18972827 INFO @ Sat, 15 Jan 2022 16:59:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:59:09: #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 16:59:10: #1 tags after filtering in treatment: 18972570 INFO @ Sat, 15 Jan 2022 16:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:59:10: #1 finished! INFO @ Sat, 15 Jan 2022 16:59:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:59:13: #2 number of paired peaks: 37398 INFO @ Sat, 15 Jan 2022 16:59:13: start model_add_line... INFO @ Sat, 15 Jan 2022 16:59:13: start X-correlation... INFO @ Sat, 15 Jan 2022 16:59:13: end of X-cor INFO @ Sat, 15 Jan 2022 16:59:13: #2 finished! INFO @ Sat, 15 Jan 2022 16:59:13: #2 predicted fragment length is 184 bps INFO @ Sat, 15 Jan 2022 16:59:13: #2 alternative fragment length(s) may be 3,184 bps INFO @ Sat, 15 Jan 2022 16:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.20_model.r INFO @ Sat, 15 Jan 2022 16:59:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.05_peaks.xls INFO @ Sat, 15 Jan 2022 16:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.05_summits.bed INFO @ Sat, 15 Jan 2022 16:59:23: Done! pass1 - making usageList (121 chroms): 5 millis pass2 - checking and writing primary data (21730 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:59:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 16:59:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.10_peaks.xls INFO @ Sat, 15 Jan 2022 16:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.10_summits.bed INFO @ Sat, 15 Jan 2022 16:59:56: Done! pass1 - making usageList (110 chroms): 4 millis pass2 - checking and writing primary data (19430 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:59:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963487/SRX9963487.20_summits.bed INFO @ Sat, 15 Jan 2022 17:00:21: Done! pass1 - making usageList (98 chroms): 4 millis pass2 - checking and writing primary data (17135 records, 4 fields): 99 millis CompletedMACS2peakCalling