Job ID = 6455241 SRX = SRX287585 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:55:40 prefetch.2.10.7: 1) Downloading 'SRR869728'... 2020-06-21T09:55:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:40 prefetch.2.10.7: 1) 'SRR869728' was downloaded successfully Read 23856669 spots for SRR869728/SRR869728.sra Written 23856669 spots for SRR869728/SRR869728.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:00 23856669 reads; of these: 23856669 (100.00%) were unpaired; of these: 1724030 (7.23%) aligned 0 times 16850738 (70.63%) aligned exactly 1 time 5281901 (22.14%) aligned >1 times 92.77% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6279059 / 22132639 = 0.2837 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:12:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:27: 1000000 INFO @ Sun, 21 Jun 2020 19:12:32: 2000000 INFO @ Sun, 21 Jun 2020 19:12:38: 3000000 INFO @ Sun, 21 Jun 2020 19:12:43: 4000000 INFO @ Sun, 21 Jun 2020 19:12:48: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:12:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:12:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:54: 6000000 INFO @ Sun, 21 Jun 2020 19:12:58: 1000000 INFO @ Sun, 21 Jun 2020 19:13:00: 7000000 INFO @ Sun, 21 Jun 2020 19:13:05: 2000000 INFO @ Sun, 21 Jun 2020 19:13:06: 8000000 INFO @ Sun, 21 Jun 2020 19:13:12: 9000000 INFO @ Sun, 21 Jun 2020 19:13:12: 3000000 INFO @ Sun, 21 Jun 2020 19:13:18: 10000000 INFO @ Sun, 21 Jun 2020 19:13:19: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:13:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:24: 11000000 INFO @ Sun, 21 Jun 2020 19:13:25: 5000000 INFO @ Sun, 21 Jun 2020 19:13:29: 1000000 INFO @ Sun, 21 Jun 2020 19:13:30: 12000000 INFO @ Sun, 21 Jun 2020 19:13:32: 6000000 INFO @ Sun, 21 Jun 2020 19:13:35: 2000000 INFO @ Sun, 21 Jun 2020 19:13:36: 13000000 INFO @ Sun, 21 Jun 2020 19:13:39: 7000000 INFO @ Sun, 21 Jun 2020 19:13:42: 14000000 INFO @ Sun, 21 Jun 2020 19:13:42: 3000000 INFO @ Sun, 21 Jun 2020 19:13:46: 8000000 INFO @ Sun, 21 Jun 2020 19:13:48: 15000000 INFO @ Sun, 21 Jun 2020 19:13:49: 4000000 INFO @ Sun, 21 Jun 2020 19:13:53: 9000000 INFO @ Sun, 21 Jun 2020 19:13:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:53: #1 total tags in treatment: 15853580 INFO @ Sun, 21 Jun 2020 19:13:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:13:54: #1 tags after filtering in treatment: 15853580 INFO @ Sun, 21 Jun 2020 19:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:55: #2 number of paired peaks: 2501 INFO @ Sun, 21 Jun 2020 19:13:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:55: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 19:13:55: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 19:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.05_model.r INFO @ Sun, 21 Jun 2020 19:13:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:56: 5000000 INFO @ Sun, 21 Jun 2020 19:14:00: 10000000 INFO @ Sun, 21 Jun 2020 19:14:03: 6000000 INFO @ Sun, 21 Jun 2020 19:14:07: 11000000 INFO @ Sun, 21 Jun 2020 19:14:10: 7000000 INFO @ Sun, 21 Jun 2020 19:14:13: 12000000 INFO @ Sun, 21 Jun 2020 19:14:17: 8000000 INFO @ Sun, 21 Jun 2020 19:14:20: 13000000 INFO @ Sun, 21 Jun 2020 19:14:24: 9000000 INFO @ Sun, 21 Jun 2020 19:14:27: 14000000 INFO @ Sun, 21 Jun 2020 19:14:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:14:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:34: 15000000 INFO @ Sun, 21 Jun 2020 19:14:37: 11000000 INFO @ Sun, 21 Jun 2020 19:14:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:40: #1 total tags in treatment: 15853580 INFO @ Sun, 21 Jun 2020 19:14:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:14:40: #1 tags after filtering in treatment: 15853580 INFO @ Sun, 21 Jun 2020 19:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:42: #2 number of paired peaks: 2501 INFO @ Sun, 21 Jun 2020 19:14:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:42: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 19:14:42: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 19:14:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.10_model.r INFO @ Sun, 21 Jun 2020 19:14:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:44: 12000000 INFO @ Sun, 21 Jun 2020 19:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:50: Done! pass1 - making usageList (626 chroms): 2 millis pass2 - checking and writing primary data (6001 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:51: 13000000 INFO @ Sun, 21 Jun 2020 19:14:57: 14000000 INFO @ Sun, 21 Jun 2020 19:15:04: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:15:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:09: #1 total tags in treatment: 15853580 INFO @ Sun, 21 Jun 2020 19:15:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:15:10: #1 tags after filtering in treatment: 15853580 INFO @ Sun, 21 Jun 2020 19:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:11: #2 number of paired peaks: 2501 INFO @ Sun, 21 Jun 2020 19:15:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:11: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 19:15:11: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 19:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.20_model.r INFO @ Sun, 21 Jun 2020 19:15:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:37: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (5175 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287585/SRX287585.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:05: Done! pass1 - making usageList (466 chroms): 1 millis pass2 - checking and writing primary data (4353 records, 4 fields): 17 millis CompletedMACS2peakCalling