Job ID = 6454594 SRX = SRX2385057 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:30:59 prefetch.2.10.7: 1) Downloading 'SRR5064688'... 2020-06-21T09:30:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:59 prefetch.2.10.7: 'SRR5064688' is valid 2020-06-21T09:32:59 prefetch.2.10.7: 1) 'SRR5064688' was downloaded successfully 2020-06-21T09:32:59 prefetch.2.10.7: 'SRR5064688' has 0 unresolved dependencies Read 17873738 spots for SRR5064688/SRR5064688.sra Written 17873738 spots for SRR5064688/SRR5064688.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: 00:04:27 17873738 reads; of these: 17873738 (100.00%) were unpaired; of these: 573628 (3.21%) aligned 0 times 14796032 (82.78%) aligned exactly 1 time 2504078 (14.01%) aligned >1 times 96.79% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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 8 files... [bam_rmdupse_core] 1856744 / 17300110 = 0.1073 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 18:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.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 18:42:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:45: 1000000 INFO @ Sun, 21 Jun 2020 18:42:52: 2000000 INFO @ Sun, 21 Jun 2020 18:42:58: 3000000 INFO @ Sun, 21 Jun 2020 18:43:04: 4000000 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 18:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.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 18:43:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:11: 5000000 INFO @ Sun, 21 Jun 2020 18:43:16: 1000000 INFO @ Sun, 21 Jun 2020 18:43:18: 6000000 INFO @ Sun, 21 Jun 2020 18:43:23: 2000000 INFO @ Sun, 21 Jun 2020 18:43:25: 7000000 INFO @ Sun, 21 Jun 2020 18:43:29: 3000000 INFO @ Sun, 21 Jun 2020 18:43:32: 8000000 INFO @ Sun, 21 Jun 2020 18:43:36: 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 18:43:38: 9000000 INFO @ Sun, 21 Jun 2020 18:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.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 18:43:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:43: 5000000 INFO @ Sun, 21 Jun 2020 18:43:45: 10000000 INFO @ Sun, 21 Jun 2020 18:43:49: 1000000 INFO @ Sun, 21 Jun 2020 18:43:50: 6000000 INFO @ Sun, 21 Jun 2020 18:43:53: 11000000 INFO @ Sun, 21 Jun 2020 18:43:56: 2000000 INFO @ Sun, 21 Jun 2020 18:43:57: 7000000 INFO @ Sun, 21 Jun 2020 18:44:00: 12000000 INFO @ Sun, 21 Jun 2020 18:44:04: 3000000 INFO @ Sun, 21 Jun 2020 18:44:04: 8000000 INFO @ Sun, 21 Jun 2020 18:44:07: 13000000 INFO @ Sun, 21 Jun 2020 18:44:11: 4000000 INFO @ Sun, 21 Jun 2020 18:44:11: 9000000 INFO @ Sun, 21 Jun 2020 18:44:14: 14000000 INFO @ Sun, 21 Jun 2020 18:44:18: 5000000 INFO @ Sun, 21 Jun 2020 18:44:19: 10000000 INFO @ Sun, 21 Jun 2020 18:44:21: 15000000 INFO @ Sun, 21 Jun 2020 18:44:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:44:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:44:25: #1 total tags in treatment: 15443366 INFO @ Sun, 21 Jun 2020 18:44:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:25: #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 18:44:25: #1 tags after filtering in treatment: 15443359 INFO @ Sun, 21 Jun 2020 18:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:26: 6000000 INFO @ Sun, 21 Jun 2020 18:44:26: 11000000 INFO @ Sun, 21 Jun 2020 18:44:27: #2 number of paired peaks: 1499 INFO @ Sun, 21 Jun 2020 18:44:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:27: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.05_model.r INFO @ Sun, 21 Jun 2020 18:44:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:33: 12000000 INFO @ Sun, 21 Jun 2020 18:44:33: 7000000 INFO @ Sun, 21 Jun 2020 18:44:40: 13000000 INFO @ Sun, 21 Jun 2020 18:44:41: 8000000 INFO @ Sun, 21 Jun 2020 18:44:47: 14000000 INFO @ Sun, 21 Jun 2020 18:44:48: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:54: 15000000 INFO @ Sun, 21 Jun 2020 18:44:56: 10000000 INFO @ Sun, 21 Jun 2020 18:44:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:44:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:44:57: #1 total tags in treatment: 15443366 INFO @ Sun, 21 Jun 2020 18:44:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:57: #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 18:44:58: #1 tags after filtering in treatment: 15443359 INFO @ Sun, 21 Jun 2020 18:44:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:59: #2 number of paired peaks: 1499 INFO @ Sun, 21 Jun 2020 18:44:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:59: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 18:44:59: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 18:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.10_model.r INFO @ Sun, 21 Jun 2020 18:44:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:03: 11000000 INFO @ Sun, 21 Jun 2020 18:45:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:10: 12000000 INFO @ Sun, 21 Jun 2020 18:45:16: 13000000 INFO @ Sun, 21 Jun 2020 18:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:23: Done! INFO @ Sun, 21 Jun 2020 18:45:23: 14000000 pass1 - making usageList (175 chroms): 2 millis pass2 - checking and writing primary data (6657 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:29: 15000000 INFO @ Sun, 21 Jun 2020 18:45:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:33: #1 total tags in treatment: 15443366 INFO @ Sun, 21 Jun 2020 18:45:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:33: #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 18:45:33: #1 tags after filtering in treatment: 15443359 INFO @ Sun, 21 Jun 2020 18:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:34: #2 number of paired peaks: 1499 INFO @ Sun, 21 Jun 2020 18:45:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:35: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 18:45:35: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 18:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.20_model.r INFO @ Sun, 21 Jun 2020 18:45:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.10_summits.bed INFO @ Sun, 21 Jun 2020 18:45:55: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (4148 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2385057/SRX2385057.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:30: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (1889 records, 4 fields): 8 millis CompletedMACS2peakCalling