Job ID = 6455150 SRX = SRX2804212 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:55 prefetch.2.10.7: 1) Downloading 'SRR5534640'... 2020-06-21T09:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:22 prefetch.2.10.7: 'SRR5534640' is valid 2020-06-21T09:52:22 prefetch.2.10.7: 1) 'SRR5534640' was downloaded successfully 2020-06-21T09:52:22 prefetch.2.10.7: 'SRR5534640' has 0 unresolved dependencies Read 27542937 spots for SRR5534640/SRR5534640.sra Written 27542937 spots for SRR5534640/SRR5534640.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: 00:06:23 27542937 reads; of these: 27542937 (100.00%) were unpaired; of these: 8874716 (32.22%) aligned 0 times 13376178 (48.56%) aligned exactly 1 time 5292043 (19.21%) aligned >1 times 67.78% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 3076308 / 18668221 = 0.1648 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 19:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.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 19:04:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:32: 1000000 INFO @ Sun, 21 Jun 2020 19:04:38: 2000000 INFO @ Sun, 21 Jun 2020 19:04:44: 3000000 INFO @ Sun, 21 Jun 2020 19:04:49: 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 19:04:54: 5000000 INFO @ Sun, 21 Jun 2020 19:04:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.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 19:04:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:00: 6000000 INFO @ Sun, 21 Jun 2020 19:05:02: 1000000 INFO @ Sun, 21 Jun 2020 19:05:06: 7000000 INFO @ Sun, 21 Jun 2020 19:05:08: 2000000 INFO @ Sun, 21 Jun 2020 19:05:11: 8000000 INFO @ Sun, 21 Jun 2020 19:05:13: 3000000 INFO @ Sun, 21 Jun 2020 19:05:17: 9000000 INFO @ Sun, 21 Jun 2020 19:05:19: 4000000 INFO @ Sun, 21 Jun 2020 19:05:22: 10000000 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 19:05:24: 5000000 INFO @ Sun, 21 Jun 2020 19:05:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.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 19:05:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:28: 11000000 INFO @ Sun, 21 Jun 2020 19:05:30: 6000000 INFO @ Sun, 21 Jun 2020 19:05:32: 1000000 INFO @ Sun, 21 Jun 2020 19:05:33: 12000000 INFO @ Sun, 21 Jun 2020 19:05:36: 7000000 INFO @ Sun, 21 Jun 2020 19:05:38: 2000000 INFO @ Sun, 21 Jun 2020 19:05:39: 13000000 INFO @ Sun, 21 Jun 2020 19:05:41: 8000000 INFO @ Sun, 21 Jun 2020 19:05:44: 3000000 INFO @ Sun, 21 Jun 2020 19:05:45: 14000000 INFO @ Sun, 21 Jun 2020 19:05:47: 9000000 INFO @ Sun, 21 Jun 2020 19:05:49: 4000000 INFO @ Sun, 21 Jun 2020 19:05:50: 15000000 INFO @ Sun, 21 Jun 2020 19:05:52: 10000000 INFO @ Sun, 21 Jun 2020 19:05:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:05:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:05:54: #1 total tags in treatment: 15591913 INFO @ Sun, 21 Jun 2020 19:05:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:54: #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 19:05:54: #1 tags after filtering in treatment: 15591912 INFO @ Sun, 21 Jun 2020 19:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:55: 5000000 INFO @ Sun, 21 Jun 2020 19:05:55: #2 number of paired peaks: 1202 INFO @ Sun, 21 Jun 2020 19:05:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:56: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 19:05:56: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 19:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.05_model.r INFO @ Sun, 21 Jun 2020 19:05:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:58: 11000000 INFO @ Sun, 21 Jun 2020 19:06:01: 6000000 INFO @ Sun, 21 Jun 2020 19:06:03: 12000000 INFO @ Sun, 21 Jun 2020 19:06:07: 7000000 INFO @ Sun, 21 Jun 2020 19:06:09: 13000000 INFO @ Sun, 21 Jun 2020 19:06:12: 8000000 INFO @ Sun, 21 Jun 2020 19:06:15: 14000000 INFO @ Sun, 21 Jun 2020 19:06:18: 9000000 INFO @ Sun, 21 Jun 2020 19:06:20: 15000000 INFO @ Sun, 21 Jun 2020 19:06:24: 10000000 INFO @ Sun, 21 Jun 2020 19:06:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:06:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:06:24: #1 total tags in treatment: 15591913 INFO @ Sun, 21 Jun 2020 19:06:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:24: #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 19:06:24: #1 tags after filtering in treatment: 15591912 INFO @ Sun, 21 Jun 2020 19:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:26: #2 number of paired peaks: 1202 INFO @ Sun, 21 Jun 2020 19:06:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:26: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 19:06:26: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 19:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.10_model.r INFO @ Sun, 21 Jun 2020 19:06:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:30: 11000000 INFO @ Sun, 21 Jun 2020 19:06:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:35: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:06:41: 13000000 INFO @ Sun, 21 Jun 2020 19:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:46: Done! pass1 - making usageList (704 chroms): 1 millis pass2 - checking and writing primary data (4924 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:47: 14000000 INFO @ Sun, 21 Jun 2020 19:06:52: 15000000 INFO @ Sun, 21 Jun 2020 19:06:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:06:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:06:56: #1 total tags in treatment: 15591913 INFO @ Sun, 21 Jun 2020 19:06:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:56: #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 19:06:56: #1 tags after filtering in treatment: 15591912 INFO @ Sun, 21 Jun 2020 19:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:57: #2 number of paired peaks: 1202 INFO @ Sun, 21 Jun 2020 19:06:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:58: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 19:06:58: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 19:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.20_model.r INFO @ Sun, 21 Jun 2020 19:06:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:16: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (3975 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804212/SRX2804212.20_summits.bed INFO @ Sun, 21 Jun 2020 19:07:49: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (2906 records, 4 fields): 17 millis CompletedMACS2peakCalling