Job ID = 6459092 SRX = SRX6386764 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:02:04 prefetch.2.10.7: 1) Downloading 'SRR9624496'... 2020-06-21T13:02:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:10:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:10:31 prefetch.2.10.7: 1) 'SRR9624496' was downloaded successfully Read 34135107 spots for SRR9624496/SRR9624496.sra Written 34135107 spots for SRR9624496/SRR9624496.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: 00:07:35 34135107 reads; of these: 34135107 (100.00%) were unpaired; of these: 6905480 (20.23%) aligned 0 times 21122877 (61.88%) aligned exactly 1 time 6106750 (17.89%) aligned >1 times 79.77% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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] 20654864 / 27229627 = 0.7585 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 22:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.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 22:24:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:52: 1000000 INFO @ Sun, 21 Jun 2020 22:24:57: 2000000 INFO @ Sun, 21 Jun 2020 22:25:03: 3000000 INFO @ Sun, 21 Jun 2020 22:25:08: 4000000 INFO @ Sun, 21 Jun 2020 22:25:14: 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 22:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.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 22:25:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:19: 6000000 INFO @ Sun, 21 Jun 2020 22:25:22: 1000000 INFO @ Sun, 21 Jun 2020 22:25:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:25:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:25:23: #1 total tags in treatment: 6574763 INFO @ Sun, 21 Jun 2020 22:25:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:25:23: #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 22:25:23: #1 tags after filtering in treatment: 6574709 INFO @ Sun, 21 Jun 2020 22:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:25:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:25:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:25:24: #2 number of paired peaks: 2646 INFO @ Sun, 21 Jun 2020 22:25:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:25:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:25:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:25:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:25:24: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 22:25:24: #2 alternative fragment length(s) may be 4,136 bps INFO @ Sun, 21 Jun 2020 22:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.05_model.r INFO @ Sun, 21 Jun 2020 22:25:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:25:28: 2000000 INFO @ Sun, 21 Jun 2020 22:25:33: 3000000 INFO @ Sun, 21 Jun 2020 22:25:39: 4000000 INFO @ Sun, 21 Jun 2020 22:25:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:25:45: 5000000 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 22:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.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 22:25:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:25:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:25:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.05_summits.bed INFO @ Sun, 21 Jun 2020 22:25:48: Done! pass1 - making usageList (902 chroms): 1 millis pass2 - checking and writing primary data (5186 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:25:50: 6000000 INFO @ Sun, 21 Jun 2020 22:25:53: 1000000 INFO @ Sun, 21 Jun 2020 22:25:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:25:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:25:54: #1 total tags in treatment: 6574763 INFO @ Sun, 21 Jun 2020 22:25:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:25:54: #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 22:25:54: #1 tags after filtering in treatment: 6574709 INFO @ Sun, 21 Jun 2020 22:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:25:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:25:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:25:55: #2 number of paired peaks: 2646 INFO @ Sun, 21 Jun 2020 22:25:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:25:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:25:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:25:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:25:55: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 22:25:55: #2 alternative fragment length(s) may be 4,136 bps INFO @ Sun, 21 Jun 2020 22:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.10_model.r INFO @ Sun, 21 Jun 2020 22:25:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:25:58: 2000000 INFO @ Sun, 21 Jun 2020 22:26:04: 3000000 INFO @ Sun, 21 Jun 2020 22:26:09: 4000000 INFO @ Sun, 21 Jun 2020 22:26:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:26:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.10_summits.bed INFO @ Sun, 21 Jun 2020 22:26:20: Done! pass1 - making usageList (694 chroms): 1 millis pass2 - checking and writing primary data (2317 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:26:21: 6000000 INFO @ Sun, 21 Jun 2020 22:26:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:26:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:26:24: #1 total tags in treatment: 6574763 INFO @ Sun, 21 Jun 2020 22:26:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:24: #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 22:26:25: #1 tags after filtering in treatment: 6574709 INFO @ Sun, 21 Jun 2020 22:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:25: #2 number of paired peaks: 2646 INFO @ Sun, 21 Jun 2020 22:26:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:26: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 22:26:26: #2 alternative fragment length(s) may be 4,136 bps INFO @ Sun, 21 Jun 2020 22:26:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.20_model.r INFO @ Sun, 21 Jun 2020 22:26:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:26:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386764/SRX6386764.20_summits.bed INFO @ Sun, 21 Jun 2020 22:26:51: Done! pass1 - making usageList (343 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 10 millis CompletedMACS2peakCalling