Job ID = 6457842 SRX = SRX4801806 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:04:53 prefetch.2.10.7: 1) Downloading 'SRR7968391'... 2020-06-21T12:04:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:22 prefetch.2.10.7: 1) 'SRR7968391' was downloaded successfully Read 18371422 spots for SRR7968391/SRR7968391.sra Written 18371422 spots for SRR7968391/SRR7968391.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:05 18371422 reads; of these: 18371422 (100.00%) were unpaired; of these: 501194 (2.73%) aligned 0 times 12282249 (66.86%) aligned exactly 1 time 5587979 (30.42%) aligned >1 times 97.27% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 2326369 / 17870228 = 0.1302 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 21:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.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 21:20:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:25: 1000000 INFO @ Sun, 21 Jun 2020 21:20:31: 2000000 INFO @ Sun, 21 Jun 2020 21:20:37: 3000000 INFO @ Sun, 21 Jun 2020 21:20:42: 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 21:20:48: 5000000 INFO @ Sun, 21 Jun 2020 21:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.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 21:20:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:54: 6000000 INFO @ Sun, 21 Jun 2020 21:20:56: 1000000 INFO @ Sun, 21 Jun 2020 21:20:59: 7000000 INFO @ Sun, 21 Jun 2020 21:21:02: 2000000 INFO @ Sun, 21 Jun 2020 21:21:05: 8000000 INFO @ Sun, 21 Jun 2020 21:21:08: 3000000 INFO @ Sun, 21 Jun 2020 21:21:11: 9000000 INFO @ Sun, 21 Jun 2020 21:21:14: 4000000 INFO @ Sun, 21 Jun 2020 21:21:16: 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 21:21:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.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 21:21:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:20: 5000000 INFO @ Sun, 21 Jun 2020 21:21:22: 11000000 INFO @ Sun, 21 Jun 2020 21:21:25: 6000000 INFO @ Sun, 21 Jun 2020 21:21:26: 1000000 INFO @ Sun, 21 Jun 2020 21:21:28: 12000000 INFO @ Sun, 21 Jun 2020 21:21:31: 7000000 INFO @ Sun, 21 Jun 2020 21:21:32: 2000000 INFO @ Sun, 21 Jun 2020 21:21:34: 13000000 INFO @ Sun, 21 Jun 2020 21:21:37: 8000000 INFO @ Sun, 21 Jun 2020 21:21:38: 3000000 INFO @ Sun, 21 Jun 2020 21:21:40: 14000000 INFO @ Sun, 21 Jun 2020 21:21:43: 9000000 INFO @ Sun, 21 Jun 2020 21:21:44: 4000000 INFO @ Sun, 21 Jun 2020 21:21:46: 15000000 INFO @ Sun, 21 Jun 2020 21:21:49: 10000000 INFO @ Sun, 21 Jun 2020 21:21:50: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:21:50: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:21:50: #1 total tags in treatment: 15543859 INFO @ Sun, 21 Jun 2020 21:21:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:50: #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 21:21:50: 5000000 INFO @ Sun, 21 Jun 2020 21:21:50: #1 tags after filtering in treatment: 15543757 INFO @ Sun, 21 Jun 2020 21:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:51: #2 number of paired peaks: 1707 INFO @ Sun, 21 Jun 2020 21:21:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:52: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:21:52: #2 alternative fragment length(s) may be 4,143 bps INFO @ Sun, 21 Jun 2020 21:21:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.05_model.r INFO @ Sun, 21 Jun 2020 21:21:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:55: 11000000 INFO @ Sun, 21 Jun 2020 21:21:56: 6000000 INFO @ Sun, 21 Jun 2020 21:22:01: 12000000 INFO @ Sun, 21 Jun 2020 21:22:02: 7000000 INFO @ Sun, 21 Jun 2020 21:22:07: 13000000 INFO @ Sun, 21 Jun 2020 21:22:08: 8000000 INFO @ Sun, 21 Jun 2020 21:22:13: 9000000 INFO @ Sun, 21 Jun 2020 21:22:13: 14000000 INFO @ Sun, 21 Jun 2020 21:22:19: 10000000 INFO @ Sun, 21 Jun 2020 21:22:20: 15000000 INFO @ Sun, 21 Jun 2020 21:22:23: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:22:23: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:22:23: #1 total tags in treatment: 15543859 INFO @ Sun, 21 Jun 2020 21:22:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:23: #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 21:22:24: #1 tags after filtering in treatment: 15543757 INFO @ Sun, 21 Jun 2020 21:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:25: #2 number of paired peaks: 1707 INFO @ Sun, 21 Jun 2020 21:22:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:25: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:22:25: #2 alternative fragment length(s) may be 4,143 bps INFO @ Sun, 21 Jun 2020 21:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.10_model.r INFO @ Sun, 21 Jun 2020 21:22:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:25: 11000000 INFO @ Sun, 21 Jun 2020 21:22:31: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:37: 13000000 INFO @ Sun, 21 Jun 2020 21:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:41: Done! pass1 - making usageList (618 chroms): 2 millis pass2 - checking and writing primary data (3570 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:44: 14000000 INFO @ Sun, 21 Jun 2020 21:22:50: 15000000 INFO @ Sun, 21 Jun 2020 21:22:53: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:22:53: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:22:53: #1 total tags in treatment: 15543859 INFO @ Sun, 21 Jun 2020 21:22:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:53: #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 21:22:54: #1 tags after filtering in treatment: 15543757 INFO @ Sun, 21 Jun 2020 21:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:55: #2 number of paired peaks: 1707 INFO @ Sun, 21 Jun 2020 21:22:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:55: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:22:55: #2 alternative fragment length(s) may be 4,143 bps INFO @ Sun, 21 Jun 2020 21:22:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.20_model.r INFO @ Sun, 21 Jun 2020 21:22:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.10_summits.bed INFO @ Sun, 21 Jun 2020 21:23:16: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (2511 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801806/SRX4801806.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:44: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1720 records, 4 fields): 13 millis CompletedMACS2peakCalling