Job ID = 6457529 SRX = SRX4669021 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:37:25 prefetch.2.10.7: 1) Downloading 'SRR7817546'... 2020-06-21T11:37:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:40:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:40:52 prefetch.2.10.7: 1) 'SRR7817546' was downloaded successfully 2020-06-21T11:40:52 prefetch.2.10.7: 'SRR7817546' has 0 unresolved dependencies Read 34560344 spots for SRR7817546/SRR7817546.sra Written 34560344 spots for SRR7817546/SRR7817546.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: 00:07:04 34560344 reads; of these: 34560344 (100.00%) were unpaired; of these: 5657783 (16.37%) aligned 0 times 24487886 (70.86%) aligned exactly 1 time 4414675 (12.77%) aligned >1 times 83.63% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 13788096 / 28902561 = 0.4771 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 20:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.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 20:54:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:54:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:28: 1000000 INFO @ Sun, 21 Jun 2020 20:54:33: 2000000 INFO @ Sun, 21 Jun 2020 20:54:39: 3000000 INFO @ Sun, 21 Jun 2020 20:54:44: 4000000 INFO @ Sun, 21 Jun 2020 20:54:49: 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 20:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.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 20:54:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:54:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:55: 6000000 INFO @ Sun, 21 Jun 2020 20:54:59: 1000000 INFO @ Sun, 21 Jun 2020 20:55:01: 7000000 INFO @ Sun, 21 Jun 2020 20:55:05: 2000000 INFO @ Sun, 21 Jun 2020 20:55:07: 8000000 INFO @ Sun, 21 Jun 2020 20:55:11: 3000000 INFO @ Sun, 21 Jun 2020 20:55:13: 9000000 INFO @ Sun, 21 Jun 2020 20:55:16: 4000000 INFO @ Sun, 21 Jun 2020 20:55:18: 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 20:55:22: 5000000 INFO @ Sun, 21 Jun 2020 20:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.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 20:55:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:55:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:55:24: 11000000 INFO @ Sun, 21 Jun 2020 20:55:28: 6000000 INFO @ Sun, 21 Jun 2020 20:55:28: 1000000 INFO @ Sun, 21 Jun 2020 20:55:31: 12000000 INFO @ Sun, 21 Jun 2020 20:55:35: 2000000 INFO @ Sun, 21 Jun 2020 20:55:35: 7000000 INFO @ Sun, 21 Jun 2020 20:55:37: 13000000 INFO @ Sun, 21 Jun 2020 20:55:41: 3000000 INFO @ Sun, 21 Jun 2020 20:55:41: 8000000 INFO @ Sun, 21 Jun 2020 20:55:44: 14000000 INFO @ Sun, 21 Jun 2020 20:55:47: 4000000 INFO @ Sun, 21 Jun 2020 20:55:47: 9000000 INFO @ Sun, 21 Jun 2020 20:55:50: 15000000 INFO @ Sun, 21 Jun 2020 20:55:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:55:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:55:51: #1 total tags in treatment: 15114465 INFO @ Sun, 21 Jun 2020 20:55:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:55:51: #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 20:55:51: #1 tags after filtering in treatment: 15114438 INFO @ Sun, 21 Jun 2020 20:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:55:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:55:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:55:52: #2 number of paired peaks: 2112 INFO @ Sun, 21 Jun 2020 20:55:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:55:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:55:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:55:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:55:52: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 20:55:52: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 20:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.05_model.r INFO @ Sun, 21 Jun 2020 20:55:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:55:53: 5000000 INFO @ Sun, 21 Jun 2020 20:55:54: 10000000 INFO @ Sun, 21 Jun 2020 20:55:59: 6000000 INFO @ Sun, 21 Jun 2020 20:56:00: 11000000 INFO @ Sun, 21 Jun 2020 20:56:06: 7000000 INFO @ Sun, 21 Jun 2020 20:56:06: 12000000 INFO @ Sun, 21 Jun 2020 20:56:12: 8000000 INFO @ Sun, 21 Jun 2020 20:56:12: 13000000 INFO @ Sun, 21 Jun 2020 20:56:18: 9000000 INFO @ Sun, 21 Jun 2020 20:56:19: 14000000 INFO @ Sun, 21 Jun 2020 20:56:24: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:56:25: 15000000 INFO @ Sun, 21 Jun 2020 20:56:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:56:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:56:26: #1 total tags in treatment: 15114465 INFO @ Sun, 21 Jun 2020 20:56:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:56:26: #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 20:56:27: #1 tags after filtering in treatment: 15114438 INFO @ Sun, 21 Jun 2020 20:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:56:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:56:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:56:28: #2 number of paired peaks: 2112 INFO @ Sun, 21 Jun 2020 20:56:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:56:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:56:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:56:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:56:28: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 20:56:28: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 20:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.10_model.r INFO @ Sun, 21 Jun 2020 20:56:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:56:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:56:31: 11000000 INFO @ Sun, 21 Jun 2020 20:56:37: 12000000 INFO @ Sun, 21 Jun 2020 20:56:43: 13000000 INFO @ Sun, 21 Jun 2020 20:56:49: 14000000 INFO @ Sun, 21 Jun 2020 20:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.05_summits.bed INFO @ Sun, 21 Jun 2020 20:56:49: Done! pass1 - making usageList (323 chroms): 3 millis pass2 - checking and writing primary data (13619 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:56:55: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:56:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:56:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:56:55: #1 total tags in treatment: 15114465 INFO @ Sun, 21 Jun 2020 20:56:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:56:55: #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 20:56:56: #1 tags after filtering in treatment: 15114438 INFO @ Sun, 21 Jun 2020 20:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:56:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:56:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:56:57: #2 number of paired peaks: 2112 INFO @ Sun, 21 Jun 2020 20:56:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:56:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:56:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:56:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:56:57: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 20:56:57: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 20:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.20_model.r INFO @ Sun, 21 Jun 2020 20:56:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.10_summits.bed INFO @ Sun, 21 Jun 2020 20:57:22: Done! pass1 - making usageList (220 chroms): 2 millis pass2 - checking and writing primary data (9329 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:57:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669021/SRX4669021.20_summits.bed INFO @ Sun, 21 Jun 2020 20:57:50: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (5449 records, 4 fields): 26 millis CompletedMACS2peakCalling