Job ID = 6458024 SRX = SRX4941148 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:54:03 prefetch.2.10.7: 1) Downloading 'SRR8114851'... 2020-06-21T11:54:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:57:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:57:22 prefetch.2.10.7: 1) 'SRR8114851' was downloaded successfully 2020-06-21T11:57:22 prefetch.2.10.7: 'SRR8114851' has 0 unresolved dependencies Read 25999231 spots for SRR8114851/SRR8114851.sra Written 25999231 spots for SRR8114851/SRR8114851.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: 00:08:33 25999231 reads; of these: 25999231 (100.00%) were unpaired; of these: 3287780 (12.65%) aligned 0 times 17444622 (67.10%) aligned exactly 1 time 5266829 (20.26%) aligned >1 times 87.35% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 7402828 / 22711451 = 0.3260 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 21:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.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 21:14:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:08: 1000000 INFO @ Sun, 21 Jun 2020 21:14:14: 2000000 INFO @ Sun, 21 Jun 2020 21:14:20: 3000000 INFO @ Sun, 21 Jun 2020 21:14:26: 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 21:14:32: 5000000 INFO @ Sun, 21 Jun 2020 21:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.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 21:14:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:38: 6000000 INFO @ Sun, 21 Jun 2020 21:14:39: 1000000 INFO @ Sun, 21 Jun 2020 21:14:44: 7000000 INFO @ Sun, 21 Jun 2020 21:14:45: 2000000 INFO @ Sun, 21 Jun 2020 21:14:51: 8000000 INFO @ Sun, 21 Jun 2020 21:14:52: 3000000 INFO @ Sun, 21 Jun 2020 21:14:58: 9000000 INFO @ Sun, 21 Jun 2020 21:14:58: 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 21:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.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 21:15:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:04: 10000000 INFO @ Sun, 21 Jun 2020 21:15:05: 5000000 INFO @ Sun, 21 Jun 2020 21:15:09: 1000000 INFO @ Sun, 21 Jun 2020 21:15:10: 11000000 INFO @ Sun, 21 Jun 2020 21:15:11: 6000000 INFO @ Sun, 21 Jun 2020 21:15:15: 2000000 INFO @ Sun, 21 Jun 2020 21:15:17: 12000000 INFO @ Sun, 21 Jun 2020 21:15:18: 7000000 INFO @ Sun, 21 Jun 2020 21:15:22: 3000000 INFO @ Sun, 21 Jun 2020 21:15:24: 13000000 INFO @ Sun, 21 Jun 2020 21:15:25: 8000000 INFO @ Sun, 21 Jun 2020 21:15:28: 4000000 INFO @ Sun, 21 Jun 2020 21:15:30: 14000000 INFO @ Sun, 21 Jun 2020 21:15:31: 9000000 INFO @ Sun, 21 Jun 2020 21:15:35: 5000000 INFO @ Sun, 21 Jun 2020 21:15:37: 15000000 INFO @ Sun, 21 Jun 2020 21:15:38: 10000000 INFO @ Sun, 21 Jun 2020 21:15:39: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:15:39: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:15:39: #1 total tags in treatment: 15308623 INFO @ Sun, 21 Jun 2020 21:15:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:39: #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 21:15:40: #1 tags after filtering in treatment: 15308447 INFO @ Sun, 21 Jun 2020 21:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:40: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:41: #2 number of paired peaks: 5896 INFO @ Sun, 21 Jun 2020 21:15:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:41: 6000000 INFO @ Sun, 21 Jun 2020 21:15:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:41: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 21:15:41: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 21:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.05_model.r INFO @ Sun, 21 Jun 2020 21:15:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:44: 11000000 INFO @ Sun, 21 Jun 2020 21:15:48: 7000000 INFO @ Sun, 21 Jun 2020 21:15:51: 12000000 INFO @ Sun, 21 Jun 2020 21:15:55: 8000000 INFO @ Sun, 21 Jun 2020 21:15:58: 13000000 INFO @ Sun, 21 Jun 2020 21:16:02: 9000000 INFO @ Sun, 21 Jun 2020 21:16:05: 14000000 INFO @ Sun, 21 Jun 2020 21:16:08: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:12: 15000000 INFO @ Sun, 21 Jun 2020 21:16:14: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:16:14: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:16:14: #1 total tags in treatment: 15308623 INFO @ Sun, 21 Jun 2020 21:16:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:14: #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 21:16:14: #1 tags after filtering in treatment: 15308447 INFO @ Sun, 21 Jun 2020 21:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:15: 11000000 INFO @ Sun, 21 Jun 2020 21:16:16: #2 number of paired peaks: 5896 INFO @ Sun, 21 Jun 2020 21:16:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:16: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 21:16:16: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 21:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.10_model.r INFO @ Sun, 21 Jun 2020 21:16:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:21: 12000000 INFO @ Sun, 21 Jun 2020 21:16:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:27: 13000000 INFO @ Sun, 21 Jun 2020 21:16:33: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:16:39: 15000000 INFO @ Sun, 21 Jun 2020 21:16:41: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:16:41: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:16:41: #1 total tags in treatment: 15308623 INFO @ Sun, 21 Jun 2020 21:16:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:41: #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 21:16:41: #1 tags after filtering in treatment: 15308447 INFO @ Sun, 21 Jun 2020 21:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:43: #2 number of paired peaks: 5896 INFO @ Sun, 21 Jun 2020 21:16:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:43: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 21:16:43: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 21:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.20_model.r INFO @ Sun, 21 Jun 2020 21:16:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.05_summits.bed INFO @ Sun, 21 Jun 2020 21:16:45: Done! pass1 - making usageList (485 chroms): 3 millis pass2 - checking and writing primary data (11068 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.10_summits.bed INFO @ Sun, 21 Jun 2020 21:17:21: Done! pass1 - making usageList (419 chroms): 2 millis pass2 - checking and writing primary data (8937 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4941148/SRX4941148.20_summits.bed INFO @ Sun, 21 Jun 2020 21:17:48: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (6466 records, 4 fields): 15 millis CompletedMACS2peakCalling