Job ID = 6456042 SRX = SRX3159492 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:27:21 prefetch.2.10.7: 1) Downloading 'SRR6004222'... 2020-06-21T10:27:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:19 prefetch.2.10.7: 1) 'SRR6004222' was downloaded successfully 2020-06-21T10:32:19 prefetch.2.10.7: 'SRR6004222' has 0 unresolved dependencies Read 46987784 spots for SRR6004222/SRR6004222.sra Written 46987784 spots for SRR6004222/SRR6004222.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: 00:09:12 46987784 reads; of these: 46987784 (100.00%) were unpaired; of these: 10516163 (22.38%) aligned 0 times 32708473 (69.61%) aligned exactly 1 time 3763148 (8.01%) aligned >1 times 77.62% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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 16 files... [bam_rmdupse_core] 15177352 / 36471621 = 0.4161 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 19:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.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 19:50:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:19: 1000000 INFO @ Sun, 21 Jun 2020 19:50:24: 2000000 INFO @ Sun, 21 Jun 2020 19:50:30: 3000000 INFO @ Sun, 21 Jun 2020 19:50:35: 4000000 INFO @ Sun, 21 Jun 2020 19:50:41: 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 19:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.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 19:50:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:47: 6000000 INFO @ Sun, 21 Jun 2020 19:50:49: 1000000 INFO @ Sun, 21 Jun 2020 19:50:53: 7000000 INFO @ Sun, 21 Jun 2020 19:50:55: 2000000 INFO @ Sun, 21 Jun 2020 19:50:59: 8000000 INFO @ Sun, 21 Jun 2020 19:51:01: 3000000 INFO @ Sun, 21 Jun 2020 19:51:05: 9000000 INFO @ Sun, 21 Jun 2020 19:51:08: 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 19:51:11: 10000000 INFO @ Sun, 21 Jun 2020 19:51:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.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 19:51:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:14: 5000000 INFO @ Sun, 21 Jun 2020 19:51:17: 11000000 INFO @ Sun, 21 Jun 2020 19:51:19: 1000000 INFO @ Sun, 21 Jun 2020 19:51:20: 6000000 INFO @ Sun, 21 Jun 2020 19:51:23: 12000000 INFO @ Sun, 21 Jun 2020 19:51:25: 2000000 INFO @ Sun, 21 Jun 2020 19:51:27: 7000000 INFO @ Sun, 21 Jun 2020 19:51:30: 13000000 INFO @ Sun, 21 Jun 2020 19:51:31: 3000000 INFO @ Sun, 21 Jun 2020 19:51:33: 8000000 INFO @ Sun, 21 Jun 2020 19:51:36: 14000000 INFO @ Sun, 21 Jun 2020 19:51:38: 4000000 INFO @ Sun, 21 Jun 2020 19:51:39: 9000000 INFO @ Sun, 21 Jun 2020 19:51:42: 15000000 INFO @ Sun, 21 Jun 2020 19:51:44: 5000000 INFO @ Sun, 21 Jun 2020 19:51:45: 10000000 INFO @ Sun, 21 Jun 2020 19:51:48: 16000000 INFO @ Sun, 21 Jun 2020 19:51:50: 6000000 INFO @ Sun, 21 Jun 2020 19:51:52: 11000000 INFO @ Sun, 21 Jun 2020 19:51:54: 17000000 INFO @ Sun, 21 Jun 2020 19:51:56: 7000000 INFO @ Sun, 21 Jun 2020 19:51:58: 12000000 INFO @ Sun, 21 Jun 2020 19:52:01: 18000000 INFO @ Sun, 21 Jun 2020 19:52:02: 8000000 INFO @ Sun, 21 Jun 2020 19:52:04: 13000000 INFO @ Sun, 21 Jun 2020 19:52:07: 19000000 INFO @ Sun, 21 Jun 2020 19:52:09: 9000000 INFO @ Sun, 21 Jun 2020 19:52:11: 14000000 INFO @ Sun, 21 Jun 2020 19:52:14: 20000000 INFO @ Sun, 21 Jun 2020 19:52:15: 10000000 INFO @ Sun, 21 Jun 2020 19:52:17: 15000000 INFO @ Sun, 21 Jun 2020 19:52:20: 21000000 INFO @ Sun, 21 Jun 2020 19:52:21: 11000000 INFO @ Sun, 21 Jun 2020 19:52:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:52:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:52:23: #1 total tags in treatment: 21294269 INFO @ Sun, 21 Jun 2020 19:52:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:23: #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 19:52:23: #1 tags after filtering in treatment: 21294252 INFO @ Sun, 21 Jun 2020 19:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:24: 16000000 INFO @ Sun, 21 Jun 2020 19:52:25: #2 number of paired peaks: 5844 INFO @ Sun, 21 Jun 2020 19:52:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:26: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 19:52:26: #2 alternative fragment length(s) may be 3,104 bps INFO @ Sun, 21 Jun 2020 19:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.05_model.r INFO @ Sun, 21 Jun 2020 19:52:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:27: 12000000 INFO @ Sun, 21 Jun 2020 19:52:30: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:52:34: 13000000 INFO @ Sun, 21 Jun 2020 19:52:37: 18000000 INFO @ Sun, 21 Jun 2020 19:52:40: 14000000 INFO @ Sun, 21 Jun 2020 19:52:44: 19000000 INFO @ Sun, 21 Jun 2020 19:52:46: 15000000 INFO @ Sun, 21 Jun 2020 19:52:50: 20000000 INFO @ Sun, 21 Jun 2020 19:52:52: 16000000 INFO @ Sun, 21 Jun 2020 19:52:57: 21000000 INFO @ Sun, 21 Jun 2020 19:52:59: 17000000 INFO @ Sun, 21 Jun 2020 19:52:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:52:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:52:59: #1 total tags in treatment: 21294269 INFO @ Sun, 21 Jun 2020 19:52:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:59: #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 19:53:00: #1 tags after filtering in treatment: 21294252 INFO @ Sun, 21 Jun 2020 19:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:02: #2 number of paired peaks: 5844 INFO @ Sun, 21 Jun 2020 19:53:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:02: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 19:53:02: #2 alternative fragment length(s) may be 3,104 bps INFO @ Sun, 21 Jun 2020 19:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.10_model.r INFO @ Sun, 21 Jun 2020 19:53:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:05: 18000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:53:10: 19000000 INFO @ Sun, 21 Jun 2020 19:53:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:16: 20000000 INFO @ Sun, 21 Jun 2020 19:53:22: 21000000 INFO @ Sun, 21 Jun 2020 19:53:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:53:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:53:24: #1 total tags in treatment: 21294269 INFO @ Sun, 21 Jun 2020 19:53:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:24: #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 19:53:24: #1 tags after filtering in treatment: 21294252 INFO @ Sun, 21 Jun 2020 19:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:27: #2 number of paired peaks: 5844 INFO @ Sun, 21 Jun 2020 19:53:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:27: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 19:53:27: #2 alternative fragment length(s) may be 3,104 bps INFO @ Sun, 21 Jun 2020 19:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.20_model.r INFO @ Sun, 21 Jun 2020 19:53:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.05_summits.bed INFO @ Sun, 21 Jun 2020 19:53:37: Done! pass1 - making usageList (429 chroms): 2 millis pass2 - checking and writing primary data (9607 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:15: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (5763 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159492/SRX3159492.20_summits.bed INFO @ Sun, 21 Jun 2020 19:54:38: Done! pass1 - making usageList (316 chroms): 2 millis pass2 - checking and writing primary data (2499 records, 4 fields): 12 millis CompletedMACS2peakCalling