Job ID = 6453918 SRX = SRX159174 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:33:39 prefetch.2.10.7: 1) Downloading 'SRR520455'... 2020-06-21T08:33:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:40 prefetch.2.10.7: 1) 'SRR520455' was downloaded successfully Read 28231400 spots for SRR520455/SRR520455.sra Written 28231400 spots for SRR520455/SRR520455.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: 00:06:46 28231400 reads; of these: 28231400 (100.00%) were unpaired; of these: 5647481 (20.00%) aligned 0 times 15656667 (55.46%) aligned exactly 1 time 6927252 (24.54%) aligned >1 times 80.00% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 4455441 / 22583919 = 0.1973 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 17:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.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 17:51:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:18: 1000000 INFO @ Sun, 21 Jun 2020 17:51:26: 2000000 INFO @ Sun, 21 Jun 2020 17:51:33: 3000000 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 17:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.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 17:51:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:41: 4000000 INFO @ Sun, 21 Jun 2020 17:51:48: 1000000 INFO @ Sun, 21 Jun 2020 17:51:49: 5000000 INFO @ Sun, 21 Jun 2020 17:51:56: 2000000 INFO @ Sun, 21 Jun 2020 17:51:57: 6000000 INFO @ Sun, 21 Jun 2020 17:52:03: 3000000 INFO @ Sun, 21 Jun 2020 17:52:04: 7000000 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 17:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.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 17:52:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:11: 4000000 INFO @ Sun, 21 Jun 2020 17:52:12: 8000000 INFO @ Sun, 21 Jun 2020 17:52:18: 1000000 INFO @ Sun, 21 Jun 2020 17:52:19: 5000000 INFO @ Sun, 21 Jun 2020 17:52:20: 9000000 INFO @ Sun, 21 Jun 2020 17:52:26: 2000000 INFO @ Sun, 21 Jun 2020 17:52:27: 6000000 INFO @ Sun, 21 Jun 2020 17:52:28: 10000000 INFO @ Sun, 21 Jun 2020 17:52:34: 3000000 INFO @ Sun, 21 Jun 2020 17:52:35: 7000000 INFO @ Sun, 21 Jun 2020 17:52:36: 11000000 INFO @ Sun, 21 Jun 2020 17:52:42: 4000000 INFO @ Sun, 21 Jun 2020 17:52:42: 8000000 INFO @ Sun, 21 Jun 2020 17:52:43: 12000000 INFO @ Sun, 21 Jun 2020 17:52:50: 9000000 INFO @ Sun, 21 Jun 2020 17:52:50: 5000000 INFO @ Sun, 21 Jun 2020 17:52:51: 13000000 INFO @ Sun, 21 Jun 2020 17:52:58: 10000000 INFO @ Sun, 21 Jun 2020 17:52:58: 6000000 INFO @ Sun, 21 Jun 2020 17:52:59: 14000000 INFO @ Sun, 21 Jun 2020 17:53:06: 11000000 INFO @ Sun, 21 Jun 2020 17:53:06: 7000000 INFO @ Sun, 21 Jun 2020 17:53:07: 15000000 INFO @ Sun, 21 Jun 2020 17:53:13: 12000000 INFO @ Sun, 21 Jun 2020 17:53:14: 8000000 INFO @ Sun, 21 Jun 2020 17:53:15: 16000000 INFO @ Sun, 21 Jun 2020 17:53:21: 13000000 INFO @ Sun, 21 Jun 2020 17:53:22: 9000000 INFO @ Sun, 21 Jun 2020 17:53:23: 17000000 INFO @ Sun, 21 Jun 2020 17:53:29: 14000000 INFO @ Sun, 21 Jun 2020 17:53:30: 10000000 INFO @ Sun, 21 Jun 2020 17:53:31: 18000000 INFO @ Sun, 21 Jun 2020 17:53:32: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 17:53:32: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 17:53:32: #1 total tags in treatment: 18128478 INFO @ Sun, 21 Jun 2020 17:53:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:32: #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 17:53:33: #1 tags after filtering in treatment: 18128413 INFO @ Sun, 21 Jun 2020 17:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:35: #2 number of paired peaks: 1535 INFO @ Sun, 21 Jun 2020 17:53:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:35: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 17:53:35: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 17:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.05_model.r INFO @ Sun, 21 Jun 2020 17:53:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:37: 15000000 INFO @ Sun, 21 Jun 2020 17:53:38: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:53:45: 16000000 INFO @ Sun, 21 Jun 2020 17:53:45: 12000000 INFO @ Sun, 21 Jun 2020 17:53:53: 17000000 INFO @ Sun, 21 Jun 2020 17:53:53: 13000000 INFO @ Sun, 21 Jun 2020 17:54:01: 14000000 INFO @ Sun, 21 Jun 2020 17:54:01: 18000000 INFO @ Sun, 21 Jun 2020 17:54:02: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 17:54:02: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 17:54:02: #1 total tags in treatment: 18128478 INFO @ Sun, 21 Jun 2020 17:54:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:02: #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 17:54:03: #1 tags after filtering in treatment: 18128413 INFO @ Sun, 21 Jun 2020 17:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:04: #2 number of paired peaks: 1535 INFO @ Sun, 21 Jun 2020 17:54:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:04: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 17:54:04: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 17:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.10_model.r INFO @ Sun, 21 Jun 2020 17:54:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:08: 15000000 INFO @ Sun, 21 Jun 2020 17:54:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:17: 16000000 INFO @ Sun, 21 Jun 2020 17:54:24: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:54:32: 18000000 INFO @ Sun, 21 Jun 2020 17:54:33: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 17:54:33: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 17:54:33: #1 total tags in treatment: 18128478 INFO @ Sun, 21 Jun 2020 17:54:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:33: #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 17:54:34: #1 tags after filtering in treatment: 18128413 INFO @ Sun, 21 Jun 2020 17:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:35: #2 number of paired peaks: 1535 INFO @ Sun, 21 Jun 2020 17:54:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:36: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 17:54:36: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 17:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.20_model.r INFO @ Sun, 21 Jun 2020 17:54:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.05_summits.bed INFO @ Sun, 21 Jun 2020 17:54:37: Done! pass1 - making usageList (682 chroms): 2 millis pass2 - checking and writing primary data (7873 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.10_summits.bed INFO @ Sun, 21 Jun 2020 17:55:07: Done! pass1 - making usageList (584 chroms): 2 millis pass2 - checking and writing primary data (5613 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:55:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159174/SRX159174.20_summits.bed INFO @ Sun, 21 Jun 2020 17:55:37: Done! pass1 - making usageList (374 chroms): 2 millis pass2 - checking and writing primary data (3449 records, 4 fields): 24 millis CompletedMACS2peakCalling