Job ID = 6454915 SRX = SRX2592497 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:32:14 prefetch.2.10.7: 1) Downloading 'SRR5289774'... 2020-06-21T09:32:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:35:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:35:37 prefetch.2.10.7: 1) 'SRR5289774' was downloaded successfully Read 18183132 spots for SRR5289774/SRR5289774.sra Written 18183132 spots for SRR5289774/SRR5289774.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: 00:03:20 18183132 reads; of these: 18183132 (100.00%) were unpaired; of these: 5394132 (29.67%) aligned 0 times 11332811 (62.33%) aligned exactly 1 time 1456189 (8.01%) aligned >1 times 70.33% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 2703614 / 12789000 = 0.2114 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 18:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.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 18:43:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:49: 1000000 INFO @ Sun, 21 Jun 2020 18:43:57: 2000000 INFO @ Sun, 21 Jun 2020 18:44:05: 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 18:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.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 18:44:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:13: 4000000 INFO @ Sun, 21 Jun 2020 18:44:20: 1000000 INFO @ Sun, 21 Jun 2020 18:44:21: 5000000 INFO @ Sun, 21 Jun 2020 18:44:29: 2000000 INFO @ Sun, 21 Jun 2020 18:44:30: 6000000 INFO @ Sun, 21 Jun 2020 18:44:37: 3000000 INFO @ Sun, 21 Jun 2020 18:44:38: 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 18:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.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 18:44:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:46: 4000000 INFO @ Sun, 21 Jun 2020 18:44:47: 8000000 INFO @ Sun, 21 Jun 2020 18:44:50: 1000000 INFO @ Sun, 21 Jun 2020 18:44:55: 5000000 INFO @ Sun, 21 Jun 2020 18:44:56: 9000000 INFO @ Sun, 21 Jun 2020 18:44:58: 2000000 INFO @ Sun, 21 Jun 2020 18:45:03: 6000000 INFO @ Sun, 21 Jun 2020 18:45:04: 10000000 INFO @ Sun, 21 Jun 2020 18:45:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:05: #1 total tags in treatment: 10085386 INFO @ Sun, 21 Jun 2020 18:45:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:05: #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 18:45:05: #1 tags after filtering in treatment: 10085197 INFO @ Sun, 21 Jun 2020 18:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:07: 3000000 INFO @ Sun, 21 Jun 2020 18:45:07: #2 number of paired peaks: 9303 INFO @ Sun, 21 Jun 2020 18:45:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:07: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 18:45:07: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 18:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.05_model.r INFO @ Sun, 21 Jun 2020 18:45:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:12: 7000000 INFO @ Sun, 21 Jun 2020 18:45:15: 4000000 INFO @ Sun, 21 Jun 2020 18:45:20: 8000000 INFO @ Sun, 21 Jun 2020 18:45:24: 5000000 INFO @ Sun, 21 Jun 2020 18:45:29: 9000000 INFO @ Sun, 21 Jun 2020 18:45:32: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:45:38: 10000000 INFO @ Sun, 21 Jun 2020 18:45:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:39: #1 total tags in treatment: 10085386 INFO @ Sun, 21 Jun 2020 18:45:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:39: #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 18:45:39: #1 tags after filtering in treatment: 10085197 INFO @ Sun, 21 Jun 2020 18:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:40: #2 number of paired peaks: 9303 INFO @ Sun, 21 Jun 2020 18:45:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:41: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 18:45:41: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 18:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.10_model.r INFO @ Sun, 21 Jun 2020 18:45:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:41: 7000000 INFO @ Sun, 21 Jun 2020 18:45:48: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:55: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (11261 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:56: 9000000 INFO @ Sun, 21 Jun 2020 18:46:04: 10000000 INFO @ Sun, 21 Jun 2020 18:46:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:04: #1 total tags in treatment: 10085386 INFO @ Sun, 21 Jun 2020 18:46:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:04: #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 18:46:05: #1 tags after filtering in treatment: 10085197 INFO @ Sun, 21 Jun 2020 18:46:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:06: #2 number of paired peaks: 9303 INFO @ Sun, 21 Jun 2020 18:46:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:06: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 18:46:06: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 18:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.20_model.r INFO @ Sun, 21 Jun 2020 18:46:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:27: Done! pass1 - making usageList (71 chroms): 2 millis pass2 - checking and writing primary data (9037 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592497/SRX2592497.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:52: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (6661 records, 4 fields): 10 millis CompletedMACS2peakCalling