Job ID = 6457094 SRX = SRX4375854 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:33:40 prefetch.2.10.7: 1) Downloading 'SRR7506508'... 2020-06-21T11:33:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:18 prefetch.2.10.7: 1) 'SRR7506508' was downloaded successfully Read 17532108 spots for SRR7506508/SRR7506508.sra Written 17532108 spots for SRR7506508/SRR7506508.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: 00:04:02 17532108 reads; of these: 17532108 (100.00%) were unpaired; of these: 1637393 (9.34%) aligned 0 times 13069603 (74.55%) aligned exactly 1 time 2825112 (16.11%) aligned >1 times 90.66% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 5869948 / 15894715 = 0.3693 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 20:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.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 20:46:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:17: 1000000 INFO @ Sun, 21 Jun 2020 20:46:23: 2000000 INFO @ Sun, 21 Jun 2020 20:46:29: 3000000 INFO @ Sun, 21 Jun 2020 20:46:34: 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 20:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.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 20:46:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:40: 5000000 INFO @ Sun, 21 Jun 2020 20:46:47: 1000000 INFO @ Sun, 21 Jun 2020 20:46:47: 6000000 INFO @ Sun, 21 Jun 2020 20:46:53: 2000000 INFO @ Sun, 21 Jun 2020 20:46:53: 7000000 INFO @ Sun, 21 Jun 2020 20:46:59: 3000000 INFO @ Sun, 21 Jun 2020 20:46:59: 8000000 INFO @ Sun, 21 Jun 2020 20:47:06: 4000000 INFO @ Sun, 21 Jun 2020 20:47:06: 9000000 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 20:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.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 20:47:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:12: 5000000 INFO @ Sun, 21 Jun 2020 20:47:13: 10000000 INFO @ Sun, 21 Jun 2020 20:47:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:47:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:47:13: #1 total tags in treatment: 10024767 INFO @ Sun, 21 Jun 2020 20:47:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:13: #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 20:47:13: #1 tags after filtering in treatment: 10024577 INFO @ Sun, 21 Jun 2020 20:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:15: #2 number of paired peaks: 8702 INFO @ Sun, 21 Jun 2020 20:47:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:15: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 20:47:15: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 20:47:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.05_model.r INFO @ Sun, 21 Jun 2020 20:47:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:17: 1000000 INFO @ Sun, 21 Jun 2020 20:47:18: 6000000 INFO @ Sun, 21 Jun 2020 20:47:23: 2000000 INFO @ Sun, 21 Jun 2020 20:47:24: 7000000 INFO @ Sun, 21 Jun 2020 20:47:30: 3000000 INFO @ Sun, 21 Jun 2020 20:47:31: 8000000 INFO @ Sun, 21 Jun 2020 20:47:36: 4000000 INFO @ Sun, 21 Jun 2020 20:47:37: 9000000 INFO @ Sun, 21 Jun 2020 20:47:42: 5000000 INFO @ Sun, 21 Jun 2020 20:47:44: 10000000 INFO @ Sun, 21 Jun 2020 20:47:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:47:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:47:44: #1 total tags in treatment: 10024767 INFO @ Sun, 21 Jun 2020 20:47:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:44: #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 20:47:45: #1 tags after filtering in treatment: 10024577 INFO @ Sun, 21 Jun 2020 20:47:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:46: #2 number of paired peaks: 8702 INFO @ Sun, 21 Jun 2020 20:47:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:46: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 20:47:46: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 20:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.10_model.r INFO @ Sun, 21 Jun 2020 20:47:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:48: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:47:54: 7000000 INFO @ Sun, 21 Jun 2020 20:48:00: 8000000 INFO @ Sun, 21 Jun 2020 20:48:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.05_summits.bed INFO @ Sun, 21 Jun 2020 20:48:01: Done! pass1 - making usageList (188 chroms): 2 millis pass2 - checking and writing primary data (9173 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:06: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:48:13: 10000000 INFO @ Sun, 21 Jun 2020 20:48:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:48:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:48:13: #1 total tags in treatment: 10024767 INFO @ Sun, 21 Jun 2020 20:48:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:48:13: #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 20:48:13: #1 tags after filtering in treatment: 10024577 INFO @ Sun, 21 Jun 2020 20:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:48:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:48:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:14: #2 number of paired peaks: 8702 INFO @ Sun, 21 Jun 2020 20:48:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:15: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 20:48:15: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 20:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.20_model.r INFO @ Sun, 21 Jun 2020 20:48:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:48:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.10_summits.bed INFO @ Sun, 21 Jun 2020 20:48:31: Done! pass1 - making usageList (140 chroms): 2 millis pass2 - checking and writing primary data (7459 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:49:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375854/SRX4375854.20_summits.bed INFO @ Sun, 21 Jun 2020 20:49:00: Done! pass1 - making usageList (109 chroms): 2 millis pass2 - checking and writing primary data (5808 records, 4 fields): 9 millis CompletedMACS2peakCalling