Job ID = 6457220 SRX = SRX457600 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:36:55 prefetch.2.10.7: 1) Downloading 'SRR1153276'... 2020-06-21T11:36:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:15 prefetch.2.10.7: 1) 'SRR1153276' was downloaded successfully Read 48729799 spots for SRR1153276/SRR1153276.sra Written 48729799 spots for SRR1153276/SRR1153276.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: 00:12:09 48729799 reads; of these: 48729799 (100.00%) were unpaired; of these: 1939209 (3.98%) aligned 0 times 41152609 (84.45%) aligned exactly 1 time 5637981 (11.57%) aligned >1 times 96.02% overall alignment rate Time searching: 00:12:09 Overall time: 00:12:09 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 20 files... [bam_rmdupse_core] 31424518 / 46790590 = 0.6716 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 21:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.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 21:09:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:09:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:09:43: 1000000 INFO @ Sun, 21 Jun 2020 21:09:48: 2000000 INFO @ Sun, 21 Jun 2020 21:09:54: 3000000 INFO @ Sun, 21 Jun 2020 21:09:59: 4000000 INFO @ Sun, 21 Jun 2020 21:10:05: 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 21:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.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 21:10:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:11: 6000000 INFO @ Sun, 21 Jun 2020 21:10:14: 1000000 INFO @ Sun, 21 Jun 2020 21:10:18: 7000000 INFO @ Sun, 21 Jun 2020 21:10:20: 2000000 INFO @ Sun, 21 Jun 2020 21:10:24: 8000000 INFO @ Sun, 21 Jun 2020 21:10:27: 3000000 INFO @ Sun, 21 Jun 2020 21:10:31: 9000000 INFO @ Sun, 21 Jun 2020 21:10:33: 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 21:10:37: 10000000 INFO @ Sun, 21 Jun 2020 21:10:40: 5000000 INFO @ Sun, 21 Jun 2020 21:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.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 21:10:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:43: 11000000 INFO @ Sun, 21 Jun 2020 21:10:46: 6000000 INFO @ Sun, 21 Jun 2020 21:10:47: 1000000 INFO @ Sun, 21 Jun 2020 21:10:50: 12000000 INFO @ Sun, 21 Jun 2020 21:10:53: 7000000 INFO @ Sun, 21 Jun 2020 21:10:53: 2000000 INFO @ Sun, 21 Jun 2020 21:10:57: 13000000 INFO @ Sun, 21 Jun 2020 21:10:59: 8000000 INFO @ Sun, 21 Jun 2020 21:11:00: 3000000 INFO @ Sun, 21 Jun 2020 21:11:04: 14000000 INFO @ Sun, 21 Jun 2020 21:11:06: 9000000 INFO @ Sun, 21 Jun 2020 21:11:07: 4000000 INFO @ Sun, 21 Jun 2020 21:11:10: 15000000 INFO @ Sun, 21 Jun 2020 21:11:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:11:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:11:13: #1 total tags in treatment: 15366072 INFO @ Sun, 21 Jun 2020 21:11:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:11:13: #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 21:11:13: 10000000 INFO @ Sun, 21 Jun 2020 21:11:13: #1 tags after filtering in treatment: 15366056 INFO @ Sun, 21 Jun 2020 21:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:11:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:11:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:11:13: 5000000 INFO @ Sun, 21 Jun 2020 21:11:15: #2 number of paired peaks: 4986 INFO @ Sun, 21 Jun 2020 21:11:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:11:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:11:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:11:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:11:15: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 21:11:15: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 21:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.05_model.r INFO @ Sun, 21 Jun 2020 21:11:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:11:19: 11000000 INFO @ Sun, 21 Jun 2020 21:11:20: 6000000 INFO @ Sun, 21 Jun 2020 21:11:26: 12000000 INFO @ Sun, 21 Jun 2020 21:11:27: 7000000 INFO @ Sun, 21 Jun 2020 21:11:33: 13000000 INFO @ Sun, 21 Jun 2020 21:11:33: 8000000 INFO @ Sun, 21 Jun 2020 21:11:40: 14000000 INFO @ Sun, 21 Jun 2020 21:11:40: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:11:46: 15000000 INFO @ Sun, 21 Jun 2020 21:11:47: 10000000 INFO @ Sun, 21 Jun 2020 21:11:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:11:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:11:49: #1 total tags in treatment: 15366072 INFO @ Sun, 21 Jun 2020 21:11:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:11:49: #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 21:11:50: #1 tags after filtering in treatment: 15366056 INFO @ Sun, 21 Jun 2020 21:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:11:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:11:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:11:51: #2 number of paired peaks: 4986 INFO @ Sun, 21 Jun 2020 21:11:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:11:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:11:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:11:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:11:51: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 21:11:51: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 21:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.10_model.r INFO @ Sun, 21 Jun 2020 21:11:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:11:54: 11000000 INFO @ Sun, 21 Jun 2020 21:11:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:12:00: 12000000 INFO @ Sun, 21 Jun 2020 21:12:07: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:12:13: 14000000 INFO @ Sun, 21 Jun 2020 21:12:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:12:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:12:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.05_summits.bed INFO @ Sun, 21 Jun 2020 21:12:16: Done! pass1 - making usageList (520 chroms): 2 millis pass2 - checking and writing primary data (10028 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:12:18: 15000000 INFO @ Sun, 21 Jun 2020 21:12:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:12:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:12:21: #1 total tags in treatment: 15366072 INFO @ Sun, 21 Jun 2020 21:12:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:21: #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 21:12:21: #1 tags after filtering in treatment: 15366056 INFO @ Sun, 21 Jun 2020 21:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:23: #2 number of paired peaks: 4986 INFO @ Sun, 21 Jun 2020 21:12:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:23: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 21:12:23: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 21:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.20_model.r INFO @ Sun, 21 Jun 2020 21:12:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.10_summits.bed INFO @ Sun, 21 Jun 2020 21:12:55: Done! pass1 - making usageList (462 chroms): 2 millis pass2 - checking and writing primary data (8247 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX457600/SRX457600.20_summits.bed INFO @ Sun, 21 Jun 2020 21:13:25: Done! pass1 - making usageList (370 chroms): 2 millis pass2 - checking and writing primary data (6489 records, 4 fields): 17 millis CompletedMACS2peakCalling