Job ID = 6454800 SRX = SRX2592399 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:24:44 prefetch.2.10.7: 1) Downloading 'SRR5289676'... 2020-06-21T09:24:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:28:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:28:46 prefetch.2.10.7: 1) 'SRR5289676' was downloaded successfully Read 22336850 spots for SRR5289676/SRR5289676.sra Written 22336850 spots for SRR5289676/SRR5289676.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: 00:06:48 22336850 reads; of these: 22336850 (100.00%) were unpaired; of these: 1707465 (7.64%) aligned 0 times 16678843 (74.67%) aligned exactly 1 time 3950542 (17.69%) aligned >1 times 92.36% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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 12 files... [bam_rmdupse_core] 7638084 / 20629385 = 0.3703 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 18:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.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 18:42:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:12: 1000000 INFO @ Sun, 21 Jun 2020 18:42:19: 2000000 INFO @ Sun, 21 Jun 2020 18:42:26: 3000000 INFO @ Sun, 21 Jun 2020 18:42:33: 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 18:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.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 18:42:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:40: 5000000 INFO @ Sun, 21 Jun 2020 18:42:42: 1000000 INFO @ Sun, 21 Jun 2020 18:42:47: 6000000 INFO @ Sun, 21 Jun 2020 18:42:49: 2000000 INFO @ Sun, 21 Jun 2020 18:42:54: 7000000 INFO @ Sun, 21 Jun 2020 18:42:56: 3000000 INFO @ Sun, 21 Jun 2020 18:43:02: 8000000 INFO @ Sun, 21 Jun 2020 18:43:02: 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 18:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.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 18:43:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:09: 5000000 INFO @ Sun, 21 Jun 2020 18:43:09: 9000000 INFO @ Sun, 21 Jun 2020 18:43:13: 1000000 INFO @ Sun, 21 Jun 2020 18:43:15: 6000000 INFO @ Sun, 21 Jun 2020 18:43:16: 10000000 INFO @ Sun, 21 Jun 2020 18:43:20: 2000000 INFO @ Sun, 21 Jun 2020 18:43:22: 7000000 INFO @ Sun, 21 Jun 2020 18:43:24: 11000000 INFO @ Sun, 21 Jun 2020 18:43:26: 3000000 INFO @ Sun, 21 Jun 2020 18:43:28: 8000000 INFO @ Sun, 21 Jun 2020 18:43:31: 12000000 INFO @ Sun, 21 Jun 2020 18:43:33: 4000000 INFO @ Sun, 21 Jun 2020 18:43:35: 9000000 INFO @ Sun, 21 Jun 2020 18:43:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:43:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:43:38: #1 total tags in treatment: 12991301 INFO @ Sun, 21 Jun 2020 18:43:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:38: #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 18:43:39: #1 tags after filtering in treatment: 12991196 INFO @ Sun, 21 Jun 2020 18:43:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:39: 5000000 INFO @ Sun, 21 Jun 2020 18:43:40: #2 number of paired peaks: 1833 INFO @ Sun, 21 Jun 2020 18:43:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:40: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 18:43:40: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 18:43:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.05_model.r INFO @ Sun, 21 Jun 2020 18:43:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:42: 10000000 INFO @ Sun, 21 Jun 2020 18:43:46: 6000000 INFO @ Sun, 21 Jun 2020 18:43:48: 11000000 INFO @ Sun, 21 Jun 2020 18:43:52: 7000000 INFO @ Sun, 21 Jun 2020 18:43:54: 12000000 INFO @ Sun, 21 Jun 2020 18:43:58: 8000000 INFO @ Sun, 21 Jun 2020 18:44:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:44:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:44:01: #1 total tags in treatment: 12991301 INFO @ Sun, 21 Jun 2020 18:44:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:01: #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 18:44:01: #1 tags after filtering in treatment: 12991196 INFO @ Sun, 21 Jun 2020 18:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:03: #2 number of paired peaks: 1833 INFO @ Sun, 21 Jun 2020 18:44:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:03: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 18:44:03: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 18:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.10_model.r INFO @ Sun, 21 Jun 2020 18:44:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:04: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:11: 10000000 INFO @ Sun, 21 Jun 2020 18:44:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:16: 11000000 INFO @ Sun, 21 Jun 2020 18:44:22: 12000000 INFO @ Sun, 21 Jun 2020 18:44:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:44:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:44:28: #1 total tags in treatment: 12991301 INFO @ Sun, 21 Jun 2020 18:44:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:28: #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 18:44:28: #1 tags after filtering in treatment: 12991196 INFO @ Sun, 21 Jun 2020 18:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:30: #2 number of paired peaks: 1833 INFO @ Sun, 21 Jun 2020 18:44:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:30: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 18:44:30: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 18:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.20_model.r INFO @ Sun, 21 Jun 2020 18:44:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.05_summits.bed INFO @ Sun, 21 Jun 2020 18:44:32: Done! pass1 - making usageList (333 chroms): 3 millis pass2 - checking and writing primary data (21430 records, 4 fields): 30 millis BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:53: Done! pass1 - making usageList (245 chroms): 4 millis pass2 - checking and writing primary data (17860 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592399/SRX2592399.20_summits.bed INFO @ Sun, 21 Jun 2020 18:45:19: Done! pass1 - making usageList (146 chroms): 3 millis pass2 - checking and writing primary data (12118 records, 4 fields): 17 millis CompletedMACS2peakCalling