Job ID = 6454699 SRX = SRX2520647 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:23:29 prefetch.2.10.7: 1) Downloading 'SRR5206766'... 2020-06-21T09:23:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:42 prefetch.2.10.7: 1) 'SRR5206766' was downloaded successfully Read 20399272 spots for SRR5206766/SRR5206766.sra Written 20399272 spots for SRR5206766/SRR5206766.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: 00:04:50 20399272 reads; of these: 20399272 (100.00%) were unpaired; of these: 289015 (1.42%) aligned 0 times 16701449 (81.87%) aligned exactly 1 time 3408808 (16.71%) aligned >1 times 98.58% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 8741658 / 20110257 = 0.4347 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 18:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.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 18:36:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:42: 1000000 INFO @ Sun, 21 Jun 2020 18:36:48: 2000000 INFO @ Sun, 21 Jun 2020 18:36:54: 3000000 INFO @ Sun, 21 Jun 2020 18:36:59: 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 18:37:05: 5000000 INFO @ Sun, 21 Jun 2020 18:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.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 18:37:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:11: 6000000 INFO @ Sun, 21 Jun 2020 18:37:13: 1000000 INFO @ Sun, 21 Jun 2020 18:37:18: 7000000 INFO @ Sun, 21 Jun 2020 18:37:20: 2000000 INFO @ Sun, 21 Jun 2020 18:37:24: 8000000 INFO @ Sun, 21 Jun 2020 18:37:27: 3000000 INFO @ Sun, 21 Jun 2020 18:37:31: 9000000 INFO @ Sun, 21 Jun 2020 18:37:34: 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 18:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.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 18:37:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:38: 10000000 INFO @ Sun, 21 Jun 2020 18:37:41: 5000000 INFO @ Sun, 21 Jun 2020 18:37:43: 1000000 INFO @ Sun, 21 Jun 2020 18:37:45: 11000000 INFO @ Sun, 21 Jun 2020 18:37:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:37:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:37:48: #1 total tags in treatment: 11368599 INFO @ Sun, 21 Jun 2020 18:37:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:48: #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 18:37:48: #1 tags after filtering in treatment: 11368493 INFO @ Sun, 21 Jun 2020 18:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:48: 6000000 INFO @ Sun, 21 Jun 2020 18:37:49: #2 number of paired peaks: 1910 INFO @ Sun, 21 Jun 2020 18:37:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:49: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 18:37:49: #2 alternative fragment length(s) may be 122,250,270 bps INFO @ Sun, 21 Jun 2020 18:37:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.05_model.r INFO @ Sun, 21 Jun 2020 18:37:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:50: 2000000 INFO @ Sun, 21 Jun 2020 18:37:55: 7000000 INFO @ Sun, 21 Jun 2020 18:37:58: 3000000 INFO @ Sun, 21 Jun 2020 18:38:02: 8000000 INFO @ Sun, 21 Jun 2020 18:38:05: 4000000 INFO @ Sun, 21 Jun 2020 18:38:09: 9000000 INFO @ Sun, 21 Jun 2020 18:38:12: 5000000 INFO @ Sun, 21 Jun 2020 18:38:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:17: 10000000 INFO @ Sun, 21 Jun 2020 18:38:19: 6000000 INFO @ Sun, 21 Jun 2020 18:38:23: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:38:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:26: #1 total tags in treatment: 11368599 INFO @ Sun, 21 Jun 2020 18:38:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:26: #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 18:38:26: 7000000 INFO @ Sun, 21 Jun 2020 18:38:27: #1 tags after filtering in treatment: 11368493 INFO @ Sun, 21 Jun 2020 18:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:28: #2 number of paired peaks: 1910 INFO @ Sun, 21 Jun 2020 18:38:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:28: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 18:38:28: #2 alternative fragment length(s) may be 122,250,270 bps INFO @ Sun, 21 Jun 2020 18:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.10_model.r INFO @ Sun, 21 Jun 2020 18:38:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.05_summits.bed INFO @ Sun, 21 Jun 2020 18:38:29: Done! pass1 - making usageList (156 chroms): 2 millis pass2 - checking and writing primary data (5875 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:38:33: 8000000 INFO @ Sun, 21 Jun 2020 18:38:39: 9000000 INFO @ Sun, 21 Jun 2020 18:38:46: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:38:52: 11000000 INFO @ Sun, 21 Jun 2020 18:38:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:54: #1 total tags in treatment: 11368599 INFO @ Sun, 21 Jun 2020 18:38:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:54: #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 18:38:55: #1 tags after filtering in treatment: 11368493 INFO @ Sun, 21 Jun 2020 18:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:56: #2 number of paired peaks: 1910 INFO @ Sun, 21 Jun 2020 18:38:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:56: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 18:38:56: #2 alternative fragment length(s) may be 122,250,270 bps INFO @ Sun, 21 Jun 2020 18:38:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.20_model.r INFO @ Sun, 21 Jun 2020 18:38:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:12: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (1422 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520647/SRX2520647.20_summits.bed INFO @ Sun, 21 Jun 2020 18:39:37: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 5 millis CompletedMACS2peakCalling