Job ID = 6458990 SRX = SRX5850002 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:56:22 prefetch.2.10.7: 1) Downloading 'SRR9074479'... 2020-06-21T12:56:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:00:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:00:14 prefetch.2.10.7: 1) 'SRR9074479' was downloaded successfully 2020-06-21T13:00:14 prefetch.2.10.7: 'SRR9074479' has 0 unresolved dependencies Read 53420599 spots for SRR9074479/SRR9074479.sra Written 53420599 spots for SRR9074479/SRR9074479.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: 00:06:14 53420599 reads; of these: 53420599 (100.00%) were unpaired; of these: 45142829 (84.50%) aligned 0 times 7111084 (13.31%) aligned exactly 1 time 1166686 (2.18%) aligned >1 times 15.50% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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_rmdupse_core] 1097773 / 8277770 = 0.1326 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 22:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.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 22:11:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:26: 1000000 INFO @ Sun, 21 Jun 2020 22:11:31: 2000000 INFO @ Sun, 21 Jun 2020 22:11:37: 3000000 INFO @ Sun, 21 Jun 2020 22:11:42: 4000000 INFO @ Sun, 21 Jun 2020 22:11:48: 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 22:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.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 22:11:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:53: 6000000 INFO @ Sun, 21 Jun 2020 22:11:56: 1000000 INFO @ Sun, 21 Jun 2020 22:12:00: 7000000 INFO @ Sun, 21 Jun 2020 22:12:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:01: #1 total tags in treatment: 7179997 INFO @ Sun, 21 Jun 2020 22:12:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:01: #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 22:12:01: #1 tags after filtering in treatment: 7179717 INFO @ Sun, 21 Jun 2020 22:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:02: #2 number of paired peaks: 11273 INFO @ Sun, 21 Jun 2020 22:12:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:03: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 22:12:03: #2 alternative fragment length(s) may be 4,193 bps INFO @ Sun, 21 Jun 2020 22:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.05_model.r INFO @ Sun, 21 Jun 2020 22:12:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:03: 2000000 INFO @ Sun, 21 Jun 2020 22:12:08: 3000000 INFO @ Sun, 21 Jun 2020 22:12:14: 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 22:12:19: 5000000 INFO @ Sun, 21 Jun 2020 22:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.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 22:12:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:25: 6000000 INFO @ Sun, 21 Jun 2020 22:12:27: 1000000 INFO @ Sun, 21 Jun 2020 22:12:32: 7000000 INFO @ Sun, 21 Jun 2020 22:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.05_summits.bed INFO @ Sun, 21 Jun 2020 22:12:32: Done! INFO @ Sun, 21 Jun 2020 22:12:33: 2000000 INFO @ Sun, 21 Jun 2020 22:12:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:33: #1 total tags in treatment: 7179997 INFO @ Sun, 21 Jun 2020 22:12:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (109 chroms): 2 millis pass2 - checking and writing primary data (7811 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:12:33: #1 tags after filtering in treatment: 7179717 INFO @ Sun, 21 Jun 2020 22:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:34: #2 number of paired peaks: 11273 INFO @ Sun, 21 Jun 2020 22:12:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:34: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 22:12:34: #2 alternative fragment length(s) may be 4,193 bps INFO @ Sun, 21 Jun 2020 22:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.10_model.r INFO @ Sun, 21 Jun 2020 22:12:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:38: 3000000 INFO @ Sun, 21 Jun 2020 22:12:44: 4000000 INFO @ Sun, 21 Jun 2020 22:12:49: 5000000 INFO @ Sun, 21 Jun 2020 22:12:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:12:55: 6000000 INFO @ Sun, 21 Jun 2020 22:13:01: 7000000 INFO @ Sun, 21 Jun 2020 22:13:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:02: #1 total tags in treatment: 7179997 INFO @ Sun, 21 Jun 2020 22:13:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:02: #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 22:13:02: #1 tags after filtering in treatment: 7179717 INFO @ Sun, 21 Jun 2020 22:13:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:03: #2 number of paired peaks: 11273 INFO @ Sun, 21 Jun 2020 22:13:03: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.10_summits.bed INFO @ Sun, 21 Jun 2020 22:13:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:03: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 22:13:03: #2 alternative fragment length(s) may be 4,193 bps INFO @ Sun, 21 Jun 2020 22:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.20_model.r INFO @ Sun, 21 Jun 2020 22:13:03: Done! INFO @ Sun, 21 Jun 2020 22:13:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:03: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (3814 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:13:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5850002/SRX5850002.20_summits.bed INFO @ Sun, 21 Jun 2020 22:13:33: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 4 millis CompletedMACS2peakCalling