Job ID = 6455343 SRX = SRX287712 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:06:25 prefetch.2.10.7: 1) Downloading 'SRR869900'... 2020-06-21T10:06:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:08:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:08:23 prefetch.2.10.7: 'SRR869900' is valid 2020-06-21T10:08:23 prefetch.2.10.7: 1) 'SRR869900' was downloaded successfully Read 9174577 spots for SRR869900/SRR869900.sra Written 9174577 spots for SRR869900/SRR869900.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: 00:02:50 9174577 reads; of these: 9174577 (100.00%) were unpaired; of these: 359505 (3.92%) aligned 0 times 6523083 (71.10%) aligned exactly 1 time 2291989 (24.98%) aligned >1 times 96.08% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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_rmdupse_core] 1358657 / 8815072 = 0.1541 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 19:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.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 19:14:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:20: 1000000 INFO @ Sun, 21 Jun 2020 19:14:25: 2000000 INFO @ Sun, 21 Jun 2020 19:14:30: 3000000 INFO @ Sun, 21 Jun 2020 19:14:34: 4000000 INFO @ Sun, 21 Jun 2020 19:14:39: 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 19:14:44: 6000000 INFO @ Sun, 21 Jun 2020 19:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.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 19:14:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:50: 7000000 INFO @ Sun, 21 Jun 2020 19:14:50: 1000000 INFO @ Sun, 21 Jun 2020 19:14:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:52: #1 total tags in treatment: 7456415 INFO @ Sun, 21 Jun 2020 19:14:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:52: #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 19:14:52: #1 tags after filtering in treatment: 7456411 INFO @ Sun, 21 Jun 2020 19:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:53: #2 number of paired peaks: 3268 INFO @ Sun, 21 Jun 2020 19:14:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:53: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 19:14:53: #2 alternative fragment length(s) may be 3,129 bps INFO @ Sun, 21 Jun 2020 19:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.05_model.r INFO @ Sun, 21 Jun 2020 19:14:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:55: 2000000 INFO @ Sun, 21 Jun 2020 19:15:00: 3000000 INFO @ Sun, 21 Jun 2020 19:15:06: 4000000 INFO @ Sun, 21 Jun 2020 19:15:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:11: 5000000 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 19:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.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 19:15:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:16: 6000000 INFO @ Sun, 21 Jun 2020 19:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:16: Done! pass1 - making usageList (633 chroms): 2 millis pass2 - checking and writing primary data (6103 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:20: 1000000 INFO @ Sun, 21 Jun 2020 19:15:21: 7000000 INFO @ Sun, 21 Jun 2020 19:15:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:24: #1 total tags in treatment: 7456415 INFO @ Sun, 21 Jun 2020 19:15:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:24: #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 19:15:24: #1 tags after filtering in treatment: 7456411 INFO @ Sun, 21 Jun 2020 19:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:25: #2 number of paired peaks: 3268 INFO @ Sun, 21 Jun 2020 19:15:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:25: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 19:15:25: #2 alternative fragment length(s) may be 3,129 bps INFO @ Sun, 21 Jun 2020 19:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.10_model.r INFO @ Sun, 21 Jun 2020 19:15:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:25: 2000000 INFO @ Sun, 21 Jun 2020 19:15:30: 3000000 INFO @ Sun, 21 Jun 2020 19:15:36: 4000000 INFO @ Sun, 21 Jun 2020 19:15:41: 5000000 INFO @ Sun, 21 Jun 2020 19:15:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:49: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (2223 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:51: 7000000 INFO @ Sun, 21 Jun 2020 19:15:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:53: #1 total tags in treatment: 7456415 INFO @ Sun, 21 Jun 2020 19:15:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:53: #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 19:15:54: #1 tags after filtering in treatment: 7456411 INFO @ Sun, 21 Jun 2020 19:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:54: #2 number of paired peaks: 3268 INFO @ Sun, 21 Jun 2020 19:15:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:55: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 19:15:55: #2 alternative fragment length(s) may be 3,129 bps INFO @ Sun, 21 Jun 2020 19:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.20_model.r INFO @ Sun, 21 Jun 2020 19:15:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287712/SRX287712.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:17: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 7 millis CompletedMACS2peakCalling