Job ID = 6455966 SRX = SRX3088628 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:23:21 prefetch.2.10.7: 1) Downloading 'SRR5928309'... 2020-06-21T10:23:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:58 prefetch.2.10.7: 1) 'SRR5928309' was downloaded successfully 2020-06-21T10:28:58 prefetch.2.10.7: 'SRR5928309' has 0 unresolved dependencies Read 39084580 spots for SRR5928309/SRR5928309.sra Written 39084580 spots for SRR5928309/SRR5928309.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:28 39084580 reads; of these: 39084580 (100.00%) were unpaired; of these: 9945737 (25.45%) aligned 0 times 26486296 (67.77%) aligned exactly 1 time 2652547 (6.79%) aligned >1 times 74.55% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 10493672 / 29138843 = 0.3601 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 19:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.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 19:44:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:28: 1000000 INFO @ Sun, 21 Jun 2020 19:44:33: 2000000 INFO @ Sun, 21 Jun 2020 19:44:39: 3000000 INFO @ Sun, 21 Jun 2020 19:44:44: 4000000 INFO @ Sun, 21 Jun 2020 19:44:50: 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 19:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.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 19:44:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:55: 6000000 INFO @ Sun, 21 Jun 2020 19:44:59: 1000000 INFO @ Sun, 21 Jun 2020 19:45:02: 7000000 INFO @ Sun, 21 Jun 2020 19:45:06: 2000000 INFO @ Sun, 21 Jun 2020 19:45:08: 8000000 INFO @ Sun, 21 Jun 2020 19:45:13: 3000000 INFO @ Sun, 21 Jun 2020 19:45:14: 9000000 INFO @ Sun, 21 Jun 2020 19:45:19: 4000000 INFO @ Sun, 21 Jun 2020 19:45:20: 10000000 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 19:45:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.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 19:45:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:26: 5000000 INFO @ Sun, 21 Jun 2020 19:45:26: 11000000 INFO @ Sun, 21 Jun 2020 19:45:29: 1000000 INFO @ Sun, 21 Jun 2020 19:45:32: 6000000 INFO @ Sun, 21 Jun 2020 19:45:32: 12000000 INFO @ Sun, 21 Jun 2020 19:45:35: 2000000 INFO @ Sun, 21 Jun 2020 19:45:38: 7000000 INFO @ Sun, 21 Jun 2020 19:45:39: 13000000 INFO @ Sun, 21 Jun 2020 19:45:41: 3000000 INFO @ Sun, 21 Jun 2020 19:45:45: 8000000 INFO @ Sun, 21 Jun 2020 19:45:45: 14000000 INFO @ Sun, 21 Jun 2020 19:45:48: 4000000 INFO @ Sun, 21 Jun 2020 19:45:51: 15000000 INFO @ Sun, 21 Jun 2020 19:45:51: 9000000 INFO @ Sun, 21 Jun 2020 19:45:54: 5000000 INFO @ Sun, 21 Jun 2020 19:45:57: 10000000 INFO @ Sun, 21 Jun 2020 19:45:58: 16000000 INFO @ Sun, 21 Jun 2020 19:46:00: 6000000 INFO @ Sun, 21 Jun 2020 19:46:04: 11000000 INFO @ Sun, 21 Jun 2020 19:46:04: 17000000 INFO @ Sun, 21 Jun 2020 19:46:06: 7000000 INFO @ Sun, 21 Jun 2020 19:46:10: 12000000 INFO @ Sun, 21 Jun 2020 19:46:10: 18000000 INFO @ Sun, 21 Jun 2020 19:46:12: 8000000 INFO @ Sun, 21 Jun 2020 19:46:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:46:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:46:14: #1 total tags in treatment: 18645171 INFO @ Sun, 21 Jun 2020 19:46:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:14: #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 19:46:15: #1 tags after filtering in treatment: 18645157 INFO @ Sun, 21 Jun 2020 19:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:16: 13000000 INFO @ Sun, 21 Jun 2020 19:46:16: #2 number of paired peaks: 3561 INFO @ Sun, 21 Jun 2020 19:46:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:17: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 19:46:17: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 19:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.05_model.r INFO @ Sun, 21 Jun 2020 19:46:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:18: 9000000 INFO @ Sun, 21 Jun 2020 19:46:22: 14000000 INFO @ Sun, 21 Jun 2020 19:46:25: 10000000 INFO @ Sun, 21 Jun 2020 19:46:28: 15000000 INFO @ Sun, 21 Jun 2020 19:46:31: 11000000 INFO @ Sun, 21 Jun 2020 19:46:34: 16000000 INFO @ Sun, 21 Jun 2020 19:46:37: 12000000 INFO @ Sun, 21 Jun 2020 19:46:40: 17000000 INFO @ Sun, 21 Jun 2020 19:46:42: 13000000 INFO @ Sun, 21 Jun 2020 19:46:46: 18000000 INFO @ Sun, 21 Jun 2020 19:46:48: 14000000 INFO @ Sun, 21 Jun 2020 19:46:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:46:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:46:51: #1 total tags in treatment: 18645171 INFO @ Sun, 21 Jun 2020 19:46:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:46:51: #1 tags after filtering in treatment: 18645157 INFO @ Sun, 21 Jun 2020 19:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:53: #2 number of paired peaks: 3561 INFO @ Sun, 21 Jun 2020 19:46:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:53: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 19:46:53: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 19:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.10_model.r INFO @ Sun, 21 Jun 2020 19:46:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:54: 15000000 INFO @ Sun, 21 Jun 2020 19:46:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:00: 16000000 INFO @ Sun, 21 Jun 2020 19:47:05: 17000000 INFO @ Sun, 21 Jun 2020 19:47:11: 18000000 INFO @ Sun, 21 Jun 2020 19:47:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:47:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:47:14: #1 total tags in treatment: 18645171 INFO @ Sun, 21 Jun 2020 19:47:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:14: #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 19:47:15: #1 tags after filtering in treatment: 18645157 INFO @ Sun, 21 Jun 2020 19:47:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:16: #2 number of paired peaks: 3561 INFO @ Sun, 21 Jun 2020 19:47:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:17: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 19:47:17: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 19:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.20_model.r INFO @ Sun, 21 Jun 2020 19:47:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:23: Done! pass1 - making usageList (442 chroms): 4 millis pass2 - checking and writing primary data (20726 records, 4 fields): 31 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:47:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.10_summits.bed INFO @ Sun, 21 Jun 2020 19:47:57: Done! pass1 - making usageList (264 chroms): 3 millis pass2 - checking and writing primary data (15815 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3088628/SRX3088628.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:20: Done! pass1 - making usageList (121 chroms): 2 millis pass2 - checking and writing primary data (11109 records, 4 fields): 16 millis CompletedMACS2peakCalling