Job ID = 6458317 SRX = SRX5011067 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:37 prefetch.2.10.7: 1) Downloading 'SRR8191516'... 2020-06-21T12:31:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:33:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:33:53 prefetch.2.10.7: 'SRR8191516' is valid 2020-06-21T12:33:53 prefetch.2.10.7: 1) 'SRR8191516' was downloaded successfully 2020-06-21T12:33:53 prefetch.2.10.7: 'SRR8191516' has 0 unresolved dependencies Read 23495495 spots for SRR8191516/SRR8191516.sra Written 23495495 spots for SRR8191516/SRR8191516.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: 00:05:18 23495495 reads; of these: 23495495 (100.00%) were unpaired; of these: 3171825 (13.50%) aligned 0 times 16305371 (69.40%) aligned exactly 1 time 4018299 (17.10%) aligned >1 times 86.50% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 9458901 / 20323670 = 0.4654 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 21:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.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 21:45:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:05: 1000000 INFO @ Sun, 21 Jun 2020 21:45:10: 2000000 INFO @ Sun, 21 Jun 2020 21:45:15: 3000000 INFO @ Sun, 21 Jun 2020 21:45:20: 4000000 INFO @ Sun, 21 Jun 2020 21:45:25: 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 21:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.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 21:45:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:30: 6000000 INFO @ Sun, 21 Jun 2020 21:45:36: 1000000 INFO @ Sun, 21 Jun 2020 21:45:36: 7000000 INFO @ Sun, 21 Jun 2020 21:45:41: 2000000 INFO @ Sun, 21 Jun 2020 21:45:41: 8000000 INFO @ Sun, 21 Jun 2020 21:45:46: 3000000 INFO @ Sun, 21 Jun 2020 21:45:47: 9000000 INFO @ Sun, 21 Jun 2020 21:45:51: 4000000 INFO @ Sun, 21 Jun 2020 21:45:53: 10000000 INFO @ Sun, 21 Jun 2020 21:45:57: 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 21:45:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:58: #1 total tags in treatment: 10864769 INFO @ Sun, 21 Jun 2020 21:45:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:58: #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 21:45:59: #1 tags after filtering in treatment: 10864641 INFO @ Sun, 21 Jun 2020 21:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:59: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.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 21:46:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:00: #2 number of paired peaks: 3630 INFO @ Sun, 21 Jun 2020 21:46:00: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:00: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:00: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:00: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:00: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 21:46:00: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 21:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.05_model.r INFO @ Sun, 21 Jun 2020 21:46:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:02: 6000000 INFO @ Sun, 21 Jun 2020 21:46:05: 1000000 INFO @ Sun, 21 Jun 2020 21:46:08: 7000000 INFO @ Sun, 21 Jun 2020 21:46:10: 2000000 INFO @ Sun, 21 Jun 2020 21:46:13: 8000000 INFO @ Sun, 21 Jun 2020 21:46:15: 3000000 INFO @ Sun, 21 Jun 2020 21:46:19: 9000000 INFO @ Sun, 21 Jun 2020 21:46:21: 4000000 INFO @ Sun, 21 Jun 2020 21:46:24: 10000000 INFO @ Sun, 21 Jun 2020 21:46:26: 5000000 INFO @ Sun, 21 Jun 2020 21:46:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:29: #1 total tags in treatment: 10864769 INFO @ Sun, 21 Jun 2020 21:46:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:29: #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 21:46:30: #1 tags after filtering in treatment: 10864641 INFO @ Sun, 21 Jun 2020 21:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:30: 6000000 INFO @ Sun, 21 Jun 2020 21:46:31: #2 number of paired peaks: 3630 INFO @ Sun, 21 Jun 2020 21:46:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:31: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 21:46:31: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 21:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.10_model.r INFO @ Sun, 21 Jun 2020 21:46:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:35: 7000000 INFO @ Sun, 21 Jun 2020 21:46:40: 8000000 INFO @ Sun, 21 Jun 2020 21:46:45: 9000000 INFO @ Sun, 21 Jun 2020 21:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.05_summits.bed INFO @ Sun, 21 Jun 2020 21:46:47: Done! pass1 - making usageList (384 chroms): 2 millis pass2 - checking and writing primary data (8571 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:46:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:46:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:55: #1 total tags in treatment: 10864769 INFO @ Sun, 21 Jun 2020 21:46:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:55: #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 21:46:55: #1 tags after filtering in treatment: 10864641 INFO @ Sun, 21 Jun 2020 21:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:56: #2 number of paired peaks: 3630 INFO @ Sun, 21 Jun 2020 21:46:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:56: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 21:46:56: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 21:46:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.20_model.r INFO @ Sun, 21 Jun 2020 21:46:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:17: Done! pass1 - making usageList (327 chroms): 2 millis pass2 - checking and writing primary data (6021 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:47:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011067/SRX5011067.20_summits.bed INFO @ Sun, 21 Jun 2020 21:47:40: Done! pass1 - making usageList (226 chroms): 2 millis pass2 - checking and writing primary data (3629 records, 4 fields): 17 millis CompletedMACS2peakCalling