Job ID = 6454737 SRX = SRX2559029 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:33:44 prefetch.2.10.7: 1) Downloading 'SRR5253493'... 2020-06-21T09:33:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:08 prefetch.2.10.7: 1) 'SRR5253493' was downloaded successfully Read 24205473 spots for SRR5253493/SRR5253493.sra Written 24205473 spots for SRR5253493/SRR5253493.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: 00:06:10 24205473 reads; of these: 24205473 (100.00%) were unpaired; of these: 1072679 (4.43%) aligned 0 times 18541962 (76.60%) aligned exactly 1 time 4590832 (18.97%) aligned >1 times 95.57% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 4653344 / 23132794 = 0.2012 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 18:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.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 18:52:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:34: 1000000 INFO @ Sun, 21 Jun 2020 18:52:39: 2000000 INFO @ Sun, 21 Jun 2020 18:52:44: 3000000 INFO @ Sun, 21 Jun 2020 18:52:49: 4000000 INFO @ Sun, 21 Jun 2020 18:52:55: 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 18:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.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 18:52:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:00: 6000000 INFO @ Sun, 21 Jun 2020 18:53:05: 1000000 INFO @ Sun, 21 Jun 2020 18:53:05: 7000000 INFO @ Sun, 21 Jun 2020 18:53:10: 2000000 INFO @ Sun, 21 Jun 2020 18:53:11: 8000000 INFO @ Sun, 21 Jun 2020 18:53:16: 3000000 INFO @ Sun, 21 Jun 2020 18:53:16: 9000000 INFO @ Sun, 21 Jun 2020 18:53:21: 4000000 INFO @ Sun, 21 Jun 2020 18:53:22: 10000000 INFO @ Sun, 21 Jun 2020 18:53:27: 5000000 INFO @ Sun, 21 Jun 2020 18:53:27: 11000000 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 18:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.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 18:53:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:32: 6000000 INFO @ Sun, 21 Jun 2020 18:53:32: 12000000 INFO @ Sun, 21 Jun 2020 18:53:35: 1000000 INFO @ Sun, 21 Jun 2020 18:53:38: 13000000 INFO @ Sun, 21 Jun 2020 18:53:38: 7000000 INFO @ Sun, 21 Jun 2020 18:53:40: 2000000 INFO @ Sun, 21 Jun 2020 18:53:43: 14000000 INFO @ Sun, 21 Jun 2020 18:53:44: 8000000 INFO @ Sun, 21 Jun 2020 18:53:46: 3000000 INFO @ Sun, 21 Jun 2020 18:53:49: 15000000 INFO @ Sun, 21 Jun 2020 18:53:49: 9000000 INFO @ Sun, 21 Jun 2020 18:53:52: 4000000 INFO @ Sun, 21 Jun 2020 18:53:55: 10000000 INFO @ Sun, 21 Jun 2020 18:53:55: 16000000 INFO @ Sun, 21 Jun 2020 18:53:57: 5000000 INFO @ Sun, 21 Jun 2020 18:54:01: 11000000 INFO @ Sun, 21 Jun 2020 18:54:01: 17000000 INFO @ Sun, 21 Jun 2020 18:54:03: 6000000 INFO @ Sun, 21 Jun 2020 18:54:06: 12000000 INFO @ Sun, 21 Jun 2020 18:54:07: 18000000 INFO @ Sun, 21 Jun 2020 18:54:08: 7000000 INFO @ Sun, 21 Jun 2020 18:54:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:10: #1 total tags in treatment: 18479450 INFO @ Sun, 21 Jun 2020 18:54:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:10: #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 18:54:10: #1 tags after filtering in treatment: 18479365 INFO @ Sun, 21 Jun 2020 18:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:12: 13000000 INFO @ Sun, 21 Jun 2020 18:54:12: #2 number of paired peaks: 1173 INFO @ Sun, 21 Jun 2020 18:54:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:12: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 18:54:12: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 21 Jun 2020 18:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.05_model.r INFO @ Sun, 21 Jun 2020 18:54:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:14: 8000000 INFO @ Sun, 21 Jun 2020 18:54:17: 14000000 INFO @ Sun, 21 Jun 2020 18:54:19: 9000000 INFO @ Sun, 21 Jun 2020 18:54:23: 15000000 INFO @ Sun, 21 Jun 2020 18:54:25: 10000000 INFO @ Sun, 21 Jun 2020 18:54:29: 16000000 INFO @ Sun, 21 Jun 2020 18:54:31: 11000000 INFO @ Sun, 21 Jun 2020 18:54:35: 17000000 INFO @ Sun, 21 Jun 2020 18:54:37: 12000000 INFO @ Sun, 21 Jun 2020 18:54:40: 18000000 INFO @ Sun, 21 Jun 2020 18:54:42: 13000000 INFO @ Sun, 21 Jun 2020 18:54:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:43: #1 total tags in treatment: 18479450 INFO @ Sun, 21 Jun 2020 18:54:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:43: #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 18:54:44: #1 tags after filtering in treatment: 18479365 INFO @ Sun, 21 Jun 2020 18:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:45: #2 number of paired peaks: 1173 INFO @ Sun, 21 Jun 2020 18:54:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:45: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 18:54:45: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 21 Jun 2020 18:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.10_model.r INFO @ Sun, 21 Jun 2020 18:54:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:48: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:54: 15000000 INFO @ Sun, 21 Jun 2020 18:54:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:00: 16000000 INFO @ Sun, 21 Jun 2020 18:55:05: 17000000 INFO @ Sun, 21 Jun 2020 18:55:11: 18000000 INFO @ Sun, 21 Jun 2020 18:55:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:55:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:55:14: #1 total tags in treatment: 18479450 INFO @ Sun, 21 Jun 2020 18:55:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:14: #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 18:55:15: #1 tags after filtering in treatment: 18479365 INFO @ Sun, 21 Jun 2020 18:55:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:16: #2 number of paired peaks: 1173 INFO @ Sun, 21 Jun 2020 18:55:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:16: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 18:55:16: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 21 Jun 2020 18:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.20_model.r INFO @ Sun, 21 Jun 2020 18:55:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.05_summits.bed INFO @ Sun, 21 Jun 2020 18:55:24: Done! pass1 - making usageList (265 chroms): 3 millis pass2 - checking and writing primary data (10319 records, 4 fields): 173 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.10_summits.bed INFO @ Sun, 21 Jun 2020 18:55:57: Done! pass1 - making usageList (184 chroms): 2 millis pass2 - checking and writing primary data (6693 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:56:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2559029/SRX2559029.20_summits.bed INFO @ Sun, 21 Jun 2020 18:56:28: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (3462 records, 4 fields): 9 millis CompletedMACS2peakCalling