Job ID = 6457897 SRX = SRX485203 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:21 prefetch.2.10.7: 1) Downloading 'SRR1187961'... 2020-06-21T12:08:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:49 prefetch.2.10.7: 1) 'SRR1187961' was downloaded successfully 2020-06-21T12:12:49 prefetch.2.10.7: 'SRR1187961' has 0 unresolved dependencies Read 27307334 spots for SRR1187961/SRR1187961.sra Written 27307334 spots for SRR1187961/SRR1187961.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: 00:06:35 27307334 reads; of these: 27307334 (100.00%) were unpaired; of these: 4461878 (16.34%) aligned 0 times 15470294 (56.65%) aligned exactly 1 time 7375162 (27.01%) aligned >1 times 83.66% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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] 9444609 / 22845456 = 0.4134 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 21:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.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 21:26:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:22: 1000000 INFO @ Sun, 21 Jun 2020 21:26:28: 2000000 INFO @ Sun, 21 Jun 2020 21:26:34: 3000000 INFO @ Sun, 21 Jun 2020 21:26:40: 4000000 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 21:26:45: 5000000 INFO @ Sun, 21 Jun 2020 21:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.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 21:26:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:51: 6000000 INFO @ Sun, 21 Jun 2020 21:26:53: 1000000 INFO @ Sun, 21 Jun 2020 21:26:57: 7000000 INFO @ Sun, 21 Jun 2020 21:26:59: 2000000 INFO @ Sun, 21 Jun 2020 21:27:03: 8000000 INFO @ Sun, 21 Jun 2020 21:27:04: 3000000 INFO @ Sun, 21 Jun 2020 21:27:10: 9000000 INFO @ Sun, 21 Jun 2020 21:27:10: 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 21:27:16: 10000000 INFO @ Sun, 21 Jun 2020 21:27:16: 5000000 INFO @ Sun, 21 Jun 2020 21:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.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 21:27:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:22: 11000000 INFO @ Sun, 21 Jun 2020 21:27:23: 6000000 INFO @ Sun, 21 Jun 2020 21:27:23: 1000000 INFO @ Sun, 21 Jun 2020 21:27:29: 7000000 INFO @ Sun, 21 Jun 2020 21:27:29: 12000000 INFO @ Sun, 21 Jun 2020 21:27:29: 2000000 INFO @ Sun, 21 Jun 2020 21:27:35: 8000000 INFO @ Sun, 21 Jun 2020 21:27:35: 13000000 INFO @ Sun, 21 Jun 2020 21:27:36: 3000000 INFO @ Sun, 21 Jun 2020 21:27:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:27:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:27:38: #1 total tags in treatment: 13400847 INFO @ Sun, 21 Jun 2020 21:27:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:38: #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 21:27:39: #1 tags after filtering in treatment: 13400816 INFO @ Sun, 21 Jun 2020 21:27:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:40: #2 number of paired peaks: 2418 INFO @ Sun, 21 Jun 2020 21:27:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:40: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:27:40: #2 alternative fragment length(s) may be 2,135 bps INFO @ Sun, 21 Jun 2020 21:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.05_model.r INFO @ Sun, 21 Jun 2020 21:27:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:42: 9000000 INFO @ Sun, 21 Jun 2020 21:27:43: 4000000 INFO @ Sun, 21 Jun 2020 21:27:48: 10000000 INFO @ Sun, 21 Jun 2020 21:27:49: 5000000 INFO @ Sun, 21 Jun 2020 21:27:55: 11000000 INFO @ Sun, 21 Jun 2020 21:27:56: 6000000 INFO @ Sun, 21 Jun 2020 21:28:01: 12000000 INFO @ Sun, 21 Jun 2020 21:28:02: 7000000 INFO @ Sun, 21 Jun 2020 21:28:08: 13000000 INFO @ Sun, 21 Jun 2020 21:28:08: 8000000 INFO @ Sun, 21 Jun 2020 21:28:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:10: #1 total tags in treatment: 13400847 INFO @ Sun, 21 Jun 2020 21:28:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:10: #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 21:28:11: #1 tags after filtering in treatment: 13400816 INFO @ Sun, 21 Jun 2020 21:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:12: #2 number of paired peaks: 2418 INFO @ Sun, 21 Jun 2020 21:28:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:12: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:28:12: #2 alternative fragment length(s) may be 2,135 bps INFO @ Sun, 21 Jun 2020 21:28:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.10_model.r INFO @ Sun, 21 Jun 2020 21:28:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:14: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:28:21: 10000000 INFO @ Sun, 21 Jun 2020 21:28:27: 11000000 INFO @ Sun, 21 Jun 2020 21:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.05_summits.bed INFO @ Sun, 21 Jun 2020 21:28:29: Done! pass1 - making usageList (736 chroms): 2 millis pass2 - checking and writing primary data (3382 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:33: 12000000 INFO @ Sun, 21 Jun 2020 21:28:39: 13000000 INFO @ Sun, 21 Jun 2020 21:28:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:41: #1 total tags in treatment: 13400847 INFO @ Sun, 21 Jun 2020 21:28:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:41: #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 21:28:41: #1 tags after filtering in treatment: 13400816 INFO @ Sun, 21 Jun 2020 21:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:43: #2 number of paired peaks: 2418 INFO @ Sun, 21 Jun 2020 21:28:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:43: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:28:43: #2 alternative fragment length(s) may be 2,135 bps INFO @ Sun, 21 Jun 2020 21:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.20_model.r INFO @ Sun, 21 Jun 2020 21:28:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.10_summits.bed INFO @ Sun, 21 Jun 2020 21:28:59: Done! pass1 - making usageList (565 chroms): 1 millis pass2 - checking and writing primary data (1911 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485203/SRX485203.20_summits.bed INFO @ Sun, 21 Jun 2020 21:29:28: Done! pass1 - making usageList (360 chroms): 1 millis pass2 - checking and writing primary data (908 records, 4 fields): 11 millis CompletedMACS2peakCalling