Job ID = 6452634 SRX = SRX020694 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:05:23 prefetch.2.10.7: 1) Downloading 'SRR060801'... 2020-06-21T08:05:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:10 prefetch.2.10.7: 'SRR060801' is valid 2020-06-21T08:07:10 prefetch.2.10.7: 1) 'SRR060801' was downloaded successfully Read 12709970 spots for SRR060801/SRR060801.sra Written 12709970 spots for SRR060801/SRR060801.sra 2020-06-21T08:07:55 prefetch.2.10.7: 1) Downloading 'SRR060802'... 2020-06-21T08:07:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:10:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:10:11 prefetch.2.10.7: 'SRR060802' is valid 2020-06-21T08:10:11 prefetch.2.10.7: 1) 'SRR060802' was downloaded successfully Read 12995670 spots for SRR060802/SRR060802.sra Written 12995670 spots for SRR060802/SRR060802.sra 2020-06-21T08:10:55 prefetch.2.10.7: 1) Downloading 'SRR060803'... 2020-06-21T08:10:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:14:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:14:28 prefetch.2.10.7: 'SRR060803' is valid 2020-06-21T08:14:28 prefetch.2.10.7: 1) 'SRR060803' was downloaded successfully Read 13335981 spots for SRR060803/SRR060803.sra Written 13335981 spots for SRR060803/SRR060803.sra 2020-06-21T08:15:12 prefetch.2.10.7: 1) Downloading 'SRR060804'... 2020-06-21T08:15:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:25 prefetch.2.10.7: 'SRR060804' is valid 2020-06-21T08:17:25 prefetch.2.10.7: 1) 'SRR060804' was downloaded successfully Read 13117930 spots for SRR060804/SRR060804.sra Written 13117930 spots for SRR060804/SRR060804.sra 2020-06-21T08:18:09 prefetch.2.10.7: 1) Downloading 'SRR060805'... 2020-06-21T08:18:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:36 prefetch.2.10.7: 'SRR060805' is valid 2020-06-21T08:21:36 prefetch.2.10.7: 1) 'SRR060805' was downloaded successfully Read 12652502 spots for SRR060805/SRR060805.sra Written 12652502 spots for SRR060805/SRR060805.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: 00:05:59 64812053 reads; of these: 64812053 (100.00%) were unpaired; of these: 41374259 (63.84%) aligned 0 times 19200667 (29.63%) aligned exactly 1 time 4237127 (6.54%) aligned >1 times 36.16% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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 8 files... [bam_rmdupse_core] 9748308 / 23437794 = 0.4159 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 17:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.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 17:33:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:09: 1000000 INFO @ Sun, 21 Jun 2020 17:33:14: 2000000 INFO @ Sun, 21 Jun 2020 17:33:18: 3000000 INFO @ Sun, 21 Jun 2020 17:33:23: 4000000 INFO @ Sun, 21 Jun 2020 17:33:27: 5000000 INFO @ Sun, 21 Jun 2020 17:33:32: 6000000 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 17:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.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 17:33:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:37: 7000000 INFO @ Sun, 21 Jun 2020 17:33:40: 1000000 INFO @ Sun, 21 Jun 2020 17:33:42: 8000000 INFO @ Sun, 21 Jun 2020 17:33:46: 2000000 INFO @ Sun, 21 Jun 2020 17:33:47: 9000000 INFO @ Sun, 21 Jun 2020 17:33:51: 3000000 INFO @ Sun, 21 Jun 2020 17:33:52: 10000000 INFO @ Sun, 21 Jun 2020 17:33:57: 11000000 INFO @ Sun, 21 Jun 2020 17:33:57: 4000000 INFO @ Sun, 21 Jun 2020 17:34:02: 12000000 INFO @ Sun, 21 Jun 2020 17:34:02: 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 17:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.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 17:34:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:07: 13000000 INFO @ Sun, 21 Jun 2020 17:34:08: 6000000 INFO @ Sun, 21 Jun 2020 17:34:10: 1000000 INFO @ Sun, 21 Jun 2020 17:34:11: #1 tag size is determined as 28 bps INFO @ Sun, 21 Jun 2020 17:34:11: #1 tag size = 28 INFO @ Sun, 21 Jun 2020 17:34:11: #1 total tags in treatment: 13689486 INFO @ Sun, 21 Jun 2020 17:34:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:11: #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 17:34:11: #1 tags after filtering in treatment: 13689484 INFO @ Sun, 21 Jun 2020 17:34:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:13: #2 number of paired peaks: 3013 INFO @ Sun, 21 Jun 2020 17:34:13: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:13: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:13: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:13: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:13: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 17:34:13: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 17:34:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.05_model.r INFO @ Sun, 21 Jun 2020 17:34:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:14: 7000000 INFO @ Sun, 21 Jun 2020 17:34:15: 2000000 INFO @ Sun, 21 Jun 2020 17:34:19: 8000000 INFO @ Sun, 21 Jun 2020 17:34:21: 3000000 INFO @ Sun, 21 Jun 2020 17:34:25: 9000000 INFO @ Sun, 21 Jun 2020 17:34:26: 4000000 INFO @ Sun, 21 Jun 2020 17:34:31: 10000000 INFO @ Sun, 21 Jun 2020 17:34:31: 5000000 INFO @ Sun, 21 Jun 2020 17:34:36: 6000000 INFO @ Sun, 21 Jun 2020 17:34:36: 11000000 INFO @ Sun, 21 Jun 2020 17:34:41: 7000000 INFO @ Sun, 21 Jun 2020 17:34:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:42: 12000000 INFO @ Sun, 21 Jun 2020 17:34:46: 8000000 INFO @ Sun, 21 Jun 2020 17:34:48: 13000000 INFO @ Sun, 21 Jun 2020 17:34:51: 9000000 INFO @ Sun, 21 Jun 2020 17:34:52: #1 tag size is determined as 28 bps INFO @ Sun, 21 Jun 2020 17:34:52: #1 tag size = 28 INFO @ Sun, 21 Jun 2020 17:34:52: #1 total tags in treatment: 13689486 INFO @ Sun, 21 Jun 2020 17:34:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:52: #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 17:34:52: #1 tags after filtering in treatment: 13689484 INFO @ Sun, 21 Jun 2020 17:34:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:54: #2 number of paired peaks: 3013 INFO @ Sun, 21 Jun 2020 17:34:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:54: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 17:34:54: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 17:34:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.10_model.r INFO @ Sun, 21 Jun 2020 17:34:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:55: 10000000 INFO @ Sun, 21 Jun 2020 17:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.05_summits.bed INFO @ Sun, 21 Jun 2020 17:34:57: Done! pass1 - making usageList (253 chroms): 3 millis pass2 - checking and writing primary data (14613 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:35:00: 11000000 INFO @ Sun, 21 Jun 2020 17:35:05: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:35:10: 13000000 INFO @ Sun, 21 Jun 2020 17:35:13: #1 tag size is determined as 28 bps INFO @ Sun, 21 Jun 2020 17:35:13: #1 tag size = 28 INFO @ Sun, 21 Jun 2020 17:35:13: #1 total tags in treatment: 13689486 INFO @ Sun, 21 Jun 2020 17:35:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:13: #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 17:35:14: #1 tags after filtering in treatment: 13689484 INFO @ Sun, 21 Jun 2020 17:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:15: #2 number of paired peaks: 3013 INFO @ Sun, 21 Jun 2020 17:35:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:15: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 17:35:15: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 17:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.20_model.r INFO @ Sun, 21 Jun 2020 17:35:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.10_summits.bed INFO @ Sun, 21 Jun 2020 17:35:38: Done! pass1 - making usageList (175 chroms): 3 millis pass2 - checking and writing primary data (9766 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:35:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:35:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020694/SRX020694.20_summits.bed INFO @ Sun, 21 Jun 2020 17:35:56: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (4352 records, 4 fields): 10 millis CompletedMACS2peakCalling