Job ID = 6456899 SRX = SRX4053306 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:25:09 prefetch.2.10.7: 1) Downloading 'SRR7132407'... 2020-06-21T11:25:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:56 prefetch.2.10.7: 'SRR7132407' is valid 2020-06-21T11:26:56 prefetch.2.10.7: 1) 'SRR7132407' was downloaded successfully 2020-06-21T11:26:56 prefetch.2.10.7: 'SRR7132407' has 0 unresolved dependencies Read 27970338 spots for SRR7132407/SRR7132407.sra Written 27970338 spots for SRR7132407/SRR7132407.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: 00:06:03 27970338 reads; of these: 27970338 (100.00%) were unpaired; of these: 1876931 (6.71%) aligned 0 times 24411953 (87.28%) aligned exactly 1 time 1681454 (6.01%) aligned >1 times 93.29% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 13986093 / 26093407 = 0.5360 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 20:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.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 20:38:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:55: 1000000 INFO @ Sun, 21 Jun 2020 20:39:02: 2000000 INFO @ Sun, 21 Jun 2020 20:39:09: 3000000 INFO @ Sun, 21 Jun 2020 20:39:16: 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 20:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.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 20:39:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:23: 5000000 INFO @ Sun, 21 Jun 2020 20:39:26: 1000000 INFO @ Sun, 21 Jun 2020 20:39:30: 6000000 INFO @ Sun, 21 Jun 2020 20:39:33: 2000000 INFO @ Sun, 21 Jun 2020 20:39:37: 7000000 INFO @ Sun, 21 Jun 2020 20:39:41: 3000000 INFO @ Sun, 21 Jun 2020 20:39:44: 8000000 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 20:39:48: 4000000 INFO @ Sun, 21 Jun 2020 20:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.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 20:39:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:51: 9000000 INFO @ Sun, 21 Jun 2020 20:39:55: 5000000 INFO @ Sun, 21 Jun 2020 20:39:56: 1000000 INFO @ Sun, 21 Jun 2020 20:39:59: 10000000 INFO @ Sun, 21 Jun 2020 20:40:03: 6000000 INFO @ Sun, 21 Jun 2020 20:40:03: 2000000 INFO @ Sun, 21 Jun 2020 20:40:06: 11000000 INFO @ Sun, 21 Jun 2020 20:40:10: 7000000 INFO @ Sun, 21 Jun 2020 20:40:10: 3000000 INFO @ Sun, 21 Jun 2020 20:40:14: 12000000 INFO @ Sun, 21 Jun 2020 20:40:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:40:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:40:15: #1 total tags in treatment: 12107314 INFO @ Sun, 21 Jun 2020 20:40:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:15: #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 20:40:15: #1 tags after filtering in treatment: 12107262 INFO @ Sun, 21 Jun 2020 20:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:17: #2 number of paired peaks: 11553 INFO @ Sun, 21 Jun 2020 20:40:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:17: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 20:40:17: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 20:40:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.05_model.r INFO @ Sun, 21 Jun 2020 20:40:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:17: 4000000 INFO @ Sun, 21 Jun 2020 20:40:17: 8000000 INFO @ Sun, 21 Jun 2020 20:40:24: 5000000 INFO @ Sun, 21 Jun 2020 20:40:24: 9000000 INFO @ Sun, 21 Jun 2020 20:40:30: 6000000 INFO @ Sun, 21 Jun 2020 20:40:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:37: 7000000 INFO @ Sun, 21 Jun 2020 20:40:39: 11000000 INFO @ Sun, 21 Jun 2020 20:40:43: 8000000 INFO @ Sun, 21 Jun 2020 20:40:46: 12000000 INFO @ Sun, 21 Jun 2020 20:40:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:40:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:40:46: #1 total tags in treatment: 12107314 INFO @ Sun, 21 Jun 2020 20:40:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:46: #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 20:40:47: #1 tags after filtering in treatment: 12107262 INFO @ Sun, 21 Jun 2020 20:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:49: #2 number of paired peaks: 11553 INFO @ Sun, 21 Jun 2020 20:40:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:49: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 20:40:49: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 20:40:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.10_model.r INFO @ Sun, 21 Jun 2020 20:40:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:49: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:40:55: 10000000 INFO @ Sun, 21 Jun 2020 20:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.05_summits.bed INFO @ Sun, 21 Jun 2020 20:41:01: Done! INFO @ Sun, 21 Jun 2020 20:41:01: 11000000 pass1 - making usageList (147 chroms): 2 millis pass2 - checking and writing primary data (6703 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:06: 12000000 INFO @ Sun, 21 Jun 2020 20:41:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:41:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:41:07: #1 total tags in treatment: 12107314 INFO @ Sun, 21 Jun 2020 20:41:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:07: #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 20:41:07: #1 tags after filtering in treatment: 12107262 INFO @ Sun, 21 Jun 2020 20:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:09: #2 number of paired peaks: 11553 INFO @ Sun, 21 Jun 2020 20:41:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:09: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:09: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:09: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:09: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 20:41:09: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 20:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.20_model.r INFO @ Sun, 21 Jun 2020 20:41:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.10_summits.bed INFO @ Sun, 21 Jun 2020 20:41:32: Done! pass1 - making usageList (102 chroms): 2 millis pass2 - checking and writing primary data (6351 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053306/SRX4053306.20_summits.bed INFO @ Sun, 21 Jun 2020 20:41:51: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (6009 records, 4 fields): 10 millis CompletedMACS2peakCalling