Job ID = 6456898 SRX = SRX4053305 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:13:39 prefetch.2.10.7: 1) Downloading 'SRR7132408'... 2020-06-21T11:13:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:44 prefetch.2.10.7: 'SRR7132408' is valid 2020-06-21T11:15:44 prefetch.2.10.7: 1) 'SRR7132408' was downloaded successfully 2020-06-21T11:15:44 prefetch.2.10.7: 'SRR7132408' has 0 unresolved dependencies Read 18863915 spots for SRR7132408/SRR7132408.sra Written 18863915 spots for SRR7132408/SRR7132408.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: 00:04:10 18863915 reads; of these: 18863915 (100.00%) were unpaired; of these: 2091006 (11.08%) aligned 0 times 15459426 (81.95%) aligned exactly 1 time 1313483 (6.96%) aligned >1 times 88.92% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 8175847 / 16772909 = 0.4874 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 20:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.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 20:24:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:44: 1000000 INFO @ Sun, 21 Jun 2020 20:24:50: 2000000 INFO @ Sun, 21 Jun 2020 20:24:56: 3000000 INFO @ Sun, 21 Jun 2020 20:25:02: 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 20:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.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 20:25:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:08: 5000000 INFO @ Sun, 21 Jun 2020 20:25:14: 1000000 INFO @ Sun, 21 Jun 2020 20:25:15: 6000000 INFO @ Sun, 21 Jun 2020 20:25:21: 2000000 INFO @ Sun, 21 Jun 2020 20:25:21: 7000000 INFO @ Sun, 21 Jun 2020 20:25:27: 3000000 INFO @ Sun, 21 Jun 2020 20:25:28: 8000000 INFO @ Sun, 21 Jun 2020 20:25:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:25:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:25:32: #1 total tags in treatment: 8597062 INFO @ Sun, 21 Jun 2020 20:25:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:32: #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 20:25:32: #1 tags after filtering in treatment: 8596997 INFO @ Sun, 21 Jun 2020 20:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:34: #2 number of paired peaks: 10634 INFO @ Sun, 21 Jun 2020 20:25:34: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:34: 4000000 INFO @ Sun, 21 Jun 2020 20:25:34: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:34: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:34: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:34: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:25:34: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 20:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.05_model.r INFO @ Sun, 21 Jun 2020 20:25:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:34: #3 Pre-compute pvalue-qvalue table... 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 20:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.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 20:25:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:40: 5000000 INFO @ Sun, 21 Jun 2020 20:25:45: 1000000 INFO @ Sun, 21 Jun 2020 20:25:46: 6000000 INFO @ Sun, 21 Jun 2020 20:25:52: 2000000 INFO @ Sun, 21 Jun 2020 20:25:53: 7000000 INFO @ Sun, 21 Jun 2020 20:25:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:59: 3000000 INFO @ Sun, 21 Jun 2020 20:26:00: 8000000 INFO @ Sun, 21 Jun 2020 20:26:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:26:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:26:05: #1 total tags in treatment: 8597062 INFO @ Sun, 21 Jun 2020 20:26:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:05: #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 20:26:05: #1 tags after filtering in treatment: 8596997 INFO @ Sun, 21 Jun 2020 20:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:05: 4000000 INFO @ Sun, 21 Jun 2020 20:26:06: #2 number of paired peaks: 10634 INFO @ Sun, 21 Jun 2020 20:26:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:06: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:26:06: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 20:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.10_model.r INFO @ Sun, 21 Jun 2020 20:26:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.05_summits.bed INFO @ Sun, 21 Jun 2020 20:26:08: Done! pass1 - making usageList (146 chroms): 2 millis pass2 - checking and writing primary data (6321 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:26:11: 5000000 INFO @ Sun, 21 Jun 2020 20:26:18: 6000000 INFO @ Sun, 21 Jun 2020 20:26:24: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:26:31: 8000000 INFO @ Sun, 21 Jun 2020 20:26:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:26:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:26:35: #1 total tags in treatment: 8597062 INFO @ Sun, 21 Jun 2020 20:26:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:35: #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 20:26:35: #1 tags after filtering in treatment: 8596997 INFO @ Sun, 21 Jun 2020 20:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:36: #2 number of paired peaks: 10634 INFO @ Sun, 21 Jun 2020 20:26:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:37: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:26:37: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 20:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.20_model.r INFO @ Sun, 21 Jun 2020 20:26:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.10_summits.bed INFO @ Sun, 21 Jun 2020 20:26:42: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (6051 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053305/SRX4053305.20_summits.bed INFO @ Sun, 21 Jun 2020 20:27:11: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (5683 records, 4 fields): 10 millis CompletedMACS2peakCalling