Job ID = 6454696 SRX = SRX2520645 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:59 prefetch.2.10.7: 1) Downloading 'SRR5206764'... 2020-06-21T09:22:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:34 prefetch.2.10.7: 'SRR5206764' is valid 2020-06-21T09:25:34 prefetch.2.10.7: 1) 'SRR5206764' was downloaded successfully Read 12815914 spots for SRR5206764/SRR5206764.sra Written 12815914 spots for SRR5206764/SRR5206764.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: 00:03:04 12815914 reads; of these: 12815914 (100.00%) were unpaired; of these: 185179 (1.44%) aligned 0 times 10421423 (81.32%) aligned exactly 1 time 2209312 (17.24%) aligned >1 times 98.56% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 4279056 / 12630735 = 0.3388 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 18:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.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 18:32:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:24: 1000000 INFO @ Sun, 21 Jun 2020 18:32:31: 2000000 INFO @ Sun, 21 Jun 2020 18:32:38: 3000000 INFO @ Sun, 21 Jun 2020 18:32:45: 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 18:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.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 18:32:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:52: 5000000 INFO @ Sun, 21 Jun 2020 18:32:55: 1000000 INFO @ Sun, 21 Jun 2020 18:33:00: 6000000 INFO @ Sun, 21 Jun 2020 18:33:03: 2000000 INFO @ Sun, 21 Jun 2020 18:33:08: 7000000 INFO @ Sun, 21 Jun 2020 18:33:11: 3000000 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 18:33:16: 8000000 INFO @ Sun, 21 Jun 2020 18:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.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 18:33:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:19: #1 total tags in treatment: 8351679 INFO @ Sun, 21 Jun 2020 18:33:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:19: #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 18:33:19: #1 tags after filtering in treatment: 8351533 INFO @ Sun, 21 Jun 2020 18:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:19: 4000000 INFO @ Sun, 21 Jun 2020 18:33:20: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 18:33:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:20: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:33:20: #2 alternative fragment length(s) may be 27,124,251,257,269,595 bps INFO @ Sun, 21 Jun 2020 18:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.05_model.r INFO @ Sun, 21 Jun 2020 18:33:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:25: 1000000 INFO @ Sun, 21 Jun 2020 18:33:27: 5000000 INFO @ Sun, 21 Jun 2020 18:33:33: 2000000 INFO @ Sun, 21 Jun 2020 18:33:35: 6000000 INFO @ Sun, 21 Jun 2020 18:33:41: 3000000 INFO @ Sun, 21 Jun 2020 18:33:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:44: 7000000 INFO @ Sun, 21 Jun 2020 18:33:49: 4000000 INFO @ Sun, 21 Jun 2020 18:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:52: Done! INFO @ Sun, 21 Jun 2020 18:33:52: 8000000 pass1 - making usageList (148 chroms): 2 millis pass2 - checking and writing primary data (4547 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:55: #1 total tags in treatment: 8351679 INFO @ Sun, 21 Jun 2020 18:33:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:55: #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 18:33:56: #1 tags after filtering in treatment: 8351533 INFO @ Sun, 21 Jun 2020 18:33:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:57: 5000000 INFO @ Sun, 21 Jun 2020 18:33:57: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 18:33:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:57: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:33:57: #2 alternative fragment length(s) may be 27,124,251,257,269,595 bps INFO @ Sun, 21 Jun 2020 18:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.10_model.r INFO @ Sun, 21 Jun 2020 18:33:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:34:04: 6000000 INFO @ Sun, 21 Jun 2020 18:34:11: 7000000 INFO @ Sun, 21 Jun 2020 18:34:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:18: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:34:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:34:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:34:21: #1 total tags in treatment: 8351679 INFO @ Sun, 21 Jun 2020 18:34:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:21: #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 18:34:21: #1 tags after filtering in treatment: 8351533 INFO @ Sun, 21 Jun 2020 18:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:22: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 18:34:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:22: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:34:22: #2 alternative fragment length(s) may be 27,124,251,257,269,595 bps INFO @ Sun, 21 Jun 2020 18:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.20_model.r INFO @ Sun, 21 Jun 2020 18:34:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:25: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (1008 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520645/SRX2520645.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:52: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 3 millis CompletedMACS2peakCalling