Job ID = 6455154 SRX = SRX2804216 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:55 prefetch.2.10.7: 1) Downloading 'SRR5534644'... 2020-06-21T09:51:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:26 prefetch.2.10.7: 'SRR5534644' is valid 2020-06-21T09:54:26 prefetch.2.10.7: 1) 'SRR5534644' was downloaded successfully 2020-06-21T09:54:26 prefetch.2.10.7: 'SRR5534644' has 0 unresolved dependencies Read 24057199 spots for SRR5534644/SRR5534644.sra Written 24057199 spots for SRR5534644/SRR5534644.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: 00:04:04 24057199 reads; of these: 24057199 (100.00%) were unpaired; of these: 12145726 (50.49%) aligned 0 times 9298400 (38.65%) aligned exactly 1 time 2613073 (10.86%) aligned >1 times 49.51% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 2569877 / 11911473 = 0.2157 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 19:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.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 19:02:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:31: 1000000 INFO @ Sun, 21 Jun 2020 19:02:36: 2000000 INFO @ Sun, 21 Jun 2020 19:02:42: 3000000 INFO @ Sun, 21 Jun 2020 19:02:47: 4000000 INFO @ Sun, 21 Jun 2020 19:02:53: 5000000 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 19:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.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 19:02:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:58: 6000000 INFO @ Sun, 21 Jun 2020 19:03:01: 1000000 INFO @ Sun, 21 Jun 2020 19:03:04: 7000000 INFO @ Sun, 21 Jun 2020 19:03:06: 2000000 INFO @ Sun, 21 Jun 2020 19:03:10: 8000000 INFO @ Sun, 21 Jun 2020 19:03:11: 3000000 INFO @ Sun, 21 Jun 2020 19:03:16: 9000000 INFO @ Sun, 21 Jun 2020 19:03:16: 4000000 INFO @ Sun, 21 Jun 2020 19:03:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:03:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:03:18: #1 total tags in treatment: 9341596 INFO @ Sun, 21 Jun 2020 19:03:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:18: #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 19:03:19: #1 tags after filtering in treatment: 9341585 INFO @ Sun, 21 Jun 2020 19:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:19: #2 number of paired peaks: 1498 INFO @ Sun, 21 Jun 2020 19:03:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:19: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:03:19: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.05_model.r INFO @ Sun, 21 Jun 2020 19:03:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:21: 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 19:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.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 19:03:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:26: 6000000 INFO @ Sun, 21 Jun 2020 19:03:31: 7000000 INFO @ Sun, 21 Jun 2020 19:03:32: 1000000 INFO @ Sun, 21 Jun 2020 19:03:36: 8000000 INFO @ Sun, 21 Jun 2020 19:03:37: 2000000 INFO @ Sun, 21 Jun 2020 19:03:41: 9000000 INFO @ Sun, 21 Jun 2020 19:03:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:43: 3000000 INFO @ Sun, 21 Jun 2020 19:03:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:03:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:03:43: #1 total tags in treatment: 9341596 INFO @ Sun, 21 Jun 2020 19:03:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:43: #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 19:03:44: #1 tags after filtering in treatment: 9341585 INFO @ Sun, 21 Jun 2020 19:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:44: #2 number of paired peaks: 1498 INFO @ Sun, 21 Jun 2020 19:03:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:45: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:03:45: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.10_model.r INFO @ Sun, 21 Jun 2020 19:03:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:48: 4000000 INFO @ Sun, 21 Jun 2020 19:03:53: 5000000 INFO @ Sun, 21 Jun 2020 19:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:54: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (5677 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:59: 6000000 INFO @ Sun, 21 Jun 2020 19:04:04: 7000000 INFO @ Sun, 21 Jun 2020 19:04:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:10: 8000000 INFO @ Sun, 21 Jun 2020 19:04:16: 9000000 INFO @ Sun, 21 Jun 2020 19:04:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:04:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:04:18: #1 total tags in treatment: 9341596 INFO @ Sun, 21 Jun 2020 19:04:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:18: #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 19:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.10_summits.bed INFO @ Sun, 21 Jun 2020 19:04:18: Done! INFO @ Sun, 21 Jun 2020 19:04:18: #1 tags after filtering in treatment: 9341585 INFO @ Sun, 21 Jun 2020 19:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:18: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (263 chroms): 2 millis pass2 - checking and writing primary data (4049 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:19: #2 number of paired peaks: 1498 INFO @ Sun, 21 Jun 2020 19:04:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:19: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:04:19: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:04:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.20_model.r INFO @ Sun, 21 Jun 2020 19:04:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804216/SRX2804216.20_summits.bed INFO @ Sun, 21 Jun 2020 19:04:50: Done! pass1 - making usageList (189 chroms): 1 millis pass2 - checking and writing primary data (2711 records, 4 fields): 9 millis CompletedMACS2peakCalling