Job ID = 6456073 SRX = SRX3167251 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:27:40 prefetch.2.10.7: 1) Downloading 'SRR6014254'... 2020-06-21T10:27:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:32 prefetch.2.10.7: 1) 'SRR6014254' was downloaded successfully Read 14187435 spots for SRR6014254/SRR6014254.sra Written 14187435 spots for SRR6014254/SRR6014254.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: 00:04:20 14187435 reads; of these: 14187435 (100.00%) were unpaired; of these: 1602003 (11.29%) aligned 0 times 7307460 (51.51%) aligned exactly 1 time 5277972 (37.20%) aligned >1 times 88.71% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 3134599 / 12585432 = 0.2491 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 19:39:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.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 19:39:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:10: 1000000 INFO @ Sun, 21 Jun 2020 19:39:15: 2000000 INFO @ Sun, 21 Jun 2020 19:39:20: 3000000 INFO @ Sun, 21 Jun 2020 19:39:26: 4000000 INFO @ Sun, 21 Jun 2020 19:39:31: 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 19:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.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 19:39:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:36: 6000000 INFO @ Sun, 21 Jun 2020 19:39:40: 1000000 INFO @ Sun, 21 Jun 2020 19:39:42: 7000000 INFO @ Sun, 21 Jun 2020 19:39:46: 2000000 INFO @ Sun, 21 Jun 2020 19:39:48: 8000000 INFO @ Sun, 21 Jun 2020 19:39:52: 3000000 INFO @ Sun, 21 Jun 2020 19:39:53: 9000000 INFO @ Sun, 21 Jun 2020 19:39:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:39:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:39:56: #1 total tags in treatment: 9450833 INFO @ Sun, 21 Jun 2020 19:39:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:56: #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 19:39:56: #1 tags after filtering in treatment: 9450745 INFO @ Sun, 21 Jun 2020 19:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:57: #2 number of paired peaks: 2264 INFO @ Sun, 21 Jun 2020 19:39:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:57: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 19:39:57: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 19:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.05_model.r INFO @ Sun, 21 Jun 2020 19:39:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:57: 4000000 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 19:40:03: 5000000 INFO @ Sun, 21 Jun 2020 19:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.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 19:40:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:08: 6000000 INFO @ Sun, 21 Jun 2020 19:40:10: 1000000 INFO @ Sun, 21 Jun 2020 19:40:14: 7000000 INFO @ Sun, 21 Jun 2020 19:40:15: 2000000 INFO @ Sun, 21 Jun 2020 19:40:19: 8000000 INFO @ Sun, 21 Jun 2020 19:40:21: 3000000 INFO @ Sun, 21 Jun 2020 19:40:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:25: 9000000 INFO @ Sun, 21 Jun 2020 19:40:26: 4000000 INFO @ Sun, 21 Jun 2020 19:40:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:40:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:40:27: #1 total tags in treatment: 9450833 INFO @ Sun, 21 Jun 2020 19:40:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:27: #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 19:40:28: #1 tags after filtering in treatment: 9450745 INFO @ Sun, 21 Jun 2020 19:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:28: #2 number of paired peaks: 2264 INFO @ Sun, 21 Jun 2020 19:40:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:29: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 19:40:29: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 19:40:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.10_model.r INFO @ Sun, 21 Jun 2020 19:40:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:31: 5000000 INFO @ Sun, 21 Jun 2020 19:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.05_summits.bed INFO @ Sun, 21 Jun 2020 19:40:32: Done! pass1 - making usageList (782 chroms): 2 millis pass2 - checking and writing primary data (3810 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:40:37: 6000000 INFO @ Sun, 21 Jun 2020 19:40:42: 7000000 INFO @ Sun, 21 Jun 2020 19:40:47: 8000000 INFO @ Sun, 21 Jun 2020 19:40:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:53: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:40:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:40:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:40:55: #1 total tags in treatment: 9450833 INFO @ Sun, 21 Jun 2020 19:40:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:55: #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 19:40:56: #1 tags after filtering in treatment: 9450745 INFO @ Sun, 21 Jun 2020 19:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:56: #2 number of paired peaks: 2264 INFO @ Sun, 21 Jun 2020 19:40:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:56: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 19:40:56: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 19:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.20_model.r INFO @ Sun, 21 Jun 2020 19:40:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:03: Done! pass1 - making usageList (731 chroms): 1 millis pass2 - checking and writing primary data (2827 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167251/SRX3167251.20_summits.bed INFO @ Sun, 21 Jun 2020 19:41:30: Done! pass1 - making usageList (644 chroms): 1 millis pass2 - checking and writing primary data (2101 records, 4 fields): 18 millis CompletedMACS2peakCalling