Job ID = 6455645 SRX = SRX287953 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:09:36 prefetch.2.10.7: 1) Downloading 'SRR870142'... 2020-06-21T10:09:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:12:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:12:18 prefetch.2.10.7: 1) 'SRR870142' was downloaded successfully Read 17623531 spots for SRR870142/SRR870142.sra Written 17623531 spots for SRR870142/SRR870142.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: 00:04:02 17623531 reads; of these: 17623531 (100.00%) were unpaired; of these: 857425 (4.87%) aligned 0 times 14841282 (84.21%) aligned exactly 1 time 1924824 (10.92%) aligned >1 times 95.13% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 1827353 / 16766106 = 0.1090 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 19:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.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 19:21:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:55: 1000000 INFO @ Sun, 21 Jun 2020 19:22:00: 2000000 INFO @ Sun, 21 Jun 2020 19:22:05: 3000000 INFO @ Sun, 21 Jun 2020 19:22:10: 4000000 INFO @ Sun, 21 Jun 2020 19:22:15: 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 19:22:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.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 19:22:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:20: 6000000 INFO @ Sun, 21 Jun 2020 19:22:25: 1000000 INFO @ Sun, 21 Jun 2020 19:22:25: 7000000 INFO @ Sun, 21 Jun 2020 19:22:30: 2000000 INFO @ Sun, 21 Jun 2020 19:22:30: 8000000 INFO @ Sun, 21 Jun 2020 19:22:35: 3000000 INFO @ Sun, 21 Jun 2020 19:22:36: 9000000 INFO @ Sun, 21 Jun 2020 19:22:40: 4000000 INFO @ Sun, 21 Jun 2020 19:22:41: 10000000 INFO @ Sun, 21 Jun 2020 19:22:45: 5000000 INFO @ Sun, 21 Jun 2020 19:22:46: 11000000 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 19:22:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.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 19:22:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:50: 6000000 INFO @ Sun, 21 Jun 2020 19:22:51: 12000000 INFO @ Sun, 21 Jun 2020 19:22:54: 1000000 INFO @ Sun, 21 Jun 2020 19:22:56: 7000000 INFO @ Sun, 21 Jun 2020 19:22:56: 13000000 INFO @ Sun, 21 Jun 2020 19:23:00: 2000000 INFO @ Sun, 21 Jun 2020 19:23:01: 8000000 INFO @ Sun, 21 Jun 2020 19:23:01: 14000000 INFO @ Sun, 21 Jun 2020 19:23:05: 3000000 INFO @ Sun, 21 Jun 2020 19:23:06: 9000000 INFO @ Sun, 21 Jun 2020 19:23:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:06: #1 total tags in treatment: 14938753 INFO @ Sun, 21 Jun 2020 19:23:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:06: #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 19:23:07: #1 tags after filtering in treatment: 14938743 INFO @ Sun, 21 Jun 2020 19:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:08: #2 number of paired peaks: 164 WARNING @ Sun, 21 Jun 2020 19:23:08: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:08: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:23:08: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 19:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.05_model.r INFO @ Sun, 21 Jun 2020 19:23:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:10: 4000000 INFO @ Sun, 21 Jun 2020 19:23:11: 10000000 INFO @ Sun, 21 Jun 2020 19:23:15: 5000000 INFO @ Sun, 21 Jun 2020 19:23:16: 11000000 INFO @ Sun, 21 Jun 2020 19:23:20: 6000000 INFO @ Sun, 21 Jun 2020 19:23:21: 12000000 INFO @ Sun, 21 Jun 2020 19:23:25: 7000000 INFO @ Sun, 21 Jun 2020 19:23:27: 13000000 INFO @ Sun, 21 Jun 2020 19:23:31: 8000000 INFO @ Sun, 21 Jun 2020 19:23:32: 14000000 INFO @ Sun, 21 Jun 2020 19:23:36: 9000000 INFO @ Sun, 21 Jun 2020 19:23:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:37: #1 total tags in treatment: 14938753 INFO @ Sun, 21 Jun 2020 19:23:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:37: #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 19:23:38: #1 tags after filtering in treatment: 14938743 INFO @ Sun, 21 Jun 2020 19:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:39: #2 number of paired peaks: 164 WARNING @ Sun, 21 Jun 2020 19:23:39: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:39: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:23:39: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 19:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.10_model.r INFO @ Sun, 21 Jun 2020 19:23:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:41: 10000000 INFO @ Sun, 21 Jun 2020 19:23:46: 11000000 INFO @ Sun, 21 Jun 2020 19:23:51: 12000000 INFO @ Sun, 21 Jun 2020 19:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.05_summits.bed INFO @ Sun, 21 Jun 2020 19:23:55: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (4688 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:57: 13000000 INFO @ Sun, 21 Jun 2020 19:24:02: 14000000 INFO @ Sun, 21 Jun 2020 19:24:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:07: #1 total tags in treatment: 14938753 INFO @ Sun, 21 Jun 2020 19:24:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:07: #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 19:24:08: #1 tags after filtering in treatment: 14938743 INFO @ Sun, 21 Jun 2020 19:24:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:09: #2 number of paired peaks: 164 WARNING @ Sun, 21 Jun 2020 19:24:09: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:09: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:24:09: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 19:24:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.20_model.r INFO @ Sun, 21 Jun 2020 19:24:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.10_summits.bed INFO @ Sun, 21 Jun 2020 19:24:27: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (1976 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:24:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287953/SRX287953.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:00: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 4 millis CompletedMACS2peakCalling