Job ID = 6455259 SRX = SRX287600 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:56:25 prefetch.2.10.7: 1) Downloading 'SRR869743'... 2020-06-21T09:56:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:17 prefetch.2.10.7: 1) 'SRR869743' was downloaded successfully Read 21552956 spots for SRR869743/SRR869743.sra Written 21552956 spots for SRR869743/SRR869743.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: 00:05:36 21552956 reads; of these: 21552956 (100.00%) were unpaired; of these: 1243752 (5.77%) aligned 0 times 17123468 (79.45%) aligned exactly 1 time 3185736 (14.78%) aligned >1 times 94.23% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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 12 files... [bam_rmdupse_core] 3982295 / 20309204 = 0.1961 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 19:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.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 19:11:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:38: 1000000 INFO @ Sun, 21 Jun 2020 19:11:45: 2000000 INFO @ Sun, 21 Jun 2020 19:11:52: 3000000 INFO @ Sun, 21 Jun 2020 19:11:58: 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 19:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.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 19:12:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:06: 5000000 INFO @ Sun, 21 Jun 2020 19:12:07: 1000000 INFO @ Sun, 21 Jun 2020 19:12:13: 6000000 INFO @ Sun, 21 Jun 2020 19:12:13: 2000000 INFO @ Sun, 21 Jun 2020 19:12:20: 7000000 INFO @ Sun, 21 Jun 2020 19:12:20: 3000000 INFO @ Sun, 21 Jun 2020 19:12:26: 4000000 INFO @ Sun, 21 Jun 2020 19:12:27: 8000000 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 19:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.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 19:12:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:33: 5000000 INFO @ Sun, 21 Jun 2020 19:12:34: 9000000 INFO @ Sun, 21 Jun 2020 19:12:37: 1000000 INFO @ Sun, 21 Jun 2020 19:12:39: 6000000 INFO @ Sun, 21 Jun 2020 19:12:41: 10000000 INFO @ Sun, 21 Jun 2020 19:12:43: 2000000 INFO @ Sun, 21 Jun 2020 19:12:45: 7000000 INFO @ Sun, 21 Jun 2020 19:12:48: 11000000 INFO @ Sun, 21 Jun 2020 19:12:50: 3000000 INFO @ Sun, 21 Jun 2020 19:12:52: 8000000 INFO @ Sun, 21 Jun 2020 19:12:56: 12000000 INFO @ Sun, 21 Jun 2020 19:12:56: 4000000 INFO @ Sun, 21 Jun 2020 19:12:58: 9000000 INFO @ Sun, 21 Jun 2020 19:13:02: 5000000 INFO @ Sun, 21 Jun 2020 19:13:03: 13000000 INFO @ Sun, 21 Jun 2020 19:13:04: 10000000 INFO @ Sun, 21 Jun 2020 19:13:08: 6000000 INFO @ Sun, 21 Jun 2020 19:13:10: 14000000 INFO @ Sun, 21 Jun 2020 19:13:11: 11000000 INFO @ Sun, 21 Jun 2020 19:13:15: 7000000 INFO @ Sun, 21 Jun 2020 19:13:17: 12000000 INFO @ Sun, 21 Jun 2020 19:13:17: 15000000 INFO @ Sun, 21 Jun 2020 19:13:21: 8000000 INFO @ Sun, 21 Jun 2020 19:13:23: 13000000 INFO @ Sun, 21 Jun 2020 19:13:24: 16000000 INFO @ Sun, 21 Jun 2020 19:13:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:27: #1 total tags in treatment: 16326909 INFO @ Sun, 21 Jun 2020 19:13:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:27: #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 19:13:27: 9000000 INFO @ Sun, 21 Jun 2020 19:13:28: #1 tags after filtering in treatment: 16326905 INFO @ Sun, 21 Jun 2020 19:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:29: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 19:13:29: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:29: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 19:13:29: #2 alternative fragment length(s) may be 4,142 bps INFO @ Sun, 21 Jun 2020 19:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.05_model.r INFO @ Sun, 21 Jun 2020 19:13:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:30: 14000000 INFO @ Sun, 21 Jun 2020 19:13:33: 10000000 INFO @ Sun, 21 Jun 2020 19:13:36: 15000000 INFO @ Sun, 21 Jun 2020 19:13:39: 11000000 INFO @ Sun, 21 Jun 2020 19:13:42: 16000000 INFO @ Sun, 21 Jun 2020 19:13:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:44: #1 total tags in treatment: 16326909 INFO @ Sun, 21 Jun 2020 19:13:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:44: #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 19:13:45: #1 tags after filtering in treatment: 16326905 INFO @ Sun, 21 Jun 2020 19:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:45: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:46: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 19:13:46: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:46: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 19:13:46: #2 alternative fragment length(s) may be 4,142 bps INFO @ Sun, 21 Jun 2020 19:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.10_model.r INFO @ Sun, 21 Jun 2020 19:13:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:51: 13000000 INFO @ Sun, 21 Jun 2020 19:13:57: 14000000 INFO @ Sun, 21 Jun 2020 19:14:03: 15000000 INFO @ Sun, 21 Jun 2020 19:14:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:08: 16000000 INFO @ Sun, 21 Jun 2020 19:14:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:10: #1 total tags in treatment: 16326909 INFO @ Sun, 21 Jun 2020 19:14:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:10: #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 19:14:11: #1 tags after filtering in treatment: 16326905 INFO @ Sun, 21 Jun 2020 19:14:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:12: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 19:14:12: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:12: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 19:14:12: #2 alternative fragment length(s) may be 4,142 bps INFO @ Sun, 21 Jun 2020 19:14:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.20_model.r INFO @ Sun, 21 Jun 2020 19:14:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:14:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:25: Done! pass1 - making usageList (423 chroms): 2 millis pass2 - checking and writing primary data (5300 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:41: Done! pass1 - making usageList (275 chroms): 1 millis pass2 - checking and writing primary data (2149 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287600/SRX287600.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:07: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 7 millis CompletedMACS2peakCalling