Job ID = 6458404 SRX = SRX512267 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:33:04 prefetch.2.10.7: 1) Downloading 'SRR1220293'... 2020-06-21T12:33:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:53 prefetch.2.10.7: 1) 'SRR1220293' was downloaded successfully Read 45861065 spots for SRR1220293/SRR1220293.sra Written 45861065 spots for SRR1220293/SRR1220293.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:30 45861065 reads; of these: 45861065 (100.00%) were unpaired; of these: 11277830 (24.59%) aligned 0 times 29920338 (65.24%) aligned exactly 1 time 4662897 (10.17%) aligned >1 times 75.41% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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 16 files... [bam_rmdupse_core] 16406399 / 34583235 = 0.4744 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 21:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.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 21:55:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:54: 1000000 INFO @ Sun, 21 Jun 2020 21:56:00: 2000000 INFO @ Sun, 21 Jun 2020 21:56:06: 3000000 INFO @ Sun, 21 Jun 2020 21:56:13: 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 21:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.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 21:56:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:19: 5000000 INFO @ Sun, 21 Jun 2020 21:56:24: 1000000 INFO @ Sun, 21 Jun 2020 21:56:26: 6000000 INFO @ Sun, 21 Jun 2020 21:56:31: 2000000 INFO @ Sun, 21 Jun 2020 21:56:32: 7000000 INFO @ Sun, 21 Jun 2020 21:56:38: 3000000 INFO @ Sun, 21 Jun 2020 21:56:39: 8000000 INFO @ Sun, 21 Jun 2020 21:56:45: 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 21:56:46: 9000000 INFO @ Sun, 21 Jun 2020 21:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.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 21:56:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:51: 5000000 INFO @ Sun, 21 Jun 2020 21:56:53: 10000000 INFO @ Sun, 21 Jun 2020 21:56:54: 1000000 INFO @ Sun, 21 Jun 2020 21:56:58: 6000000 INFO @ Sun, 21 Jun 2020 21:57:00: 11000000 INFO @ Sun, 21 Jun 2020 21:57:00: 2000000 INFO @ Sun, 21 Jun 2020 21:57:05: 7000000 INFO @ Sun, 21 Jun 2020 21:57:06: 3000000 INFO @ Sun, 21 Jun 2020 21:57:06: 12000000 INFO @ Sun, 21 Jun 2020 21:57:12: 4000000 INFO @ Sun, 21 Jun 2020 21:57:12: 8000000 INFO @ Sun, 21 Jun 2020 21:57:13: 13000000 INFO @ Sun, 21 Jun 2020 21:57:18: 5000000 INFO @ Sun, 21 Jun 2020 21:57:19: 9000000 INFO @ Sun, 21 Jun 2020 21:57:20: 14000000 INFO @ Sun, 21 Jun 2020 21:57:24: 6000000 INFO @ Sun, 21 Jun 2020 21:57:26: 10000000 INFO @ Sun, 21 Jun 2020 21:57:27: 15000000 INFO @ Sun, 21 Jun 2020 21:57:30: 7000000 INFO @ Sun, 21 Jun 2020 21:57:32: 11000000 INFO @ Sun, 21 Jun 2020 21:57:34: 16000000 INFO @ Sun, 21 Jun 2020 21:57:36: 8000000 INFO @ Sun, 21 Jun 2020 21:57:39: 12000000 INFO @ Sun, 21 Jun 2020 21:57:40: 17000000 INFO @ Sun, 21 Jun 2020 21:57:42: 9000000 INFO @ Sun, 21 Jun 2020 21:57:46: 13000000 INFO @ Sun, 21 Jun 2020 21:57:47: 18000000 INFO @ Sun, 21 Jun 2020 21:57:48: 10000000 INFO @ Sun, 21 Jun 2020 21:57:49: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 21:57:49: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 21:57:49: #1 total tags in treatment: 18176836 INFO @ Sun, 21 Jun 2020 21:57:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:49: #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 21:57:49: #1 tags after filtering in treatment: 18176814 INFO @ Sun, 21 Jun 2020 21:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:51: #2 number of paired peaks: 966 WARNING @ Sun, 21 Jun 2020 21:57:51: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sun, 21 Jun 2020 21:57:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:51: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 21:57:51: #2 alternative fragment length(s) may be 4,139 bps INFO @ Sun, 21 Jun 2020 21:57:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.05_model.r INFO @ Sun, 21 Jun 2020 21:57:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:57:53: 14000000 INFO @ Sun, 21 Jun 2020 21:57:54: 11000000 INFO @ Sun, 21 Jun 2020 21:58:00: 12000000 INFO @ Sun, 21 Jun 2020 21:58:00: 15000000 INFO @ Sun, 21 Jun 2020 21:58:05: 13000000 INFO @ Sun, 21 Jun 2020 21:58:06: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:58:11: 14000000 INFO @ Sun, 21 Jun 2020 21:58:13: 17000000 INFO @ Sun, 21 Jun 2020 21:58:18: 15000000 INFO @ Sun, 21 Jun 2020 21:58:20: 18000000 INFO @ Sun, 21 Jun 2020 21:58:22: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 21:58:22: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 21:58:22: #1 total tags in treatment: 18176836 INFO @ Sun, 21 Jun 2020 21:58:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:22: #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 21:58:22: #1 tags after filtering in treatment: 18176814 INFO @ Sun, 21 Jun 2020 21:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:24: 16000000 INFO @ Sun, 21 Jun 2020 21:58:24: #2 number of paired peaks: 966 WARNING @ Sun, 21 Jun 2020 21:58:24: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:24: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 21:58:24: #2 alternative fragment length(s) may be 4,139 bps INFO @ Sun, 21 Jun 2020 21:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.10_model.r INFO @ Sun, 21 Jun 2020 21:58:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:29: 17000000 INFO @ Sun, 21 Jun 2020 21:58:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:34: 18000000 INFO @ Sun, 21 Jun 2020 21:58:35: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 21:58:35: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 21:58:35: #1 total tags in treatment: 18176836 INFO @ Sun, 21 Jun 2020 21:58:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:35: #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 21:58:36: #1 tags after filtering in treatment: 18176814 INFO @ Sun, 21 Jun 2020 21:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:37: #2 number of paired peaks: 966 WARNING @ Sun, 21 Jun 2020 21:58:37: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:37: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 21:58:37: #2 alternative fragment length(s) may be 4,139 bps INFO @ Sun, 21 Jun 2020 21:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.20_model.r INFO @ Sun, 21 Jun 2020 21:58:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.05_summits.bed INFO @ Sun, 21 Jun 2020 21:58:49: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (6598 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.10_summits.bed INFO @ Sun, 21 Jun 2020 21:59:24: Done! pass1 - making usageList (284 chroms): 1 millis pass2 - checking and writing primary data (2157 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX512267/SRX512267.20_summits.bed INFO @ Sun, 21 Jun 2020 21:59:36: Done! pass1 - making usageList (193 chroms): 1 millis pass2 - checking and writing primary data (581 records, 4 fields): 7 millis CompletedMACS2peakCalling