Job ID = 6455693 SRX = SRX287994 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:06 prefetch.2.10.7: 1) Downloading 'SRR870183'... 2020-06-21T10:15:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:46 prefetch.2.10.7: 1) 'SRR870183' was downloaded successfully Read 17887932 spots for SRR870183/SRR870183.sra Written 17887932 spots for SRR870183/SRR870183.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: 00:05:08 17887932 reads; of these: 17887932 (100.00%) were unpaired; of these: 1599205 (8.94%) aligned 0 times 11589541 (64.79%) aligned exactly 1 time 4699186 (26.27%) aligned >1 times 91.06% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 2057005 / 16288727 = 0.1263 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 19:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.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 19:31:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:51: 1000000 INFO @ Sun, 21 Jun 2020 19:32:00: 2000000 INFO @ Sun, 21 Jun 2020 19:32:09: 3000000 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 19:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.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 19:32:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:17: 4000000 INFO @ Sun, 21 Jun 2020 19:32:22: 1000000 INFO @ Sun, 21 Jun 2020 19:32:26: 5000000 INFO @ Sun, 21 Jun 2020 19:32:30: 2000000 INFO @ Sun, 21 Jun 2020 19:32:34: 6000000 INFO @ Sun, 21 Jun 2020 19:32:39: 3000000 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 19:32:43: 7000000 INFO @ Sun, 21 Jun 2020 19:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.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 19:32:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:48: 4000000 INFO @ Sun, 21 Jun 2020 19:32:49: 1000000 INFO @ Sun, 21 Jun 2020 19:32:52: 8000000 INFO @ Sun, 21 Jun 2020 19:32:56: 5000000 INFO @ Sun, 21 Jun 2020 19:32:58: 2000000 INFO @ Sun, 21 Jun 2020 19:33:01: 9000000 INFO @ Sun, 21 Jun 2020 19:33:05: 6000000 INFO @ Sun, 21 Jun 2020 19:33:07: 3000000 INFO @ Sun, 21 Jun 2020 19:33:09: 10000000 INFO @ Sun, 21 Jun 2020 19:33:13: 7000000 INFO @ Sun, 21 Jun 2020 19:33:16: 4000000 INFO @ Sun, 21 Jun 2020 19:33:17: 11000000 INFO @ Sun, 21 Jun 2020 19:33:21: 8000000 INFO @ Sun, 21 Jun 2020 19:33:25: 5000000 INFO @ Sun, 21 Jun 2020 19:33:26: 12000000 INFO @ Sun, 21 Jun 2020 19:33:29: 9000000 INFO @ Sun, 21 Jun 2020 19:33:34: 6000000 INFO @ Sun, 21 Jun 2020 19:33:35: 13000000 INFO @ Sun, 21 Jun 2020 19:33:37: 10000000 INFO @ Sun, 21 Jun 2020 19:33:43: 14000000 INFO @ Sun, 21 Jun 2020 19:33:43: 7000000 INFO @ Sun, 21 Jun 2020 19:33:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:45: #1 total tags in treatment: 14231722 INFO @ Sun, 21 Jun 2020 19:33:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:45: #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 19:33:45: 11000000 INFO @ Sun, 21 Jun 2020 19:33:46: #1 tags after filtering in treatment: 14231722 INFO @ Sun, 21 Jun 2020 19:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:47: #2 number of paired peaks: 1125 INFO @ Sun, 21 Jun 2020 19:33:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:47: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 19:33:47: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 19:33:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.05_model.r INFO @ Sun, 21 Jun 2020 19:33:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:52: 8000000 INFO @ Sun, 21 Jun 2020 19:33:53: 12000000 INFO @ Sun, 21 Jun 2020 19:34:01: 9000000 INFO @ Sun, 21 Jun 2020 19:34:01: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:09: 14000000 INFO @ Sun, 21 Jun 2020 19:34:10: 10000000 INFO @ Sun, 21 Jun 2020 19:34:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:11: #1 total tags in treatment: 14231722 INFO @ Sun, 21 Jun 2020 19:34:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:11: #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 19:34:12: #1 tags after filtering in treatment: 14231722 INFO @ Sun, 21 Jun 2020 19:34:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:13: #2 number of paired peaks: 1125 INFO @ Sun, 21 Jun 2020 19:34:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:13: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 19:34:13: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 19:34:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.10_model.r INFO @ Sun, 21 Jun 2020 19:34:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:18: 11000000 INFO @ Sun, 21 Jun 2020 19:34:27: 12000000 INFO @ Sun, 21 Jun 2020 19:34:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:34: Done! pass1 - making usageList (687 chroms): 2 millis pass2 - checking and writing primary data (4877 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:35: 13000000 INFO @ Sun, 21 Jun 2020 19:34:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:34:44: 14000000 INFO @ Sun, 21 Jun 2020 19:34:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:47: #1 total tags in treatment: 14231722 INFO @ Sun, 21 Jun 2020 19:34:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:47: #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 19:34:47: #1 tags after filtering in treatment: 14231722 INFO @ Sun, 21 Jun 2020 19:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:48: #2 number of paired peaks: 1125 INFO @ Sun, 21 Jun 2020 19:34:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:49: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 19:34:49: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 19:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.20_model.r INFO @ Sun, 21 Jun 2020 19:34:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:00: Done! pass1 - making usageList (599 chroms): 1 millis pass2 - checking and writing primary data (3711 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287994/SRX287994.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:35: Done! pass1 - making usageList (494 chroms): 2 millis pass2 - checking and writing primary data (2635 records, 4 fields): 28 millis CompletedMACS2peakCalling