Job ID = 6455550 SRX = SRX287876 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:22:09 prefetch.2.10.7: 1) Downloading 'SRR870065'... 2020-06-21T10:22:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:01 prefetch.2.10.7: 1) 'SRR870065' was downloaded successfully Read 23049469 spots for SRR870065/SRR870065.sra Written 23049469 spots for SRR870065/SRR870065.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: 00:06:01 23049469 reads; of these: 23049469 (100.00%) were unpaired; of these: 1522380 (6.60%) aligned 0 times 15234536 (66.09%) aligned exactly 1 time 6292553 (27.30%) aligned >1 times 93.40% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 3631514 / 21527089 = 0.1687 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 19:38:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.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 19:38:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:40: 1000000 INFO @ Sun, 21 Jun 2020 19:38:45: 2000000 INFO @ Sun, 21 Jun 2020 19:38:50: 3000000 INFO @ Sun, 21 Jun 2020 19:38:55: 4000000 INFO @ Sun, 21 Jun 2020 19:39:00: 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 19:39:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.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 19:39:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:05: 6000000 INFO @ Sun, 21 Jun 2020 19:39:11: 7000000 INFO @ Sun, 21 Jun 2020 19:39:11: 1000000 INFO @ Sun, 21 Jun 2020 19:39:16: 8000000 INFO @ Sun, 21 Jun 2020 19:39:17: 2000000 INFO @ Sun, 21 Jun 2020 19:39:22: 9000000 INFO @ Sun, 21 Jun 2020 19:39:24: 3000000 INFO @ Sun, 21 Jun 2020 19:39:27: 10000000 INFO @ Sun, 21 Jun 2020 19:39:30: 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 19:39:33: 11000000 INFO @ Sun, 21 Jun 2020 19:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.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 19:39:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:36: 5000000 INFO @ Sun, 21 Jun 2020 19:39:39: 12000000 INFO @ Sun, 21 Jun 2020 19:39:41: 1000000 INFO @ Sun, 21 Jun 2020 19:39:43: 6000000 INFO @ Sun, 21 Jun 2020 19:39:44: 13000000 INFO @ Sun, 21 Jun 2020 19:39:46: 2000000 INFO @ Sun, 21 Jun 2020 19:39:50: 7000000 INFO @ Sun, 21 Jun 2020 19:39:50: 14000000 INFO @ Sun, 21 Jun 2020 19:39:52: 3000000 INFO @ Sun, 21 Jun 2020 19:39:56: 15000000 INFO @ Sun, 21 Jun 2020 19:39:56: 8000000 INFO @ Sun, 21 Jun 2020 19:39:57: 4000000 INFO @ Sun, 21 Jun 2020 19:40:02: 16000000 INFO @ Sun, 21 Jun 2020 19:40:02: 9000000 INFO @ Sun, 21 Jun 2020 19:40:03: 5000000 INFO @ Sun, 21 Jun 2020 19:40:07: 17000000 INFO @ Sun, 21 Jun 2020 19:40:09: 6000000 INFO @ Sun, 21 Jun 2020 19:40:09: 10000000 INFO @ Sun, 21 Jun 2020 19:40:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:13: #1 total tags in treatment: 17895575 INFO @ Sun, 21 Jun 2020 19:40:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:13: #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 19:40:13: #1 tags after filtering in treatment: 17895573 INFO @ Sun, 21 Jun 2020 19:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:15: 7000000 INFO @ Sun, 21 Jun 2020 19:40:15: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 19:40:15: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 19:40:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:15: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 19:40:15: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 19:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.05_model.r INFO @ Sun, 21 Jun 2020 19:40:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:16: 11000000 INFO @ Sun, 21 Jun 2020 19:40:20: 8000000 INFO @ Sun, 21 Jun 2020 19:40:22: 12000000 INFO @ Sun, 21 Jun 2020 19:40:26: 9000000 INFO @ Sun, 21 Jun 2020 19:40:29: 13000000 INFO @ Sun, 21 Jun 2020 19:40:31: 10000000 INFO @ Sun, 21 Jun 2020 19:40:35: 14000000 INFO @ Sun, 21 Jun 2020 19:40:37: 11000000 INFO @ Sun, 21 Jun 2020 19:40:42: 15000000 INFO @ Sun, 21 Jun 2020 19:40:42: 12000000 INFO @ Sun, 21 Jun 2020 19:40:48: 13000000 INFO @ Sun, 21 Jun 2020 19:40:48: 16000000 INFO @ Sun, 21 Jun 2020 19:40:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:40:53: 14000000 INFO @ Sun, 21 Jun 2020 19:40:55: 17000000 INFO @ Sun, 21 Jun 2020 19:40:59: 15000000 INFO @ Sun, 21 Jun 2020 19:41:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:00: #1 total tags in treatment: 17895575 INFO @ Sun, 21 Jun 2020 19:41:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:00: #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 19:41:01: #1 tags after filtering in treatment: 17895573 INFO @ Sun, 21 Jun 2020 19:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:02: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 19:41:02: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 19:41:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:02: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 19:41:02: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 19:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.10_model.r INFO @ Sun, 21 Jun 2020 19:41:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:05: 16000000 INFO @ Sun, 21 Jun 2020 19:41:10: 17000000 INFO @ Sun, 21 Jun 2020 19:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.05_summits.bed INFO @ Sun, 21 Jun 2020 19:41:11: Done! pass1 - making usageList (783 chroms): 1 millis pass2 - checking and writing primary data (5035 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:15: #1 total tags in treatment: 17895575 INFO @ Sun, 21 Jun 2020 19:41:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:15: #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 19:41:16: #1 tags after filtering in treatment: 17895573 INFO @ Sun, 21 Jun 2020 19:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:17: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 19:41:17: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 19:41:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:17: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 19:41:17: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 19:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.20_model.r INFO @ Sun, 21 Jun 2020 19:41:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:56: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (3091 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287876/SRX287876.20_summits.bed INFO @ Sun, 21 Jun 2020 19:42:12: Done! pass1 - making usageList (362 chroms): 1 millis pass2 - checking and writing primary data (1596 records, 4 fields): 11 millis CompletedMACS2peakCalling