Job ID = 6458709 SRX = SRX5416210 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:36:48 prefetch.2.10.7: 1) Downloading 'SRR8617260'... 2020-06-21T12:36:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:58 prefetch.2.10.7: 1) 'SRR8617260' was downloaded successfully Read 50454880 spots for SRR8617260/SRR8617260.sra Written 50454880 spots for SRR8617260/SRR8617260.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: 00:21:03 50454880 reads; of these: 50454880 (100.00%) were unpaired; of these: 4192264 (8.31%) aligned 0 times 24301776 (48.17%) aligned exactly 1 time 21960840 (43.53%) aligned >1 times 91.69% overall alignment rate Time searching: 00:21:03 Overall time: 00:21:03 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 20 files... [bam_rmdupse_core] 25018307 / 46262616 = 0.5408 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 22:19:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.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 22:19:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:26: 1000000 INFO @ Sun, 21 Jun 2020 22:19:32: 2000000 INFO @ Sun, 21 Jun 2020 22:19:38: 3000000 INFO @ Sun, 21 Jun 2020 22:19:44: 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 22:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.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 22:19:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:50: 5000000 INFO @ Sun, 21 Jun 2020 22:19:56: 1000000 INFO @ Sun, 21 Jun 2020 22:19:56: 6000000 INFO @ Sun, 21 Jun 2020 22:20:01: 2000000 INFO @ Sun, 21 Jun 2020 22:20:03: 7000000 INFO @ Sun, 21 Jun 2020 22:20:07: 3000000 INFO @ Sun, 21 Jun 2020 22:20:09: 8000000 INFO @ Sun, 21 Jun 2020 22:20:13: 4000000 INFO @ Sun, 21 Jun 2020 22:20:15: 9000000 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 22:20:19: 5000000 INFO @ Sun, 21 Jun 2020 22:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.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 22:20:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:20:22: 10000000 INFO @ Sun, 21 Jun 2020 22:20:24: 6000000 INFO @ Sun, 21 Jun 2020 22:20:26: 1000000 INFO @ Sun, 21 Jun 2020 22:20:28: 11000000 INFO @ Sun, 21 Jun 2020 22:20:30: 7000000 INFO @ Sun, 21 Jun 2020 22:20:32: 2000000 INFO @ Sun, 21 Jun 2020 22:20:34: 12000000 INFO @ Sun, 21 Jun 2020 22:20:36: 8000000 INFO @ Sun, 21 Jun 2020 22:20:37: 3000000 INFO @ Sun, 21 Jun 2020 22:20:40: 13000000 INFO @ Sun, 21 Jun 2020 22:20:42: 9000000 INFO @ Sun, 21 Jun 2020 22:20:43: 4000000 INFO @ Sun, 21 Jun 2020 22:20:47: 14000000 INFO @ Sun, 21 Jun 2020 22:20:48: 10000000 INFO @ Sun, 21 Jun 2020 22:20:49: 5000000 INFO @ Sun, 21 Jun 2020 22:20:53: 15000000 INFO @ Sun, 21 Jun 2020 22:20:53: 11000000 INFO @ Sun, 21 Jun 2020 22:20:55: 6000000 INFO @ Sun, 21 Jun 2020 22:20:59: 16000000 INFO @ Sun, 21 Jun 2020 22:20:59: 12000000 INFO @ Sun, 21 Jun 2020 22:21:01: 7000000 INFO @ Sun, 21 Jun 2020 22:21:05: 13000000 INFO @ Sun, 21 Jun 2020 22:21:06: 17000000 INFO @ Sun, 21 Jun 2020 22:21:07: 8000000 INFO @ Sun, 21 Jun 2020 22:21:10: 14000000 INFO @ Sun, 21 Jun 2020 22:21:12: 18000000 INFO @ Sun, 21 Jun 2020 22:21:12: 9000000 INFO @ Sun, 21 Jun 2020 22:21:16: 15000000 INFO @ Sun, 21 Jun 2020 22:21:18: 19000000 INFO @ Sun, 21 Jun 2020 22:21:18: 10000000 INFO @ Sun, 21 Jun 2020 22:21:22: 16000000 INFO @ Sun, 21 Jun 2020 22:21:24: 11000000 INFO @ Sun, 21 Jun 2020 22:21:24: 20000000 INFO @ Sun, 21 Jun 2020 22:21:28: 17000000 INFO @ Sun, 21 Jun 2020 22:21:30: 12000000 INFO @ Sun, 21 Jun 2020 22:21:31: 21000000 INFO @ Sun, 21 Jun 2020 22:21:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:21:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:21:33: #1 total tags in treatment: 21244309 INFO @ Sun, 21 Jun 2020 22:21:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:21:33: #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 22:21:33: #1 tags after filtering in treatment: 21244307 INFO @ Sun, 21 Jun 2020 22:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:21:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:21:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:21:34: 18000000 INFO @ Sun, 21 Jun 2020 22:21:34: #2 number of paired peaks: 858 WARNING @ Sun, 21 Jun 2020 22:21:34: Fewer paired peaks (858) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 858 pairs to build model! INFO @ Sun, 21 Jun 2020 22:21:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:21:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:21:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:21:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:21:35: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:21:35: #2 alternative fragment length(s) may be 4,111 bps INFO @ Sun, 21 Jun 2020 22:21:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.05_model.r INFO @ Sun, 21 Jun 2020 22:21:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:21:36: 13000000 INFO @ Sun, 21 Jun 2020 22:21:39: 19000000 INFO @ Sun, 21 Jun 2020 22:21:41: 14000000 INFO @ Sun, 21 Jun 2020 22:21:45: 20000000 INFO @ Sun, 21 Jun 2020 22:21:47: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:21:51: 21000000 INFO @ Sun, 21 Jun 2020 22:21:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:21:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:21:52: #1 total tags in treatment: 21244309 INFO @ Sun, 21 Jun 2020 22:21:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:21:52: #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 22:21:52: 16000000 INFO @ Sun, 21 Jun 2020 22:21:53: #1 tags after filtering in treatment: 21244307 INFO @ Sun, 21 Jun 2020 22:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:21:53: #1 finished! INFO @ Sun, 21 Jun 2020 22:21:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:21:54: #2 number of paired peaks: 858 WARNING @ Sun, 21 Jun 2020 22:21:54: Fewer paired peaks (858) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 858 pairs to build model! INFO @ Sun, 21 Jun 2020 22:21:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:21:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:21:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:21:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:21:55: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:21:55: #2 alternative fragment length(s) may be 4,111 bps INFO @ Sun, 21 Jun 2020 22:21:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.10_model.r INFO @ Sun, 21 Jun 2020 22:21:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:21:58: 17000000 INFO @ Sun, 21 Jun 2020 22:22:04: 18000000 INFO @ Sun, 21 Jun 2020 22:22:09: 19000000 INFO @ Sun, 21 Jun 2020 22:22:14: 20000000 INFO @ Sun, 21 Jun 2020 22:22:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:20: 21000000 INFO @ Sun, 21 Jun 2020 22:22:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:22:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:22:21: #1 total tags in treatment: 21244309 INFO @ Sun, 21 Jun 2020 22:22:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:21: #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 22:22:22: #1 tags after filtering in treatment: 21244307 INFO @ Sun, 21 Jun 2020 22:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:23: #2 number of paired peaks: 858 WARNING @ Sun, 21 Jun 2020 22:22:23: Fewer paired peaks (858) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 858 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:23: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:22:23: #2 alternative fragment length(s) may be 4,111 bps INFO @ Sun, 21 Jun 2020 22:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.20_model.r INFO @ Sun, 21 Jun 2020 22:22:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:22:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:34: Done! pass1 - making usageList (1011 chroms): 3 millis pass2 - checking and writing primary data (9847 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.10_summits.bed INFO @ Sun, 21 Jun 2020 22:22:52: Done! pass1 - making usageList (825 chroms): 2 millis pass2 - checking and writing primary data (4767 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416210/SRX5416210.20_summits.bed INFO @ Sun, 21 Jun 2020 22:23:21: Done! pass1 - making usageList (510 chroms): 2 millis pass2 - checking and writing primary data (1687 records, 4 fields): 13 millis CompletedMACS2peakCalling