Job ID = 6453966 SRX = SRX1715679 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:46:17 prefetch.2.10.7: 1) Downloading 'SRR3405220'... 2020-06-21T08:46:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:15 prefetch.2.10.7: 1) 'SRR3405220' was downloaded successfully Read 38082740 spots for SRR3405220/SRR3405220.sra Written 38082740 spots for SRR3405220/SRR3405220.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: 00:09:40 38082740 reads; of these: 38082740 (100.00%) were unpaired; of these: 881298 (2.31%) aligned 0 times 30249261 (79.43%) aligned exactly 1 time 6952181 (18.26%) aligned >1 times 97.69% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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] 17720831 / 37201442 = 0.4763 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 18:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.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 18:19:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:53: 1000000 INFO @ Sun, 21 Jun 2020 18:19:58: 2000000 INFO @ Sun, 21 Jun 2020 18:20:03: 3000000 INFO @ Sun, 21 Jun 2020 18:20:08: 4000000 INFO @ Sun, 21 Jun 2020 18:20:14: 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 18:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.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 18:20:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:19: 6000000 INFO @ Sun, 21 Jun 2020 18:20:23: 1000000 INFO @ Sun, 21 Jun 2020 18:20:25: 7000000 INFO @ Sun, 21 Jun 2020 18:20:29: 2000000 INFO @ Sun, 21 Jun 2020 18:20:30: 8000000 INFO @ Sun, 21 Jun 2020 18:20:34: 3000000 INFO @ Sun, 21 Jun 2020 18:20:36: 9000000 INFO @ Sun, 21 Jun 2020 18:20:40: 4000000 INFO @ Sun, 21 Jun 2020 18:20:41: 10000000 INFO @ Sun, 21 Jun 2020 18:20:45: 5000000 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 18:20:46: 11000000 INFO @ Sun, 21 Jun 2020 18:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.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 18:20:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:50: 6000000 INFO @ Sun, 21 Jun 2020 18:20:52: 12000000 INFO @ Sun, 21 Jun 2020 18:20:54: 1000000 INFO @ Sun, 21 Jun 2020 18:20:56: 7000000 INFO @ Sun, 21 Jun 2020 18:20:57: 13000000 INFO @ Sun, 21 Jun 2020 18:21:00: 2000000 INFO @ Sun, 21 Jun 2020 18:21:02: 8000000 INFO @ Sun, 21 Jun 2020 18:21:03: 14000000 INFO @ Sun, 21 Jun 2020 18:21:06: 3000000 INFO @ Sun, 21 Jun 2020 18:21:07: 9000000 INFO @ Sun, 21 Jun 2020 18:21:08: 15000000 INFO @ Sun, 21 Jun 2020 18:21:12: 4000000 INFO @ Sun, 21 Jun 2020 18:21:12: 10000000 INFO @ Sun, 21 Jun 2020 18:21:14: 16000000 INFO @ Sun, 21 Jun 2020 18:21:18: 11000000 INFO @ Sun, 21 Jun 2020 18:21:18: 5000000 INFO @ Sun, 21 Jun 2020 18:21:19: 17000000 INFO @ Sun, 21 Jun 2020 18:21:23: 12000000 INFO @ Sun, 21 Jun 2020 18:21:24: 6000000 INFO @ Sun, 21 Jun 2020 18:21:25: 18000000 INFO @ Sun, 21 Jun 2020 18:21:29: 13000000 INFO @ Sun, 21 Jun 2020 18:21:30: 7000000 INFO @ Sun, 21 Jun 2020 18:21:30: 19000000 INFO @ Sun, 21 Jun 2020 18:21:33: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:21:33: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:21:33: #1 total tags in treatment: 19480611 INFO @ Sun, 21 Jun 2020 18:21:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:33: #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 18:21:34: #1 tags after filtering in treatment: 19480611 INFO @ Sun, 21 Jun 2020 18:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:34: 14000000 INFO @ Sun, 21 Jun 2020 18:21:35: #2 number of paired peaks: 551 WARNING @ Sun, 21 Jun 2020 18:21:35: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:35: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 18:21:35: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 18:21:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.05_model.r INFO @ Sun, 21 Jun 2020 18:21:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:36: 8000000 INFO @ Sun, 21 Jun 2020 18:21:39: 15000000 INFO @ Sun, 21 Jun 2020 18:21:42: 9000000 INFO @ Sun, 21 Jun 2020 18:21:45: 16000000 INFO @ Sun, 21 Jun 2020 18:21:48: 10000000 INFO @ Sun, 21 Jun 2020 18:21:51: 17000000 INFO @ Sun, 21 Jun 2020 18:21:54: 11000000 INFO @ Sun, 21 Jun 2020 18:21:56: 18000000 INFO @ Sun, 21 Jun 2020 18:22:00: 12000000 INFO @ Sun, 21 Jun 2020 18:22:02: 19000000 INFO @ Sun, 21 Jun 2020 18:22:05: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:22:05: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:22:05: #1 total tags in treatment: 19480611 INFO @ Sun, 21 Jun 2020 18:22:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:05: #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 18:22:05: #1 tags after filtering in treatment: 19480611 INFO @ Sun, 21 Jun 2020 18:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:06: 13000000 INFO @ Sun, 21 Jun 2020 18:22:07: #2 number of paired peaks: 551 WARNING @ Sun, 21 Jun 2020 18:22:07: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Sun, 21 Jun 2020 18:22:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:07: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 18:22:07: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 18:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.10_model.r INFO @ Sun, 21 Jun 2020 18:22:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:22:12: 14000000 INFO @ Sun, 21 Jun 2020 18:22:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:18: 15000000 INFO @ Sun, 21 Jun 2020 18:22:24: 16000000 INFO @ Sun, 21 Jun 2020 18:22:29: 17000000 INFO @ Sun, 21 Jun 2020 18:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.05_summits.bed INFO @ Sun, 21 Jun 2020 18:22:33: Done! pass1 - making usageList (617 chroms): 2 millis pass2 - checking and writing primary data (8808 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:35: 18000000 INFO @ Sun, 21 Jun 2020 18:22:42: 19000000 INFO @ Sun, 21 Jun 2020 18:22:45: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:22:45: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:22:45: #1 total tags in treatment: 19480611 INFO @ Sun, 21 Jun 2020 18:22:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:45: #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 18:22:45: #1 tags after filtering in treatment: 19480611 INFO @ Sun, 21 Jun 2020 18:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:46: #2 number of paired peaks: 551 WARNING @ Sun, 21 Jun 2020 18:22:46: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Sun, 21 Jun 2020 18:22:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:47: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 18:22:47: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 18:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.20_model.r INFO @ Sun, 21 Jun 2020 18:22:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.10_summits.bed INFO @ Sun, 21 Jun 2020 18:23:04: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (6733 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715679/SRX1715679.20_summits.bed INFO @ Sun, 21 Jun 2020 18:23:47: Done! pass1 - making usageList (203 chroms): 1 millis pass2 - checking and writing primary data (3268 records, 4 fields): 9 millis CompletedMACS2peakCalling