Job ID = 6459083 SRX = SRX6386760 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:55:52 prefetch.2.10.7: 1) Downloading 'SRR9624492'... 2020-06-21T12:55:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:26 prefetch.2.10.7: 1) 'SRR9624492' was downloaded successfully Read 21915615 spots for SRR9624492/SRR9624492.sra Written 21915615 spots for SRR9624492/SRR9624492.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: 00:05:32 21915615 reads; of these: 21915615 (100.00%) were unpaired; of these: 3075409 (14.03%) aligned 0 times 13911140 (63.48%) aligned exactly 1 time 4929066 (22.49%) aligned >1 times 85.97% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 6597717 / 18840206 = 0.3502 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 22:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.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 22:12:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:39: 1000000 INFO @ Sun, 21 Jun 2020 22:12:44: 2000000 INFO @ Sun, 21 Jun 2020 22:12:49: 3000000 INFO @ Sun, 21 Jun 2020 22:12:54: 4000000 INFO @ Sun, 21 Jun 2020 22:12:59: 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 22:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.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 22:13:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:04: 6000000 INFO @ Sun, 21 Jun 2020 22:13:09: 1000000 INFO @ Sun, 21 Jun 2020 22:13:10: 7000000 INFO @ Sun, 21 Jun 2020 22:13:15: 2000000 INFO @ Sun, 21 Jun 2020 22:13:15: 8000000 INFO @ Sun, 21 Jun 2020 22:13:20: 9000000 INFO @ Sun, 21 Jun 2020 22:13:20: 3000000 INFO @ Sun, 21 Jun 2020 22:13:25: 4000000 INFO @ Sun, 21 Jun 2020 22:13:26: 10000000 INFO @ Sun, 21 Jun 2020 22:13:31: 5000000 INFO @ Sun, 21 Jun 2020 22:13:31: 11000000 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 22:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.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 22:13:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:36: 6000000 INFO @ Sun, 21 Jun 2020 22:13:37: 12000000 INFO @ Sun, 21 Jun 2020 22:13:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:13:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:13:38: #1 total tags in treatment: 12242489 INFO @ Sun, 21 Jun 2020 22:13:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:38: #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 22:13:39: #1 tags after filtering in treatment: 12242488 INFO @ Sun, 21 Jun 2020 22:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:39: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:39: #2 number of paired peaks: 827 WARNING @ Sun, 21 Jun 2020 22:13:39: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:39: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:40: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:40: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:40: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:40: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 22:13:40: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 22:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.05_model.r INFO @ Sun, 21 Jun 2020 22:13:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:40: 1000000 INFO @ Sun, 21 Jun 2020 22:13:41: 7000000 INFO @ Sun, 21 Jun 2020 22:13:46: 2000000 INFO @ Sun, 21 Jun 2020 22:13:47: 8000000 INFO @ Sun, 21 Jun 2020 22:13:52: 3000000 INFO @ Sun, 21 Jun 2020 22:13:52: 9000000 INFO @ Sun, 21 Jun 2020 22:13:58: 4000000 INFO @ Sun, 21 Jun 2020 22:13:58: 10000000 INFO @ Sun, 21 Jun 2020 22:14:04: 11000000 INFO @ Sun, 21 Jun 2020 22:14:04: 5000000 INFO @ Sun, 21 Jun 2020 22:14:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:09: 12000000 INFO @ Sun, 21 Jun 2020 22:14:10: 6000000 INFO @ Sun, 21 Jun 2020 22:14:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:14:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:14:11: #1 total tags in treatment: 12242489 INFO @ Sun, 21 Jun 2020 22:14:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:11: #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 22:14:11: #1 tags after filtering in treatment: 12242488 INFO @ Sun, 21 Jun 2020 22:14:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:12: #2 number of paired peaks: 827 WARNING @ Sun, 21 Jun 2020 22:14:12: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:12: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 22:14:12: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 22:14:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.10_model.r INFO @ Sun, 21 Jun 2020 22:14:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:16: 7000000 INFO @ Sun, 21 Jun 2020 22:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.05_summits.bed INFO @ Sun, 21 Jun 2020 22:14:19: Done! pass1 - making usageList (798 chroms): 2 millis pass2 - checking and writing primary data (4695 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:22: 8000000 INFO @ Sun, 21 Jun 2020 22:14:28: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:14:34: 10000000 INFO @ Sun, 21 Jun 2020 22:14:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:41: 11000000 INFO @ Sun, 21 Jun 2020 22:14:47: 12000000 INFO @ Sun, 21 Jun 2020 22:14:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:14:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:14:48: #1 total tags in treatment: 12242489 INFO @ Sun, 21 Jun 2020 22:14:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:48: #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 22:14:49: #1 tags after filtering in treatment: 12242488 INFO @ Sun, 21 Jun 2020 22:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:49: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:50: #2 number of paired peaks: 827 WARNING @ Sun, 21 Jun 2020 22:14:50: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:50: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 22:14:50: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 22:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.20_model.r INFO @ Sun, 21 Jun 2020 22:14:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.10_summits.bed INFO @ Sun, 21 Jun 2020 22:14:53: Done! pass1 - making usageList (658 chroms): 1 millis pass2 - checking and writing primary data (3004 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:15:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386760/SRX6386760.20_summits.bed INFO @ Sun, 21 Jun 2020 22:15:29: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1732 records, 4 fields): 15 millis CompletedMACS2peakCalling