Job ID = 6452814 SRX = SRX040616 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:43:21 prefetch.2.10.7: 1) Downloading 'SRR097985'... 2020-06-21T07:43:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:46:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:46:59 prefetch.2.10.7: 1) 'SRR097985' was downloaded successfully Read 31394442 spots for SRR097985/SRR097985.sra Written 31394442 spots for SRR097985/SRR097985.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: 00:06:22 31394442 reads; of these: 31394442 (100.00%) were unpaired; of these: 1784039 (5.68%) aligned 0 times 24825853 (79.08%) aligned exactly 1 time 4784550 (15.24%) aligned >1 times 94.32% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 15687057 / 29610403 = 0.5298 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 17:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.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 17:00:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:08: 1000000 INFO @ Sun, 21 Jun 2020 17:00:14: 2000000 INFO @ Sun, 21 Jun 2020 17:00:20: 3000000 INFO @ Sun, 21 Jun 2020 17:00:25: 4000000 INFO @ Sun, 21 Jun 2020 17:00:30: 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 17:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.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 17:00:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:36: 6000000 INFO @ Sun, 21 Jun 2020 17:00:38: 1000000 INFO @ Sun, 21 Jun 2020 17:00:41: 7000000 INFO @ Sun, 21 Jun 2020 17:00:43: 2000000 INFO @ Sun, 21 Jun 2020 17:00:47: 8000000 INFO @ Sun, 21 Jun 2020 17:00:49: 3000000 INFO @ Sun, 21 Jun 2020 17:00:52: 9000000 INFO @ Sun, 21 Jun 2020 17:00:55: 4000000 INFO @ Sun, 21 Jun 2020 17:00:58: 10000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 17:01:00: 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 17:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.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 17:01:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:01:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:01:04: 11000000 INFO @ Sun, 21 Jun 2020 17:01:06: 6000000 INFO @ Sun, 21 Jun 2020 17:01:08: 1000000 INFO @ Sun, 21 Jun 2020 17:01:10: 12000000 INFO @ Sun, 21 Jun 2020 17:01:12: 7000000 INFO @ Sun, 21 Jun 2020 17:01:14: 2000000 INFO @ Sun, 21 Jun 2020 17:01:15: 13000000 INFO @ Sun, 21 Jun 2020 17:01:18: 8000000 INFO @ Sun, 21 Jun 2020 17:01:20: 3000000 INFO @ Sun, 21 Jun 2020 17:01:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:01:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:01:21: #1 total tags in treatment: 13923346 INFO @ Sun, 21 Jun 2020 17:01:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:01:21: #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 17:01:21: #1 tags after filtering in treatment: 13923287 INFO @ Sun, 21 Jun 2020 17:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:01:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:01:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:01:23: #2 number of paired peaks: 1473 INFO @ Sun, 21 Jun 2020 17:01:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:01:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:01:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:01:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:01:23: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 17:01:23: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 17:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.05_model.r INFO @ Sun, 21 Jun 2020 17:01:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:01:23: 9000000 INFO @ Sun, 21 Jun 2020 17:01:25: 4000000 INFO @ Sun, 21 Jun 2020 17:01:29: 10000000 INFO @ Sun, 21 Jun 2020 17:01:31: 5000000 INFO @ Sun, 21 Jun 2020 17:01:35: 11000000 INFO @ Sun, 21 Jun 2020 17:01:37: 6000000 INFO @ Sun, 21 Jun 2020 17:01:41: 12000000 INFO @ Sun, 21 Jun 2020 17:01:42: 7000000 INFO @ Sun, 21 Jun 2020 17:01:46: 13000000 INFO @ Sun, 21 Jun 2020 17:01:48: 8000000 INFO @ Sun, 21 Jun 2020 17:01:52: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:01:52: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:01:52: #1 total tags in treatment: 13923346 INFO @ Sun, 21 Jun 2020 17:01:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:01:52: #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 17:01:52: #1 tags after filtering in treatment: 13923287 INFO @ Sun, 21 Jun 2020 17:01:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:01:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:01:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:01:53: 9000000 INFO @ Sun, 21 Jun 2020 17:01:53: #2 number of paired peaks: 1473 INFO @ Sun, 21 Jun 2020 17:01:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:01:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:01:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:01:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:01:53: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 17:01:53: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 17:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.10_model.r INFO @ Sun, 21 Jun 2020 17:01:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:01:54: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:01:59: 10000000 INFO @ Sun, 21 Jun 2020 17:02:05: 11000000 INFO @ Sun, 21 Jun 2020 17:02:10: 12000000 INFO @ Sun, 21 Jun 2020 17:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:02:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.05_summits.bed INFO @ Sun, 21 Jun 2020 17:02:11: Done! pass1 - making usageList (818 chroms): 6 millis pass2 - checking and writing primary data (35703 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:02:16: 13000000 INFO @ Sun, 21 Jun 2020 17:02:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:02:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:02:21: #1 total tags in treatment: 13923346 INFO @ Sun, 21 Jun 2020 17:02:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:02:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:02:22: #1 tags after filtering in treatment: 13923287 INFO @ Sun, 21 Jun 2020 17:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:02:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:02:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:02:23: #2 number of paired peaks: 1473 INFO @ Sun, 21 Jun 2020 17:02:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:02:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:02:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:02:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:02:23: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 17:02:23: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 17:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.20_model.r INFO @ Sun, 21 Jun 2020 17:02:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:02:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.10_summits.bed INFO @ Sun, 21 Jun 2020 17:02:42: Done! pass1 - making usageList (725 chroms): 4 millis pass2 - checking and writing primary data (18737 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:02:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:03:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040616/SRX040616.20_summits.bed INFO @ Sun, 21 Jun 2020 17:03:11: Done! pass1 - making usageList (529 chroms): 2 millis pass2 - checking and writing primary data (7030 records, 4 fields): 20 millis CompletedMACS2peakCalling