Job ID = 6454920 SRX = SRX2592502 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:10 prefetch.2.10.7: 1) Downloading 'SRR5289779'... 2020-06-21T09:36:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:23 prefetch.2.10.7: 'SRR5289779' is valid 2020-06-21T09:39:23 prefetch.2.10.7: 1) 'SRR5289779' was downloaded successfully Read 15211150 spots for SRR5289779/SRR5289779.sra Written 15211150 spots for SRR5289779/SRR5289779.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: 00:00:01 Multiseed full-index search: 00:02:46 15211150 reads; of these: 15211150 (100.00%) were unpaired; of these: 4999700 (32.87%) aligned 0 times 9028772 (59.36%) aligned exactly 1 time 1182678 (7.78%) aligned >1 times 67.13% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 1841539 / 10211450 = 0.1803 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 18:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.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 18:45:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:59: 1000000 INFO @ Sun, 21 Jun 2020 18:46:05: 2000000 INFO @ Sun, 21 Jun 2020 18:46:10: 3000000 INFO @ Sun, 21 Jun 2020 18:46:15: 4000000 INFO @ Sun, 21 Jun 2020 18:46:21: 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 18:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.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 18:46:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:26: 6000000 INFO @ Sun, 21 Jun 2020 18:46:29: 1000000 INFO @ Sun, 21 Jun 2020 18:46:32: 7000000 INFO @ Sun, 21 Jun 2020 18:46:35: 2000000 INFO @ Sun, 21 Jun 2020 18:46:37: 8000000 INFO @ Sun, 21 Jun 2020 18:46:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:39: #1 total tags in treatment: 8369911 INFO @ Sun, 21 Jun 2020 18:46:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:39: #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 18:46:40: #1 tags after filtering in treatment: 8369667 INFO @ Sun, 21 Jun 2020 18:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:40: 3000000 INFO @ Sun, 21 Jun 2020 18:46:41: #2 number of paired peaks: 9280 INFO @ Sun, 21 Jun 2020 18:46:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:41: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:46:41: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.05_model.r INFO @ Sun, 21 Jun 2020 18:46:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:45: 4000000 INFO @ Sun, 21 Jun 2020 18:46:51: 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 18:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.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 18:46:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:56: 6000000 INFO @ Sun, 21 Jun 2020 18:47:00: 1000000 INFO @ Sun, 21 Jun 2020 18:47:02: 7000000 INFO @ Sun, 21 Jun 2020 18:47:05: 2000000 INFO @ Sun, 21 Jun 2020 18:47:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:08: 8000000 INFO @ Sun, 21 Jun 2020 18:47:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:10: #1 total tags in treatment: 8369911 INFO @ Sun, 21 Jun 2020 18:47:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:10: #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 18:47:10: #1 tags after filtering in treatment: 8369667 INFO @ Sun, 21 Jun 2020 18:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:11: 3000000 INFO @ Sun, 21 Jun 2020 18:47:11: #2 number of paired peaks: 9280 INFO @ Sun, 21 Jun 2020 18:47:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:12: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:47:12: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.10_model.r INFO @ Sun, 21 Jun 2020 18:47:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:16: 4000000 INFO @ Sun, 21 Jun 2020 18:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:18: Done! pass1 - making usageList (90 chroms): 2 millis pass2 - checking and writing primary data (10244 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:47:22: 5000000 INFO @ Sun, 21 Jun 2020 18:47:27: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:47:33: 7000000 INFO @ Sun, 21 Jun 2020 18:47:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:38: 8000000 INFO @ Sun, 21 Jun 2020 18:47:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:40: #1 total tags in treatment: 8369911 INFO @ Sun, 21 Jun 2020 18:47:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:40: #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 18:47:40: #1 tags after filtering in treatment: 8369667 INFO @ Sun, 21 Jun 2020 18:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:42: #2 number of paired peaks: 9280 INFO @ Sun, 21 Jun 2020 18:47:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:42: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:47:42: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.20_model.r INFO @ Sun, 21 Jun 2020 18:47:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.10_summits.bed INFO @ Sun, 21 Jun 2020 18:47:49: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (8022 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592502/SRX2592502.20_summits.bed INFO @ Sun, 21 Jun 2020 18:48:18: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (5895 records, 4 fields): 7 millis CompletedMACS2peakCalling