Job ID = 6452004 SRX = ERX1430250 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:24:47 prefetch.2.10.7: 1) Downloading 'ERR1358775'... 2020-06-21T07:24:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:21 prefetch.2.10.7: 1) 'ERR1358775' was downloaded successfully Read 23182678 spots for ERR1358775/ERR1358775.sra Written 23182678 spots for ERR1358775/ERR1358775.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: 00:04:33 23182678 reads; of these: 23182678 (100.00%) were unpaired; of these: 1060124 (4.57%) aligned 0 times 18165831 (78.36%) aligned exactly 1 time 3956723 (17.07%) aligned >1 times 95.43% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 16942984 / 22122554 = 0.7659 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 16:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.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 16:40:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:57: 1000000 INFO @ Sun, 21 Jun 2020 16:41:01: 2000000 INFO @ Sun, 21 Jun 2020 16:41:06: 3000000 INFO @ Sun, 21 Jun 2020 16:41:12: 4000000 INFO @ Sun, 21 Jun 2020 16:41:17: 5000000 INFO @ Sun, 21 Jun 2020 16:41:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:17: #1 total tags in treatment: 5179570 INFO @ Sun, 21 Jun 2020 16:41:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:17: #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 16:41:18: #1 tags after filtering in treatment: 5179495 INFO @ Sun, 21 Jun 2020 16:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:18: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:18: #2 number of paired peaks: 3165 INFO @ Sun, 21 Jun 2020 16:41:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:18: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 16:41:18: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 21 Jun 2020 16:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.05_model.r INFO @ Sun, 21 Jun 2020 16:41:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:19: #3 Pre-compute pvalue-qvalue table... 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 16:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.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 16:41:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:27: 1000000 INFO @ Sun, 21 Jun 2020 16:41:32: 2000000 INFO @ Sun, 21 Jun 2020 16:41:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:38: 3000000 INFO @ Sun, 21 Jun 2020 16:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.05_summits.bed INFO @ Sun, 21 Jun 2020 16:41:40: Done! pass1 - making usageList (690 chroms): 2 millis pass2 - checking and writing primary data (6162 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:41:44: 4000000 INFO @ Sun, 21 Jun 2020 16:41:49: 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 16:41:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:50: #1 total tags in treatment: 5179570 INFO @ Sun, 21 Jun 2020 16:41:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:50: #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 16:41:50: #1 tags after filtering in treatment: 5179495 INFO @ Sun, 21 Jun 2020 16:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:50: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:51: #2 number of paired peaks: 3165 INFO @ Sun, 21 Jun 2020 16:41:51: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:51: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:51: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:51: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:51: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 16:41:51: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 21 Jun 2020 16:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.10_model.r INFO @ Sun, 21 Jun 2020 16:41:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.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 16:41:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:58: 1000000 INFO @ Sun, 21 Jun 2020 16:42:03: 2000000 INFO @ Sun, 21 Jun 2020 16:42:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:09: 3000000 INFO @ Sun, 21 Jun 2020 16:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.10_summits.bed INFO @ Sun, 21 Jun 2020 16:42:12: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (3286 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:42:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:42:20: 5000000 INFO @ Sun, 21 Jun 2020 16:42:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:42:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:42:21: #1 total tags in treatment: 5179570 INFO @ Sun, 21 Jun 2020 16:42:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:42:21: #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 16:42:21: #1 tags after filtering in treatment: 5179495 INFO @ Sun, 21 Jun 2020 16:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:42:21: #1 finished! INFO @ Sun, 21 Jun 2020 16:42:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:42:22: #2 number of paired peaks: 3165 INFO @ Sun, 21 Jun 2020 16:42:22: start model_add_line... INFO @ Sun, 21 Jun 2020 16:42:22: start X-correlation... INFO @ Sun, 21 Jun 2020 16:42:22: end of X-cor INFO @ Sun, 21 Jun 2020 16:42:22: #2 finished! INFO @ Sun, 21 Jun 2020 16:42:22: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 16:42:22: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 21 Jun 2020 16:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.20_model.r INFO @ Sun, 21 Jun 2020 16:42:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:42:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:42:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430250/ERX1430250.20_summits.bed INFO @ Sun, 21 Jun 2020 16:42:42: Done! pass1 - making usageList (305 chroms): 1 millis pass2 - checking and writing primary data (1449 records, 4 fields): 10 millis CompletedMACS2peakCalling