Job ID = 6456056 SRX = SRX3167240 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:27:06 prefetch.2.10.7: 1) Downloading 'SRR6014243'... 2020-06-21T10:27:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:53 prefetch.2.10.7: 1) 'SRR6014243' was downloaded successfully Read 32185369 spots for SRR6014243/SRR6014243.sra Written 32185369 spots for SRR6014243/SRR6014243.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: 00:10:44 32185369 reads; of these: 32185369 (100.00%) were unpaired; of these: 10375339 (32.24%) aligned 0 times 11129688 (34.58%) aligned exactly 1 time 10680342 (33.18%) aligned >1 times 67.76% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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 12 files... [bam_rmdupse_core] 18892971 / 21810030 = 0.8663 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 19:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.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 19:50:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:29: 1000000 INFO @ Sun, 21 Jun 2020 19:50:35: 2000000 INFO @ Sun, 21 Jun 2020 19:50:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:40: #1 total tags in treatment: 2917059 INFO @ Sun, 21 Jun 2020 19:50:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:40: #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 19:50:41: #1 tags after filtering in treatment: 2916831 INFO @ Sun, 21 Jun 2020 19:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:41: #2 number of paired peaks: 4646 INFO @ Sun, 21 Jun 2020 19:50:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:41: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 19:50:41: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 19:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.05_model.r INFO @ Sun, 21 Jun 2020 19:50:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:50: #3 Call peaks for each chromosome... 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 19:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.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 19:50:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:54: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (4981 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:59: 1000000 INFO @ Sun, 21 Jun 2020 19:51:05: 2000000 INFO @ Sun, 21 Jun 2020 19:51:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:51:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:51:10: #1 total tags in treatment: 2917059 INFO @ Sun, 21 Jun 2020 19:51:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:10: #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 19:51:10: #1 tags after filtering in treatment: 2916831 INFO @ Sun, 21 Jun 2020 19:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:11: #2 number of paired peaks: 4646 INFO @ Sun, 21 Jun 2020 19:51:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:11: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 19:51:11: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 19:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.10_model.r INFO @ Sun, 21 Jun 2020 19:51:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:20: #3 Call peaks for each chromosome... 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 19:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:23: Done! INFO @ Sun, 21 Jun 2020 19:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.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 19:51:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:24: #1 read treatment tags... pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (3362 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:29: 1000000 INFO @ Sun, 21 Jun 2020 19:51:34: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:51:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:51:40: #1 total tags in treatment: 2917059 INFO @ Sun, 21 Jun 2020 19:51:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:40: #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 19:51:40: #1 tags after filtering in treatment: 2916831 INFO @ Sun, 21 Jun 2020 19:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:40: #2 number of paired peaks: 4646 INFO @ Sun, 21 Jun 2020 19:51:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:41: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 19:51:41: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 19:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.20_model.r INFO @ Sun, 21 Jun 2020 19:51:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167240/SRX3167240.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:53: Done! pass1 - making usageList (301 chroms): 1 millis pass2 - checking and writing primary data (1992 records, 4 fields): 11 millis CompletedMACS2peakCalling