Job ID = 6457048 SRX = SRX4375816 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:22:54 prefetch.2.10.7: 1) Downloading 'SRR7506470'... 2020-06-21T11:22:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:42 prefetch.2.10.7: 'SRR7506470' is valid 2020-06-21T11:24:42 prefetch.2.10.7: 1) 'SRR7506470' was downloaded successfully Read 7584800 spots for SRR7506470/SRR7506470.sra Written 7584800 spots for SRR7506470/SRR7506470.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:44 7584800 reads; of these: 7584800 (100.00%) were unpaired; of these: 6296713 (83.02%) aligned 0 times 1039492 (13.70%) aligned exactly 1 time 248595 (3.28%) aligned >1 times 16.98% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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_rmdupse_core] 443268 / 1288087 = 0.3441 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 20:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.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 20:26:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:26:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:26:45: #1 total tags in treatment: 844819 INFO @ Sun, 21 Jun 2020 20:26:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:45: #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 20:26:45: #1 tags after filtering in treatment: 844389 INFO @ Sun, 21 Jun 2020 20:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:45: #2 number of paired peaks: 2700 INFO @ Sun, 21 Jun 2020 20:26:45: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:45: #2 predicted fragment length is 297 bps INFO @ Sun, 21 Jun 2020 20:26:45: #2 alternative fragment length(s) may be 297 bps INFO @ Sun, 21 Jun 2020 20:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.05_model.r INFO @ Sun, 21 Jun 2020 20:26:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:26:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.05_summits.bed INFO @ Sun, 21 Jun 2020 20:26:49: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (1103 records, 4 fields): 13 millis CompletedMACS2peakCalling 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 20:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.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 20:27:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:27:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:27:15: #1 total tags in treatment: 844819 INFO @ Sun, 21 Jun 2020 20:27:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:15: #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 20:27:15: #1 tags after filtering in treatment: 844389 INFO @ Sun, 21 Jun 2020 20:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:15: #2 number of paired peaks: 2700 INFO @ Sun, 21 Jun 2020 20:27:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:15: #2 predicted fragment length is 297 bps INFO @ Sun, 21 Jun 2020 20:27:15: #2 alternative fragment length(s) may be 297 bps INFO @ Sun, 21 Jun 2020 20:27:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.10_model.r INFO @ Sun, 21 Jun 2020 20:27:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.10_summits.bed INFO @ Sun, 21 Jun 2020 20:27:19: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 20:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.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 20:27:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:40: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:27:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:27:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:27:46: #1 total tags in treatment: 844819 INFO @ Sun, 21 Jun 2020 20:27:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:46: #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 20:27:46: #1 tags after filtering in treatment: 844389 INFO @ Sun, 21 Jun 2020 20:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:46: #2 number of paired peaks: 2700 INFO @ Sun, 21 Jun 2020 20:27:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:46: #2 predicted fragment length is 297 bps INFO @ Sun, 21 Jun 2020 20:27:46: #2 alternative fragment length(s) may be 297 bps INFO @ Sun, 21 Jun 2020 20:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.20_model.r INFO @ Sun, 21 Jun 2020 20:27:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375816/SRX4375816.20_summits.bed INFO @ Sun, 21 Jun 2020 20:27:50: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling