Job ID = 6457790 SRX = SRX4798827 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:07:51 prefetch.2.10.7: 1) Downloading 'SRR7965242'... 2020-06-21T12:07:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:09:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:09:50 prefetch.2.10.7: 'SRR7965242' is valid 2020-06-21T12:09:50 prefetch.2.10.7: 1) 'SRR7965242' was downloaded successfully Read 10824599 spots for SRR7965242/SRR7965242.sra Written 10824599 spots for SRR7965242/SRR7965242.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: 00:02:23 10824599 reads; of these: 10824599 (100.00%) were unpaired; of these: 1152286 (10.65%) aligned 0 times 8338756 (77.04%) aligned exactly 1 time 1333557 (12.32%) aligned >1 times 89.35% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 2488615 / 9672313 = 0.2573 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 21:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.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 21:16:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:28: 1000000 INFO @ Sun, 21 Jun 2020 21:16:34: 2000000 INFO @ Sun, 21 Jun 2020 21:16:40: 3000000 INFO @ Sun, 21 Jun 2020 21:16:46: 4000000 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 21:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.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 21:16:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:53: 5000000 INFO @ Sun, 21 Jun 2020 21:16:58: 1000000 INFO @ Sun, 21 Jun 2020 21:17:00: 6000000 INFO @ Sun, 21 Jun 2020 21:17:05: 2000000 INFO @ Sun, 21 Jun 2020 21:17:07: 7000000 INFO @ Sun, 21 Jun 2020 21:17:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:17:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:17:09: #1 total tags in treatment: 7183698 INFO @ Sun, 21 Jun 2020 21:17:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:09: #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 21:17:09: #1 tags after filtering in treatment: 7183576 INFO @ Sun, 21 Jun 2020 21:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:10: #2 number of paired peaks: 1994 INFO @ Sun, 21 Jun 2020 21:17:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:10: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:17:10: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.05_model.r INFO @ Sun, 21 Jun 2020 21:17:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:11: 3000000 INFO @ Sun, 21 Jun 2020 21:17:17: 4000000 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 21:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.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 21:17:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:24: 5000000 INFO @ Sun, 21 Jun 2020 21:17:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:28: 1000000 INFO @ Sun, 21 Jun 2020 21:17:31: 6000000 INFO @ Sun, 21 Jun 2020 21:17:35: 2000000 INFO @ Sun, 21 Jun 2020 21:17:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.05_summits.bed INFO @ Sun, 21 Jun 2020 21:17:37: Done! pass1 - making usageList (311 chroms): 2 millis pass2 - checking and writing primary data (4624 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:38: 7000000 INFO @ Sun, 21 Jun 2020 21:17:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:17:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:17:40: #1 total tags in treatment: 7183698 INFO @ Sun, 21 Jun 2020 21:17:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:40: #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 21:17:40: #1 tags after filtering in treatment: 7183576 INFO @ Sun, 21 Jun 2020 21:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:40: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:41: #2 number of paired peaks: 1994 INFO @ Sun, 21 Jun 2020 21:17:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:41: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:17:41: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.10_model.r INFO @ Sun, 21 Jun 2020 21:17:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:42: 3000000 INFO @ Sun, 21 Jun 2020 21:17:48: 4000000 INFO @ Sun, 21 Jun 2020 21:17:54: 5000000 INFO @ Sun, 21 Jun 2020 21:17:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:18:01: 6000000 INFO @ Sun, 21 Jun 2020 21:18:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.10_summits.bed INFO @ Sun, 21 Jun 2020 21:18:07: Done! pass1 - making usageList (205 chroms): 1 millis pass2 - checking and writing primary data (1447 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:07: 7000000 INFO @ Sun, 21 Jun 2020 21:18:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:18:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:18:09: #1 total tags in treatment: 7183698 INFO @ Sun, 21 Jun 2020 21:18:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:09: #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 21:18:09: #1 tags after filtering in treatment: 7183576 INFO @ Sun, 21 Jun 2020 21:18:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:18:10: #2 number of paired peaks: 1994 INFO @ Sun, 21 Jun 2020 21:18:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:10: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:18:10: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.20_model.r INFO @ Sun, 21 Jun 2020 21:18:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:18:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798827/SRX4798827.20_summits.bed INFO @ Sun, 21 Jun 2020 21:18:35: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 7 millis CompletedMACS2peakCalling