Job ID = 6455939 SRX = SRX3068975 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:36 prefetch.2.10.7: 1) Downloading 'SRR5907451'... 2020-06-21T10:30:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:31 prefetch.2.10.7: 'SRR5907451' is valid 2020-06-21T10:32:31 prefetch.2.10.7: 1) 'SRR5907451' was downloaded successfully Read 10498282 spots for SRR5907451/SRR5907451.sra Written 10498282 spots for SRR5907451/SRR5907451.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: 00:02:30 10498282 reads; of these: 10498282 (100.00%) were unpaired; of these: 2663704 (25.37%) aligned 0 times 6668102 (63.52%) aligned exactly 1 time 1166476 (11.11%) aligned >1 times 74.63% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 3638150 / 7834578 = 0.4644 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 19:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.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 19:37:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:51: 1000000 INFO @ Sun, 21 Jun 2020 19:37:57: 2000000 INFO @ Sun, 21 Jun 2020 19:38:03: 3000000 INFO @ Sun, 21 Jun 2020 19:38:08: 4000000 INFO @ Sun, 21 Jun 2020 19:38:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:10: #1 total tags in treatment: 4196428 INFO @ Sun, 21 Jun 2020 19:38:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:10: #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 19:38:10: #1 tags after filtering in treatment: 4196378 INFO @ Sun, 21 Jun 2020 19:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:10: #2 number of paired peaks: 2201 INFO @ Sun, 21 Jun 2020 19:38:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:10: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 19:38:10: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 19:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.05_model.r INFO @ Sun, 21 Jun 2020 19:38:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:10: #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 19:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.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 19:38:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:21: 1000000 INFO @ Sun, 21 Jun 2020 19:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:25: Done! pass1 - making usageList (448 chroms): 2 millis pass2 - checking and writing primary data (4837 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:27: 2000000 INFO @ Sun, 21 Jun 2020 19:38:32: 3000000 INFO @ Sun, 21 Jun 2020 19:38:38: 4000000 INFO @ Sun, 21 Jun 2020 19:38:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:39: #1 total tags in treatment: 4196428 INFO @ Sun, 21 Jun 2020 19:38:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:39: #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 19:38:40: #1 tags after filtering in treatment: 4196378 INFO @ Sun, 21 Jun 2020 19:38:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:40: #2 number of paired peaks: 2201 INFO @ Sun, 21 Jun 2020 19:38:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:40: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 19:38:40: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 19:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.10_model.r INFO @ Sun, 21 Jun 2020 19:38:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:40: #3 Pre-compute pvalue-qvalue table... 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 19:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.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 19:38:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:51: 1000000 INFO @ Sun, 21 Jun 2020 19:38:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:55: Done! pass1 - making usageList (377 chroms): 2 millis pass2 - checking and writing primary data (2614 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:57: 2000000 INFO @ Sun, 21 Jun 2020 19:39:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:39:08: 4000000 INFO @ Sun, 21 Jun 2020 19:39:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:39:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:39:10: #1 total tags in treatment: 4196428 INFO @ Sun, 21 Jun 2020 19:39:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:10: #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 19:39:10: #1 tags after filtering in treatment: 4196378 INFO @ Sun, 21 Jun 2020 19:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:10: #2 number of paired peaks: 2201 INFO @ Sun, 21 Jun 2020 19:39:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:10: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 19:39:10: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 19:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.20_model.r INFO @ Sun, 21 Jun 2020 19:39:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068975/SRX3068975.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:25: Done! pass1 - making usageList (195 chroms): 2 millis pass2 - checking and writing primary data (953 records, 4 fields): 7 millis CompletedMACS2peakCalling