Job ID = 6453248 SRX = SRX110767 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:18:47 prefetch.2.10.7: 1) Downloading 'SRR388349'... 2020-06-21T08:18:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:19:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:19:48 prefetch.2.10.7: 'SRR388349' is valid 2020-06-21T08:19:48 prefetch.2.10.7: 1) 'SRR388349' was downloaded successfully Read 16332772 spots for SRR388349/SRR388349.sra Written 16332772 spots for SRR388349/SRR388349.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: 00:04:50 16332772 reads; of these: 16332772 (100.00%) were unpaired; of these: 1407763 (8.62%) aligned 0 times 8353727 (51.15%) aligned exactly 1 time 6571282 (40.23%) aligned >1 times 91.38% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 5298995 / 14925009 = 0.3550 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 17:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.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 17:28:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:09: 1000000 INFO @ Sun, 21 Jun 2020 17:28:15: 2000000 INFO @ Sun, 21 Jun 2020 17:28:20: 3000000 INFO @ Sun, 21 Jun 2020 17:28:26: 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 17:28:31: 5000000 INFO @ Sun, 21 Jun 2020 17:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.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 17:28:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:38: 6000000 INFO @ Sun, 21 Jun 2020 17:28:39: 1000000 INFO @ Sun, 21 Jun 2020 17:28:44: 7000000 INFO @ Sun, 21 Jun 2020 17:28:46: 2000000 INFO @ Sun, 21 Jun 2020 17:28:50: 8000000 INFO @ Sun, 21 Jun 2020 17:28:52: 3000000 INFO @ Sun, 21 Jun 2020 17:28:57: 9000000 INFO @ Sun, 21 Jun 2020 17:28:59: 4000000 INFO @ Sun, 21 Jun 2020 17:29:01: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:29:01: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:29:01: #1 total tags in treatment: 9626014 INFO @ Sun, 21 Jun 2020 17:29:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:01: #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 17:29:01: #1 tags after filtering in treatment: 9626013 INFO @ Sun, 21 Jun 2020 17:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:01: #2 looking for paired plus/minus strand peaks... 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 17:29:02: #2 number of paired peaks: 4474 INFO @ Sun, 21 Jun 2020 17:29:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:02: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:29:02: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 17:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.05_model.r INFO @ Sun, 21 Jun 2020 17:29:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.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 17:29:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:05: 5000000 INFO @ Sun, 21 Jun 2020 17:29:09: 1000000 INFO @ Sun, 21 Jun 2020 17:29:12: 6000000 INFO @ Sun, 21 Jun 2020 17:29:16: 2000000 INFO @ Sun, 21 Jun 2020 17:29:18: 7000000 INFO @ Sun, 21 Jun 2020 17:29:22: 3000000 INFO @ Sun, 21 Jun 2020 17:29:25: 8000000 INFO @ Sun, 21 Jun 2020 17:29:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:29: 4000000 INFO @ Sun, 21 Jun 2020 17:29:31: 9000000 INFO @ Sun, 21 Jun 2020 17:29:35: 5000000 INFO @ Sun, 21 Jun 2020 17:29:35: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:29:35: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:29:35: #1 total tags in treatment: 9626014 INFO @ Sun, 21 Jun 2020 17:29:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:35: #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 17:29:36: #1 tags after filtering in treatment: 9626013 INFO @ Sun, 21 Jun 2020 17:29:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:36: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:37: #2 number of paired peaks: 4474 INFO @ Sun, 21 Jun 2020 17:29:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:37: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:29:37: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 17:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.10_model.r INFO @ Sun, 21 Jun 2020 17:29:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.05_summits.bed INFO @ Sun, 21 Jun 2020 17:29:38: Done! pass1 - making usageList (167 chroms): 2 millis pass2 - checking and writing primary data (8849 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:29:41: 6000000 INFO @ Sun, 21 Jun 2020 17:29:47: 7000000 INFO @ Sun, 21 Jun 2020 17:29:53: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:58: 9000000 INFO @ Sun, 21 Jun 2020 17:30:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:02: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:30:02: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:30:02: #1 total tags in treatment: 9626014 INFO @ Sun, 21 Jun 2020 17:30:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:02: #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 17:30:02: #1 tags after filtering in treatment: 9626013 INFO @ Sun, 21 Jun 2020 17:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:03: #2 number of paired peaks: 4474 INFO @ Sun, 21 Jun 2020 17:30:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:03: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:30:03: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 17:30:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.20_model.r INFO @ Sun, 21 Jun 2020 17:30:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.10_summits.bed INFO @ Sun, 21 Jun 2020 17:30:11: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (6674 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110767/SRX110767.20_summits.bed INFO @ Sun, 21 Jun 2020 17:30:39: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (4690 records, 4 fields): 10 millis CompletedMACS2peakCalling