Job ID = 6457819 SRX = SRX4798862 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:52 prefetch.2.10.7: 1) Downloading 'SRR7965207'... 2020-06-21T12:08:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:11:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:11:06 prefetch.2.10.7: 'SRR7965207' is valid 2020-06-21T12:11:06 prefetch.2.10.7: 1) 'SRR7965207' was downloaded successfully Read 14837133 spots for SRR7965207/SRR7965207.sra Written 14837133 spots for SRR7965207/SRR7965207.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: 00:01:30 14837133 reads; of these: 14837133 (100.00%) were unpaired; of these: 11001961 (74.15%) aligned 0 times 3554494 (23.96%) aligned exactly 1 time 280678 (1.89%) aligned >1 times 25.85% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 972821 / 3835172 = 0.2537 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 21:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.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 21:14:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:52: 1000000 INFO @ Sun, 21 Jun 2020 21:14:57: 2000000 INFO @ Sun, 21 Jun 2020 21:15:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:15:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:15:02: #1 total tags in treatment: 2862351 INFO @ Sun, 21 Jun 2020 21:15:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:02: #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 21:15:03: #1 tags after filtering in treatment: 2862006 INFO @ Sun, 21 Jun 2020 21:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:03: #2 number of paired peaks: 3933 INFO @ Sun, 21 Jun 2020 21:15:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:03: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 21:15:03: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 21:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.05_model.r INFO @ Sun, 21 Jun 2020 21:15:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.05_summits.bed INFO @ Sun, 21 Jun 2020 21:15:13: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (5169 records, 4 fields): 49 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 21:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.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 21:15:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:22: 1000000 INFO @ Sun, 21 Jun 2020 21:15:27: 2000000 INFO @ Sun, 21 Jun 2020 21:15:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:15:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:15:32: #1 total tags in treatment: 2862351 INFO @ Sun, 21 Jun 2020 21:15:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:32: #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 21:15:33: #1 tags after filtering in treatment: 2862006 INFO @ Sun, 21 Jun 2020 21:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:33: #2 number of paired peaks: 3933 INFO @ Sun, 21 Jun 2020 21:15:33: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:33: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:33: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 21:15:33: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 21:15:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.10_model.r INFO @ Sun, 21 Jun 2020 21:15:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.10_summits.bed INFO @ Sun, 21 Jun 2020 21:15:44: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (2827 records, 4 fields): 5 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 21:15:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.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 21:15:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:52: 1000000 INFO @ Sun, 21 Jun 2020 21:15:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:16:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:16:02: #1 total tags in treatment: 2862351 INFO @ Sun, 21 Jun 2020 21:16:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:02: #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 21:16:02: #1 tags after filtering in treatment: 2862006 INFO @ Sun, 21 Jun 2020 21:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:03: #2 number of paired peaks: 3933 INFO @ Sun, 21 Jun 2020 21:16:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:03: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 21:16:03: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 21:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.20_model.r INFO @ Sun, 21 Jun 2020 21:16:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:16:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798862/SRX4798862.20_summits.bed INFO @ Sun, 21 Jun 2020 21:16:13: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (1238 records, 4 fields): 3 millis CompletedMACS2peakCalling