Job ID = 6453776 SRX = SRX147003 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:32:26 prefetch.2.10.7: 1) Downloading 'SRR495377'... 2020-06-21T08:32:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:01 prefetch.2.10.7: 1) 'SRR495377' was downloaded successfully Read 21545230 spots for SRR495377/SRR495377.sra Written 21545230 spots for SRR495377/SRR495377.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: 00:05:32 21545230 reads; of these: 21545230 (100.00%) were unpaired; of these: 769628 (3.57%) aligned 0 times 14856458 (68.95%) aligned exactly 1 time 5919144 (27.47%) aligned >1 times 96.43% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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_sort_core] merging from 12 files... [bam_rmdupse_core] 5573220 / 20775602 = 0.2683 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 17:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.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 17:47:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:14: 1000000 INFO @ Sun, 21 Jun 2020 17:47:20: 2000000 INFO @ Sun, 21 Jun 2020 17:47:25: 3000000 INFO @ Sun, 21 Jun 2020 17:47:31: 4000000 INFO @ Sun, 21 Jun 2020 17:47:36: 5000000 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 17:47:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.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 17:47:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:42: 6000000 INFO @ Sun, 21 Jun 2020 17:47:45: 1000000 INFO @ Sun, 21 Jun 2020 17:47:47: 7000000 INFO @ Sun, 21 Jun 2020 17:47:50: 2000000 INFO @ Sun, 21 Jun 2020 17:47:53: 8000000 INFO @ Sun, 21 Jun 2020 17:47:56: 3000000 INFO @ Sun, 21 Jun 2020 17:47:58: 9000000 INFO @ Sun, 21 Jun 2020 17:48:01: 4000000 INFO @ Sun, 21 Jun 2020 17:48:04: 10000000 INFO @ Sun, 21 Jun 2020 17:48:07: 5000000 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 17:48:09: 11000000 INFO @ Sun, 21 Jun 2020 17:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.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 17:48:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:12: 6000000 INFO @ Sun, 21 Jun 2020 17:48:14: 12000000 INFO @ Sun, 21 Jun 2020 17:48:15: 1000000 INFO @ Sun, 21 Jun 2020 17:48:18: 7000000 INFO @ Sun, 21 Jun 2020 17:48:20: 13000000 INFO @ Sun, 21 Jun 2020 17:48:21: 2000000 INFO @ Sun, 21 Jun 2020 17:48:24: 8000000 INFO @ Sun, 21 Jun 2020 17:48:26: 14000000 INFO @ Sun, 21 Jun 2020 17:48:27: 3000000 INFO @ Sun, 21 Jun 2020 17:48:29: 9000000 INFO @ Sun, 21 Jun 2020 17:48:32: 15000000 INFO @ Sun, 21 Jun 2020 17:48:32: 4000000 INFO @ Sun, 21 Jun 2020 17:48:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:48:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:48:33: #1 total tags in treatment: 15202382 INFO @ Sun, 21 Jun 2020 17:48:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:33: #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 17:48:34: #1 tags after filtering in treatment: 15202276 INFO @ Sun, 21 Jun 2020 17:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:35: 10000000 INFO @ Sun, 21 Jun 2020 17:48:35: #2 number of paired peaks: 2857 INFO @ Sun, 21 Jun 2020 17:48:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:35: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 17:48:35: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 17:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.05_model.r INFO @ Sun, 21 Jun 2020 17:48:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:38: 5000000 INFO @ Sun, 21 Jun 2020 17:48:40: 11000000 INFO @ Sun, 21 Jun 2020 17:48:44: 6000000 INFO @ Sun, 21 Jun 2020 17:48:45: 12000000 INFO @ Sun, 21 Jun 2020 17:48:49: 7000000 INFO @ Sun, 21 Jun 2020 17:48:51: 13000000 INFO @ Sun, 21 Jun 2020 17:48:55: 8000000 INFO @ Sun, 21 Jun 2020 17:48:56: 14000000 INFO @ Sun, 21 Jun 2020 17:49:00: 9000000 INFO @ Sun, 21 Jun 2020 17:49:02: 15000000 INFO @ Sun, 21 Jun 2020 17:49:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:49:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:49:03: #1 total tags in treatment: 15202382 INFO @ Sun, 21 Jun 2020 17:49:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:03: #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 17:49:04: #1 tags after filtering in treatment: 15202276 INFO @ Sun, 21 Jun 2020 17:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:04: 10000000 INFO @ Sun, 21 Jun 2020 17:49:05: #2 number of paired peaks: 2857 INFO @ Sun, 21 Jun 2020 17:49:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:05: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 17:49:05: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 17:49:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.10_model.r INFO @ Sun, 21 Jun 2020 17:49:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:09: 11000000 INFO @ Sun, 21 Jun 2020 17:49:14: 12000000 INFO @ Sun, 21 Jun 2020 17:49:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:19: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:23: 14000000 INFO @ Sun, 21 Jun 2020 17:49:28: 15000000 INFO @ Sun, 21 Jun 2020 17:49:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:49:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:49:29: #1 total tags in treatment: 15202382 INFO @ Sun, 21 Jun 2020 17:49:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:29: #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 17:49:30: #1 tags after filtering in treatment: 15202276 INFO @ Sun, 21 Jun 2020 17:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:31: #2 number of paired peaks: 2857 INFO @ Sun, 21 Jun 2020 17:49:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:31: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 17:49:31: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 17:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.20_model.r INFO @ Sun, 21 Jun 2020 17:49:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:32: Done! pass1 - making usageList (373 chroms): 2 millis pass2 - checking and writing primary data (8885 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:01: Done! pass1 - making usageList (257 chroms): 2 millis pass2 - checking and writing primary data (6463 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX147003/SRX147003.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:28: Done! pass1 - making usageList (175 chroms): 1 millis pass2 - checking and writing primary data (4357 records, 4 fields): 10 millis CompletedMACS2peakCalling