Job ID = 6457493 SRX = SRX4664648 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:00:32 prefetch.2.10.7: 1) Downloading 'SRR7813075'... 2020-06-21T12:00:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:03:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:03:39 prefetch.2.10.7: 'SRR7813075' is valid 2020-06-21T12:03:39 prefetch.2.10.7: 1) 'SRR7813075' was downloaded successfully Read 20216769 spots for SRR7813075/SRR7813075.sra Written 20216769 spots for SRR7813075/SRR7813075.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: 00:05:26 20216769 reads; of these: 20216769 (100.00%) were unpaired; of these: 1233473 (6.10%) aligned 0 times 14169947 (70.09%) aligned exactly 1 time 4813349 (23.81%) aligned >1 times 93.90% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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 8 files... [bam_rmdupse_core] 4634090 / 18983296 = 0.2441 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 21:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.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 21:14:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:30: 1000000 INFO @ Sun, 21 Jun 2020 21:14:36: 2000000 INFO @ Sun, 21 Jun 2020 21:14:42: 3000000 INFO @ Sun, 21 Jun 2020 21:14:47: 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 21:14:53: 5000000 INFO @ Sun, 21 Jun 2020 21:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.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 21:14:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:59: 6000000 INFO @ Sun, 21 Jun 2020 21:15:02: 1000000 INFO @ Sun, 21 Jun 2020 21:15:05: 7000000 INFO @ Sun, 21 Jun 2020 21:15:08: 2000000 INFO @ Sun, 21 Jun 2020 21:15:12: 8000000 INFO @ Sun, 21 Jun 2020 21:15:15: 3000000 INFO @ Sun, 21 Jun 2020 21:15:18: 9000000 INFO @ Sun, 21 Jun 2020 21:15:21: 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 21:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.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 21:15:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:25: 10000000 INFO @ Sun, 21 Jun 2020 21:15:28: 5000000 INFO @ Sun, 21 Jun 2020 21:15:31: 11000000 INFO @ Sun, 21 Jun 2020 21:15:31: 1000000 INFO @ Sun, 21 Jun 2020 21:15:34: 6000000 INFO @ Sun, 21 Jun 2020 21:15:38: 2000000 INFO @ Sun, 21 Jun 2020 21:15:38: 12000000 INFO @ Sun, 21 Jun 2020 21:15:41: 7000000 INFO @ Sun, 21 Jun 2020 21:15:44: 13000000 INFO @ Sun, 21 Jun 2020 21:15:45: 3000000 INFO @ Sun, 21 Jun 2020 21:15:47: 8000000 INFO @ Sun, 21 Jun 2020 21:15:51: 14000000 INFO @ Sun, 21 Jun 2020 21:15:51: 4000000 INFO @ Sun, 21 Jun 2020 21:15:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:15:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:15:53: #1 total tags in treatment: 14349206 INFO @ Sun, 21 Jun 2020 21:15:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:53: #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 21:15:54: #1 tags after filtering in treatment: 14349104 INFO @ Sun, 21 Jun 2020 21:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:54: 9000000 INFO @ Sun, 21 Jun 2020 21:15:55: #2 number of paired peaks: 2740 INFO @ Sun, 21 Jun 2020 21:15:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:55: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 21:15:55: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 21:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.05_model.r INFO @ Sun, 21 Jun 2020 21:15:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:58: 5000000 INFO @ Sun, 21 Jun 2020 21:16:00: 10000000 INFO @ Sun, 21 Jun 2020 21:16:04: 6000000 INFO @ Sun, 21 Jun 2020 21:16:06: 11000000 INFO @ Sun, 21 Jun 2020 21:16:10: 7000000 INFO @ Sun, 21 Jun 2020 21:16:13: 12000000 INFO @ Sun, 21 Jun 2020 21:16:16: 8000000 INFO @ Sun, 21 Jun 2020 21:16:19: 13000000 INFO @ Sun, 21 Jun 2020 21:16:22: 9000000 INFO @ Sun, 21 Jun 2020 21:16:25: 14000000 INFO @ Sun, 21 Jun 2020 21:16:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:27: #1 total tags in treatment: 14349206 INFO @ Sun, 21 Jun 2020 21:16:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:27: #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 21:16:27: #1 tags after filtering in treatment: 14349104 INFO @ Sun, 21 Jun 2020 21:16:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:28: 10000000 INFO @ Sun, 21 Jun 2020 21:16:29: #2 number of paired peaks: 2740 INFO @ Sun, 21 Jun 2020 21:16:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:29: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 21:16:29: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 21:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.10_model.r INFO @ Sun, 21 Jun 2020 21:16:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:34: 11000000 INFO @ Sun, 21 Jun 2020 21:16:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:46: 13000000 INFO @ Sun, 21 Jun 2020 21:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.05_summits.bed INFO @ Sun, 21 Jun 2020 21:16:48: Done! pass1 - making usageList (567 chroms): 3 millis pass2 - checking and writing primary data (10748 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:16:51: 14000000 INFO @ Sun, 21 Jun 2020 21:16:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:54: #1 total tags in treatment: 14349206 INFO @ Sun, 21 Jun 2020 21:16:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:54: #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 21:16:54: #1 tags after filtering in treatment: 14349104 INFO @ Sun, 21 Jun 2020 21:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:55: #2 number of paired peaks: 2740 INFO @ Sun, 21 Jun 2020 21:16:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:56: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 21:16:56: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 21:16:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.20_model.r INFO @ Sun, 21 Jun 2020 21:16:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.10_summits.bed INFO @ Sun, 21 Jun 2020 21:17:22: Done! pass1 - making usageList (492 chroms): 2 millis pass2 - checking and writing primary data (8219 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664648/SRX4664648.20_summits.bed INFO @ Sun, 21 Jun 2020 21:17:47: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (5473 records, 4 fields): 17 millis CompletedMACS2peakCalling