Job ID = 6456350 SRX = SRX3380797 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:45:38 prefetch.2.10.7: 1) Downloading 'SRR6278160'... 2020-06-21T10:45:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:47:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:47:33 prefetch.2.10.7: 'SRR6278160' is valid 2020-06-21T10:47:33 prefetch.2.10.7: 1) 'SRR6278160' was downloaded successfully Read 10507971 spots for SRR6278160/SRR6278160.sra Written 10507971 spots for SRR6278160/SRR6278160.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: 00:02:45 10507971 reads; of these: 10507971 (100.00%) were unpaired; of these: 776233 (7.39%) aligned 0 times 7125170 (67.81%) aligned exactly 1 time 2606568 (24.81%) aligned >1 times 92.61% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1554134 / 9731738 = 0.1597 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 19:53:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.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 19:53:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:42: 1000000 INFO @ Sun, 21 Jun 2020 19:53:48: 2000000 INFO @ Sun, 21 Jun 2020 19:53:54: 3000000 INFO @ Sun, 21 Jun 2020 19:54:00: 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 19:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.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 19:54:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:07: 5000000 INFO @ Sun, 21 Jun 2020 19:54:13: 1000000 INFO @ Sun, 21 Jun 2020 19:54:13: 6000000 INFO @ Sun, 21 Jun 2020 19:54:19: 2000000 INFO @ Sun, 21 Jun 2020 19:54:20: 7000000 INFO @ Sun, 21 Jun 2020 19:54:25: 3000000 INFO @ Sun, 21 Jun 2020 19:54:26: 8000000 INFO @ Sun, 21 Jun 2020 19:54:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:54:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:54:27: #1 total tags in treatment: 8177604 INFO @ Sun, 21 Jun 2020 19:54:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:27: #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 19:54:28: #1 tags after filtering in treatment: 8177398 INFO @ Sun, 21 Jun 2020 19:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:29: #2 number of paired peaks: 5989 INFO @ Sun, 21 Jun 2020 19:54:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:29: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 19:54:29: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 19:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.05_model.r INFO @ Sun, 21 Jun 2020 19:54:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:31: 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 19:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.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 19:54:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:38: 5000000 INFO @ Sun, 21 Jun 2020 19:54:42: 1000000 INFO @ Sun, 21 Jun 2020 19:54:44: 6000000 INFO @ Sun, 21 Jun 2020 19:54:48: 2000000 INFO @ Sun, 21 Jun 2020 19:54:51: 7000000 INFO @ Sun, 21 Jun 2020 19:54:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:54: 3000000 INFO @ Sun, 21 Jun 2020 19:54:57: 8000000 INFO @ Sun, 21 Jun 2020 19:54:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:54:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:54:58: #1 total tags in treatment: 8177604 INFO @ Sun, 21 Jun 2020 19:54:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:58: #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 19:54:58: #1 tags after filtering in treatment: 8177398 INFO @ Sun, 21 Jun 2020 19:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:59: #2 number of paired peaks: 5989 INFO @ Sun, 21 Jun 2020 19:54:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:00: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 19:55:00: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 19:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.10_model.r INFO @ Sun, 21 Jun 2020 19:55:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:00: 4000000 INFO @ Sun, 21 Jun 2020 19:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.05_summits.bed INFO @ Sun, 21 Jun 2020 19:55:03: Done! pass1 - making usageList (263 chroms): 2 millis pass2 - checking and writing primary data (7105 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:05: 5000000 INFO @ Sun, 21 Jun 2020 19:55:11: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:55:17: 7000000 INFO @ Sun, 21 Jun 2020 19:55:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:22: 8000000 INFO @ Sun, 21 Jun 2020 19:55:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:23: #1 total tags in treatment: 8177604 INFO @ Sun, 21 Jun 2020 19:55:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:23: #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 19:55:23: #1 tags after filtering in treatment: 8177398 INFO @ Sun, 21 Jun 2020 19:55:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:24: #2 number of paired peaks: 5989 INFO @ Sun, 21 Jun 2020 19:55:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:24: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 19:55:24: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 19:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.20_model.r INFO @ Sun, 21 Jun 2020 19:55:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.10_summits.bed INFO @ Sun, 21 Jun 2020 19:55:32: Done! BigWig に変換しました。 pass1 - making usageList (210 chroms): 1 millis pass2 - checking and writing primary data (3717 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380797/SRX3380797.20_summits.bed INFO @ Sun, 21 Jun 2020 19:55:57: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (1447 records, 4 fields): 7 millis CompletedMACS2peakCalling