Job ID = 6458959 SRX = SRX5827828 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:01:05 prefetch.2.10.7: 1) Downloading 'SRR9051579'... 2020-06-21T13:01:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:04:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:04:42 prefetch.2.10.7: 'SRR9051579' is valid 2020-06-21T13:04:42 prefetch.2.10.7: 1) 'SRR9051579' was downloaded successfully 2020-06-21T13:04:42 prefetch.2.10.7: 'SRR9051579' has 0 unresolved dependencies Read 20657033 spots for SRR9051579/SRR9051579.sra Written 20657033 spots for SRR9051579/SRR9051579.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: 00:00:01 Multiseed full-index search: 00:04:58 20657033 reads; of these: 20657033 (100.00%) were unpaired; of these: 2015685 (9.76%) aligned 0 times 16133106 (78.10%) aligned exactly 1 time 2508242 (12.14%) aligned >1 times 90.24% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 6083187 / 18641348 = 0.3263 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 22:16:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.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 22:16:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:16:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:16:35: 1000000 INFO @ Sun, 21 Jun 2020 22:16:41: 2000000 INFO @ Sun, 21 Jun 2020 22:16:47: 3000000 INFO @ Sun, 21 Jun 2020 22:16:53: 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 22:16:58: 5000000 INFO @ Sun, 21 Jun 2020 22:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.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 22:16:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:16:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:04: 1000000 INFO @ Sun, 21 Jun 2020 22:17:05: 6000000 INFO @ Sun, 21 Jun 2020 22:17:09: 2000000 INFO @ Sun, 21 Jun 2020 22:17:10: 7000000 INFO @ Sun, 21 Jun 2020 22:17:14: 3000000 INFO @ Sun, 21 Jun 2020 22:17:16: 8000000 INFO @ Sun, 21 Jun 2020 22:17:19: 4000000 INFO @ Sun, 21 Jun 2020 22:17:22: 9000000 INFO @ Sun, 21 Jun 2020 22:17:24: 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 22:17:28: 10000000 INFO @ Sun, 21 Jun 2020 22:17:29: 6000000 INFO @ Sun, 21 Jun 2020 22:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.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 22:17:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:33: 7000000 INFO @ Sun, 21 Jun 2020 22:17:34: 11000000 INFO @ Sun, 21 Jun 2020 22:17:34: 1000000 INFO @ Sun, 21 Jun 2020 22:17:38: 8000000 INFO @ Sun, 21 Jun 2020 22:17:40: 2000000 INFO @ Sun, 21 Jun 2020 22:17:40: 12000000 INFO @ Sun, 21 Jun 2020 22:17:43: 9000000 INFO @ Sun, 21 Jun 2020 22:17:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:17:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:17:44: #1 total tags in treatment: 12558161 INFO @ Sun, 21 Jun 2020 22:17:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:44: #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 22:17:44: #1 tags after filtering in treatment: 12558155 INFO @ Sun, 21 Jun 2020 22:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:45: 3000000 INFO @ Sun, 21 Jun 2020 22:17:45: #2 number of paired peaks: 1816 INFO @ Sun, 21 Jun 2020 22:17:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:46: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:17:46: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.05_model.r INFO @ Sun, 21 Jun 2020 22:17:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:48: 10000000 INFO @ Sun, 21 Jun 2020 22:17:50: 4000000 INFO @ Sun, 21 Jun 2020 22:17:53: 11000000 INFO @ Sun, 21 Jun 2020 22:17:55: 5000000 INFO @ Sun, 21 Jun 2020 22:17:58: 12000000 INFO @ Sun, 21 Jun 2020 22:18:00: 6000000 INFO @ Sun, 21 Jun 2020 22:18:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:18:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:18:01: #1 total tags in treatment: 12558161 INFO @ Sun, 21 Jun 2020 22:18:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:01: #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 22:18:02: #1 tags after filtering in treatment: 12558155 INFO @ Sun, 21 Jun 2020 22:18:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:03: #2 number of paired peaks: 1816 INFO @ Sun, 21 Jun 2020 22:18:03: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:03: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:18:03: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.10_model.r INFO @ Sun, 21 Jun 2020 22:18:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:05: 7000000 INFO @ Sun, 21 Jun 2020 22:18:10: 8000000 INFO @ Sun, 21 Jun 2020 22:18:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:15: 9000000 INFO @ Sun, 21 Jun 2020 22:18:20: 10000000 INFO @ Sun, 21 Jun 2020 22:18:25: 11000000 INFO @ Sun, 21 Jun 2020 22:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:30: 12000000 INFO @ Sun, 21 Jun 2020 22:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.05_summits.bed INFO @ Sun, 21 Jun 2020 22:18:30: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (3566 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:18:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:18:33: #1 total tags in treatment: 12558161 INFO @ Sun, 21 Jun 2020 22:18:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:33: #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 22:18:33: #1 tags after filtering in treatment: 12558155 INFO @ Sun, 21 Jun 2020 22:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:34: #2 number of paired peaks: 1816 INFO @ Sun, 21 Jun 2020 22:18:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:34: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:18:34: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.20_model.r INFO @ Sun, 21 Jun 2020 22:18:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:44: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (2191 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:19:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827828/SRX5827828.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:15: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (1345 records, 4 fields): 6 millis CompletedMACS2peakCalling