Job ID = 6454107 SRX = SRX183520 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:52:04 prefetch.2.10.7: 1) Downloading 'SRR567536'... 2020-06-21T08:52:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:05 prefetch.2.10.7: 1) 'SRR567536' was downloaded successfully Read 26129655 spots for SRR567536/SRR567536.sra Written 26129655 spots for SRR567536/SRR567536.sra 2020-06-21T08:57:27 prefetch.2.10.7: 1) Downloading 'SRR567537'... 2020-06-21T08:57:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:59:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:59:42 prefetch.2.10.7: 1) 'SRR567537' was downloaded successfully Read 21770338 spots for SRR567537/SRR567537.sra Written 21770338 spots for SRR567537/SRR567537.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: 00:08:14 47899993 reads; of these: 47899993 (100.00%) were unpaired; of these: 32015974 (66.84%) aligned 0 times 10748968 (22.44%) aligned exactly 1 time 5135051 (10.72%) aligned >1 times 33.16% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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] 10750632 / 15884019 = 0.6768 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 18:12:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.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 18:12:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:02: 1000000 INFO @ Sun, 21 Jun 2020 18:13:08: 2000000 INFO @ Sun, 21 Jun 2020 18:13:13: 3000000 INFO @ Sun, 21 Jun 2020 18:13:19: 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 18:13:25: 5000000 INFO @ Sun, 21 Jun 2020 18:13:25: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 18:13:25: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 18:13:25: #1 total tags in treatment: 5133387 INFO @ Sun, 21 Jun 2020 18:13:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:25: #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 18:13:26: #1 tags after filtering in treatment: 5133278 INFO @ Sun, 21 Jun 2020 18:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:26: #2 number of paired peaks: 5873 INFO @ Sun, 21 Jun 2020 18:13:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.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 18:13:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:27: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 18:13:27: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 18:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.05_model.r INFO @ Sun, 21 Jun 2020 18:13:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:32: 1000000 INFO @ Sun, 21 Jun 2020 18:13:38: 2000000 INFO @ Sun, 21 Jun 2020 18:13:43: 3000000 INFO @ Sun, 21 Jun 2020 18:13:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:48: 4000000 INFO @ Sun, 21 Jun 2020 18:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.05_summits.bed INFO @ Sun, 21 Jun 2020 18:13:51: Done! pass1 - making usageList (596 chroms): 2 millis pass2 - checking and writing primary data (6015 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:13:54: 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 18:13:55: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 18:13:55: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 18:13:55: #1 total tags in treatment: 5133387 INFO @ Sun, 21 Jun 2020 18:13:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:55: #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 18:13:56: #1 tags after filtering in treatment: 5133278 INFO @ Sun, 21 Jun 2020 18:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:56: #2 number of paired peaks: 5873 INFO @ Sun, 21 Jun 2020 18:13:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:56: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 18:13:56: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 18:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.10_model.r INFO @ Sun, 21 Jun 2020 18:13:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.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 18:13:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:03: 1000000 INFO @ Sun, 21 Jun 2020 18:14:09: 2000000 INFO @ Sun, 21 Jun 2020 18:14:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:15: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:14:21: 4000000 INFO @ Sun, 21 Jun 2020 18:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.10_summits.bed INFO @ Sun, 21 Jun 2020 18:14:22: Done! pass1 - making usageList (495 chroms): 2 millis pass2 - checking and writing primary data (4927 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:28: 5000000 INFO @ Sun, 21 Jun 2020 18:14:29: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 18:14:29: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 18:14:29: #1 total tags in treatment: 5133387 INFO @ Sun, 21 Jun 2020 18:14:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:29: #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 18:14:29: #1 tags after filtering in treatment: 5133278 INFO @ Sun, 21 Jun 2020 18:14:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:30: #2 number of paired peaks: 5873 INFO @ Sun, 21 Jun 2020 18:14:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:30: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 18:14:30: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 18:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.20_model.r INFO @ Sun, 21 Jun 2020 18:14:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:14:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183520/SRX183520.20_summits.bed INFO @ Sun, 21 Jun 2020 18:14:53: Done! pass1 - making usageList (256 chroms): 1 millis pass2 - checking and writing primary data (3690 records, 4 fields): 13 millis CompletedMACS2peakCalling