Job ID = 6455230 SRX = SRX287575 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:45:25 prefetch.2.10.7: 1) Downloading 'SRR869718'... 2020-06-21T09:45:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:25 prefetch.2.10.7: 'SRR869718' is valid 2020-06-21T09:46:25 prefetch.2.10.7: 1) 'SRR869718' was downloaded successfully Read 7903645 spots for SRR869718/SRR869718.sra Written 7903645 spots for SRR869718/SRR869718.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: 00:03:15 7903645 reads; of these: 7903645 (100.00%) were unpaired; of these: 279855 (3.54%) aligned 0 times 2939930 (37.20%) aligned exactly 1 time 4683860 (59.26%) aligned >1 times 96.46% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 1928682 / 7623790 = 0.2530 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 18:52:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.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 18:52:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:13: 1000000 INFO @ Sun, 21 Jun 2020 18:52:18: 2000000 INFO @ Sun, 21 Jun 2020 18:52:24: 3000000 INFO @ Sun, 21 Jun 2020 18:52:29: 4000000 INFO @ Sun, 21 Jun 2020 18:52:35: 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 18:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.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 18:52:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:52:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:52:39: #1 total tags in treatment: 5695108 INFO @ Sun, 21 Jun 2020 18:52:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:39: #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 18:52:39: #1 tags after filtering in treatment: 5695108 INFO @ Sun, 21 Jun 2020 18:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:40: #2 number of paired peaks: 2858 INFO @ Sun, 21 Jun 2020 18:52:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:40: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 18:52:40: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 18:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.05_model.r INFO @ Sun, 21 Jun 2020 18:52:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:44: 1000000 INFO @ Sun, 21 Jun 2020 18:52:50: 2000000 INFO @ Sun, 21 Jun 2020 18:52:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:56: 3000000 INFO @ Sun, 21 Jun 2020 18:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.05_summits.bed INFO @ Sun, 21 Jun 2020 18:53:01: Done! pass1 - making usageList (974 chroms): 1 millis pass2 - checking and writing primary data (4397 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:02: 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 18:53:08: 5000000 INFO @ Sun, 21 Jun 2020 18:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.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 18:53:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:53:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:53:12: #1 total tags in treatment: 5695108 INFO @ Sun, 21 Jun 2020 18:53:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:12: #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 18:53:13: #1 tags after filtering in treatment: 5695108 INFO @ Sun, 21 Jun 2020 18:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:13: #2 number of paired peaks: 2858 INFO @ Sun, 21 Jun 2020 18:53:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:13: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 18:53:13: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 18:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.10_model.r INFO @ Sun, 21 Jun 2020 18:53:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:14: 1000000 INFO @ Sun, 21 Jun 2020 18:53:19: 2000000 INFO @ Sun, 21 Jun 2020 18:53:25: 3000000 INFO @ Sun, 21 Jun 2020 18:53:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:30: 4000000 INFO @ Sun, 21 Jun 2020 18:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:34: Done! pass1 - making usageList (751 chroms): 2 millis pass2 - checking and writing primary data (3009 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:35: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:53:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:53:39: #1 total tags in treatment: 5695108 INFO @ Sun, 21 Jun 2020 18:53:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:39: #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 18:53:40: #1 tags after filtering in treatment: 5695108 INFO @ Sun, 21 Jun 2020 18:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:40: #2 number of paired peaks: 2858 INFO @ Sun, 21 Jun 2020 18:53:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:40: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 18:53:40: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 18:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.20_model.r INFO @ Sun, 21 Jun 2020 18:53:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287575/SRX287575.20_summits.bed INFO @ Sun, 21 Jun 2020 18:54:01: Done! pass1 - making usageList (598 chroms): 4 millis pass2 - checking and writing primary data (1963 records, 4 fields): 17 millis CompletedMACS2peakCalling