Job ID = 6455890 SRX = SRX3032294 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:19:36 prefetch.2.10.7: 1) Downloading 'SRR5863984'... 2020-06-21T10:19:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:55 prefetch.2.10.7: 'SRR5863984' is valid 2020-06-21T10:20:55 prefetch.2.10.7: 1) 'SRR5863984' was downloaded successfully 2020-06-21T10:20:55 prefetch.2.10.7: 'SRR5863984' has 0 unresolved dependencies Read 7618844 spots for SRR5863984/SRR5863984.sra Written 7618844 spots for SRR5863984/SRR5863984.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:30 7618844 reads; of these: 7618844 (100.00%) were unpaired; of these: 1253832 (16.46%) aligned 0 times 5674132 (74.47%) aligned exactly 1 time 690880 (9.07%) aligned >1 times 83.54% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 3394128 / 6365012 = 0.5332 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 19:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.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 19:25:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:00: 1000000 INFO @ Sun, 21 Jun 2020 19:26:06: 2000000 INFO @ Sun, 21 Jun 2020 19:26:12: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:26:12: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:26:12: #1 total tags in treatment: 2970884 INFO @ Sun, 21 Jun 2020 19:26:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:12: #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 19:26:12: #1 tags after filtering in treatment: 2970533 INFO @ Sun, 21 Jun 2020 19:26:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:13: #2 number of paired peaks: 7561 INFO @ Sun, 21 Jun 2020 19:26:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:13: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:26:13: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.05_model.r INFO @ Sun, 21 Jun 2020 19:26:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:21: #3 Call peaks for each chromosome... 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 19:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.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 19:26:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:25: Done! pass1 - making usageList (141 chroms): 2 millis pass2 - checking and writing primary data (6826 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:30: 1000000 INFO @ Sun, 21 Jun 2020 19:26:35: 2000000 INFO @ Sun, 21 Jun 2020 19:26:41: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:26:41: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:26:41: #1 total tags in treatment: 2970884 INFO @ Sun, 21 Jun 2020 19:26:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:41: #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 19:26:42: #1 tags after filtering in treatment: 2970533 INFO @ Sun, 21 Jun 2020 19:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:42: #2 number of paired peaks: 7561 INFO @ Sun, 21 Jun 2020 19:26:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:42: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:26:42: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.10_model.r INFO @ Sun, 21 Jun 2020 19:26:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:50: #3 Call peaks for each chromosome... 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 19:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.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 19:26:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.10_summits.bed INFO @ Sun, 21 Jun 2020 19:26:54: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (4621 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:59: 1000000 INFO @ Sun, 21 Jun 2020 19:27:05: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:27:11: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:27:11: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:27:11: #1 total tags in treatment: 2970884 INFO @ Sun, 21 Jun 2020 19:27:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:11: #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 19:27:12: #1 tags after filtering in treatment: 2970533 INFO @ Sun, 21 Jun 2020 19:27:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:12: #2 number of paired peaks: 7561 INFO @ Sun, 21 Jun 2020 19:27:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:12: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:27:12: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.20_model.r INFO @ Sun, 21 Jun 2020 19:27:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032294/SRX3032294.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:24: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (2460 records, 4 fields): 6 millis CompletedMACS2peakCalling