Job ID = 6453793 SRX = SRX1490785 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:33:09 prefetch.2.10.7: 1) Downloading 'SRR3031652'... 2020-06-21T08:33:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:35:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:35:49 prefetch.2.10.7: 'SRR3031652' is valid 2020-06-21T08:35:49 prefetch.2.10.7: 1) 'SRR3031652' was downloaded successfully Read 14143419 spots for SRR3031652/SRR3031652.sra Written 14143419 spots for SRR3031652/SRR3031652.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 14143419 reads; of these: 14143419 (100.00%) were unpaired; of these: 1492189 (10.55%) aligned 0 times 10226166 (72.30%) aligned exactly 1 time 2425064 (17.15%) aligned >1 times 89.45% 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7941092 / 12651230 = 0.6277 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 17:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.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 17:42:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:26: 1000000 INFO @ Sun, 21 Jun 2020 17:42:31: 2000000 INFO @ Sun, 21 Jun 2020 17:42:37: 3000000 INFO @ Sun, 21 Jun 2020 17:42:42: 4000000 INFO @ Sun, 21 Jun 2020 17:42:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:46: #1 total tags in treatment: 4710138 INFO @ Sun, 21 Jun 2020 17:42:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:46: #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 17:42:46: #1 tags after filtering in treatment: 4710065 INFO @ Sun, 21 Jun 2020 17:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:46: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:47: #2 number of paired peaks: 7020 INFO @ Sun, 21 Jun 2020 17:42:47: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:47: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 17:42:47: #2 alternative fragment length(s) may be 4,202 bps INFO @ Sun, 21 Jun 2020 17:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.05_model.r INFO @ Sun, 21 Jun 2020 17:42:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:47: #3 Pre-compute pvalue-qvalue table... 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 17:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.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 17:42:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:56: 1000000 INFO @ Sun, 21 Jun 2020 17:43:02: 2000000 INFO @ Sun, 21 Jun 2020 17:43:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:07: 3000000 INFO @ Sun, 21 Jun 2020 17:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.05_summits.bed INFO @ Sun, 21 Jun 2020 17:43:10: Done! pass1 - making usageList (164 chroms): 1 millis pass2 - checking and writing primary data (1905 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:43:13: 4000000 INFO @ Sun, 21 Jun 2020 17:43:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:43:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:43:17: #1 total tags in treatment: 4710138 INFO @ Sun, 21 Jun 2020 17:43:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:17: #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 17:43:17: #1 tags after filtering in treatment: 4710065 INFO @ Sun, 21 Jun 2020 17:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:18: #2 number of paired peaks: 7020 INFO @ Sun, 21 Jun 2020 17:43:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:18: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 17:43:18: #2 alternative fragment length(s) may be 4,202 bps INFO @ Sun, 21 Jun 2020 17:43:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.10_model.r INFO @ Sun, 21 Jun 2020 17:43:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:18: #3 Pre-compute pvalue-qvalue table... 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 17:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.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 17:43:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:26: 1000000 INFO @ Sun, 21 Jun 2020 17:43:32: 2000000 INFO @ Sun, 21 Jun 2020 17:43:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:38: 3000000 INFO @ Sun, 21 Jun 2020 17:43:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.10_summits.bed INFO @ Sun, 21 Jun 2020 17:43:42: Done! pass1 - making usageList (149 chroms): 2 millis pass2 - checking and writing primary data (1162 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:43:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:43:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:43:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:43:48: #1 total tags in treatment: 4710138 INFO @ Sun, 21 Jun 2020 17:43:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:48: #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 17:43:48: #1 tags after filtering in treatment: 4710065 INFO @ Sun, 21 Jun 2020 17:43:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:49: #2 number of paired peaks: 7020 INFO @ Sun, 21 Jun 2020 17:43:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:49: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 17:43:49: #2 alternative fragment length(s) may be 4,202 bps INFO @ Sun, 21 Jun 2020 17:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.20_model.r INFO @ Sun, 21 Jun 2020 17:43:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:44:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490785/SRX1490785.20_summits.bed INFO @ Sun, 21 Jun 2020 17:44:13: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 5 millis CompletedMACS2peakCalling