Job ID = 6455943 SRX = SRX3068979 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:25:51 prefetch.2.10.7: 1) Downloading 'SRR5907455'... 2020-06-21T10:25:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:00 prefetch.2.10.7: 'SRR5907455' is valid 2020-06-21T10:27:00 prefetch.2.10.7: 1) 'SRR5907455' was downloaded successfully Read 7494587 spots for SRR5907455/SRR5907455.sra Written 7494587 spots for SRR5907455/SRR5907455.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: 00:01:27 7494587 reads; of these: 7494587 (100.00%) were unpaired; of these: 3847905 (51.34%) aligned 0 times 3075510 (41.04%) aligned exactly 1 time 571172 (7.62%) aligned >1 times 48.66% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 1428059 / 3646682 = 0.3916 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 19:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.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 19:30:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:33: 1000000 INFO @ Sun, 21 Jun 2020 19:30:39: 2000000 INFO @ Sun, 21 Jun 2020 19:30:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:30:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:30:41: #1 total tags in treatment: 2218623 INFO @ Sun, 21 Jun 2020 19:30:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:41: #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 19:30:41: #1 tags after filtering in treatment: 2218418 INFO @ Sun, 21 Jun 2020 19:30:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:42: #2 number of paired peaks: 1110 INFO @ Sun, 21 Jun 2020 19:30:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:42: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 19:30:42: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 19:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.05_model.r INFO @ Sun, 21 Jun 2020 19:30:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:49: Done! pass1 - making usageList (361 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 21 millis CompletedMACS2peakCalling 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 19:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.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 19:30:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:03: 1000000 INFO @ Sun, 21 Jun 2020 19:31:09: 2000000 INFO @ Sun, 21 Jun 2020 19:31:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:31:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:31:11: #1 total tags in treatment: 2218623 INFO @ Sun, 21 Jun 2020 19:31:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:11: #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 19:31:11: #1 tags after filtering in treatment: 2218418 INFO @ Sun, 21 Jun 2020 19:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:12: #2 number of paired peaks: 1110 INFO @ Sun, 21 Jun 2020 19:31:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:12: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 19:31:12: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 19:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.10_model.r INFO @ Sun, 21 Jun 2020 19:31:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:19: Done! pass1 - making usageList (189 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 19:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.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 19:31:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:33: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:31:40: 2000000 INFO @ Sun, 21 Jun 2020 19:31:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:31:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:31:41: #1 total tags in treatment: 2218623 INFO @ Sun, 21 Jun 2020 19:31:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:41: #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 19:31:42: #1 tags after filtering in treatment: 2218418 INFO @ Sun, 21 Jun 2020 19:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:42: #2 number of paired peaks: 1110 INFO @ Sun, 21 Jun 2020 19:31:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:42: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 19:31:42: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 19:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.20_model.r INFO @ Sun, 21 Jun 2020 19:31:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068979/SRX3068979.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:49: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 5 millis CompletedMACS2peakCalling