Job ID = 6456057 SRX = SRX3167241 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:38:44 prefetch.2.10.7: 1) Downloading 'SRR6014244'... 2020-06-21T10:38:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:22 prefetch.2.10.7: 'SRR6014244' is valid 2020-06-21T10:41:22 prefetch.2.10.7: 1) 'SRR6014244' was downloaded successfully Read 11548577 spots for SRR6014244/SRR6014244.sra Written 11548577 spots for SRR6014244/SRR6014244.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: 00:03:10 11548577 reads; of these: 11548577 (100.00%) were unpaired; of these: 1412338 (12.23%) aligned 0 times 6666917 (57.73%) aligned exactly 1 time 3469322 (30.04%) aligned >1 times 87.77% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 6794283 / 10136239 = 0.6703 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 19:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.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 19:47:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:34: 1000000 INFO @ Sun, 21 Jun 2020 19:47:41: 2000000 INFO @ Sun, 21 Jun 2020 19:47:48: 3000000 INFO @ Sun, 21 Jun 2020 19:47:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:47:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:47:50: #1 total tags in treatment: 3341956 INFO @ Sun, 21 Jun 2020 19:47:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:50: #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 19:47:50: #1 tags after filtering in treatment: 3341838 INFO @ Sun, 21 Jun 2020 19:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:51: #2 number of paired peaks: 3928 INFO @ Sun, 21 Jun 2020 19:47:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:51: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 19:47:51: #2 alternative fragment length(s) may be 4,133 bps INFO @ Sun, 21 Jun 2020 19:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.05_model.r INFO @ Sun, 21 Jun 2020 19:47:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:51: #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 19:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.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 19:47:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.05_summits.bed INFO @ Sun, 21 Jun 2020 19:48:03: Done! pass1 - making usageList (808 chroms): 1 millis pass2 - checking and writing primary data (3127 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:48:04: 1000000 INFO @ Sun, 21 Jun 2020 19:48:10: 2000000 INFO @ Sun, 21 Jun 2020 19:48:17: 3000000 INFO @ Sun, 21 Jun 2020 19:48:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:48:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:48:19: #1 total tags in treatment: 3341956 INFO @ Sun, 21 Jun 2020 19:48:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:19: #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 19:48:19: #1 tags after filtering in treatment: 3341838 INFO @ Sun, 21 Jun 2020 19:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:20: #2 number of paired peaks: 3928 INFO @ Sun, 21 Jun 2020 19:48:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:20: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 19:48:20: #2 alternative fragment length(s) may be 4,133 bps INFO @ Sun, 21 Jun 2020 19:48:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.10_model.r INFO @ Sun, 21 Jun 2020 19:48:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:20: #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 19:48:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.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 19:48:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:32: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (1931 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:48:35: 1000000 INFO @ Sun, 21 Jun 2020 19:48:41: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:48:48: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:48:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:48:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:48:50: #1 total tags in treatment: 3341956 INFO @ Sun, 21 Jun 2020 19:48:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:50: #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 19:48:51: #1 tags after filtering in treatment: 3341838 INFO @ Sun, 21 Jun 2020 19:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:51: #2 number of paired peaks: 3928 INFO @ Sun, 21 Jun 2020 19:48:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:51: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 19:48:51: #2 alternative fragment length(s) may be 4,133 bps INFO @ Sun, 21 Jun 2020 19:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.20_model.r INFO @ Sun, 21 Jun 2020 19:48:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167241/SRX3167241.20_summits.bed INFO @ Sun, 21 Jun 2020 19:49:03: Done! pass1 - making usageList (516 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 13 millis CompletedMACS2peakCalling