Job ID = 6455752 SRX = SRX288046 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:21 prefetch.2.10.7: 1) Downloading 'SRR870235'... 2020-06-21T10:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:38 prefetch.2.10.7: 1) 'SRR870235' was downloaded successfully Read 17315235 spots for SRR870235/SRR870235.sra Written 17315235 spots for SRR870235/SRR870235.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: 00:04:03 17315235 reads; of these: 17315235 (100.00%) were unpaired; of these: 878466 (5.07%) aligned 0 times 14026475 (81.01%) aligned exactly 1 time 2410294 (13.92%) aligned >1 times 94.93% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 2471043 / 16436769 = 0.1503 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 19:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.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 19:27:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:59: 1000000 INFO @ Sun, 21 Jun 2020 19:28:05: 2000000 INFO @ Sun, 21 Jun 2020 19:28:11: 3000000 INFO @ Sun, 21 Jun 2020 19:28:18: 4000000 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 19:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.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 19:28:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:24: 5000000 INFO @ Sun, 21 Jun 2020 19:28:30: 1000000 INFO @ Sun, 21 Jun 2020 19:28:32: 6000000 INFO @ Sun, 21 Jun 2020 19:28:37: 2000000 INFO @ Sun, 21 Jun 2020 19:28:39: 7000000 INFO @ Sun, 21 Jun 2020 19:28:44: 3000000 INFO @ Sun, 21 Jun 2020 19:28:46: 8000000 INFO @ Sun, 21 Jun 2020 19:28:50: 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 19:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.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 19:28:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:53: 9000000 INFO @ Sun, 21 Jun 2020 19:28:57: 5000000 INFO @ Sun, 21 Jun 2020 19:29:00: 1000000 INFO @ Sun, 21 Jun 2020 19:29:00: 10000000 INFO @ Sun, 21 Jun 2020 19:29:04: 6000000 INFO @ Sun, 21 Jun 2020 19:29:07: 2000000 INFO @ Sun, 21 Jun 2020 19:29:07: 11000000 INFO @ Sun, 21 Jun 2020 19:29:11: 7000000 INFO @ Sun, 21 Jun 2020 19:29:14: 3000000 INFO @ Sun, 21 Jun 2020 19:29:14: 12000000 INFO @ Sun, 21 Jun 2020 19:29:18: 8000000 INFO @ Sun, 21 Jun 2020 19:29:21: 4000000 INFO @ Sun, 21 Jun 2020 19:29:22: 13000000 INFO @ Sun, 21 Jun 2020 19:29:24: 9000000 INFO @ Sun, 21 Jun 2020 19:29:28: 5000000 INFO @ Sun, 21 Jun 2020 19:29:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:29: #1 total tags in treatment: 13965726 INFO @ Sun, 21 Jun 2020 19:29:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:29: #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 19:29:29: #1 tags after filtering in treatment: 13965712 INFO @ Sun, 21 Jun 2020 19:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:31: #2 number of paired peaks: 3583 INFO @ Sun, 21 Jun 2020 19:29:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:31: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 19:29:31: #2 alternative fragment length(s) may be 2,208,225 bps INFO @ Sun, 21 Jun 2020 19:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.05_model.r INFO @ Sun, 21 Jun 2020 19:29:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:31: 10000000 INFO @ Sun, 21 Jun 2020 19:29:35: 6000000 INFO @ Sun, 21 Jun 2020 19:29:37: 11000000 INFO @ Sun, 21 Jun 2020 19:29:41: 7000000 INFO @ Sun, 21 Jun 2020 19:29:44: 12000000 INFO @ Sun, 21 Jun 2020 19:29:48: 8000000 INFO @ Sun, 21 Jun 2020 19:29:51: 13000000 INFO @ Sun, 21 Jun 2020 19:29:55: 9000000 INFO @ Sun, 21 Jun 2020 19:29:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:58: #1 total tags in treatment: 13965726 INFO @ Sun, 21 Jun 2020 19:29:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:58: #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 19:29:58: #1 tags after filtering in treatment: 13965712 INFO @ Sun, 21 Jun 2020 19:29:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:00: #2 number of paired peaks: 3583 INFO @ Sun, 21 Jun 2020 19:30:00: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:00: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 19:30:00: #2 alternative fragment length(s) may be 2,208,225 bps INFO @ Sun, 21 Jun 2020 19:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.10_model.r INFO @ Sun, 21 Jun 2020 19:30:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:01: 10000000 INFO @ Sun, 21 Jun 2020 19:30:08: 11000000 INFO @ Sun, 21 Jun 2020 19:30:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:14: 12000000 INFO @ Sun, 21 Jun 2020 19:30:20: 13000000 INFO @ Sun, 21 Jun 2020 19:30:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:27: #1 total tags in treatment: 13965726 INFO @ Sun, 21 Jun 2020 19:30:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:27: #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 19:30:27: #1 tags after filtering in treatment: 13965712 INFO @ Sun, 21 Jun 2020 19:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:27: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:28: #2 number of paired peaks: 3583 INFO @ Sun, 21 Jun 2020 19:30:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:29: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 19:30:29: #2 alternative fragment length(s) may be 2,208,225 bps INFO @ Sun, 21 Jun 2020 19:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.20_model.r INFO @ Sun, 21 Jun 2020 19:30:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:29: Done! pass1 - making usageList (100 chroms): 2 millis pass2 - checking and writing primary data (9184 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:59: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (4920 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288046/SRX288046.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:27: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 5 millis CompletedMACS2peakCalling