Job ID = 6456357 SRX = SRX3380801 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:13:39 prefetch.2.10.7: 1) Downloading 'SRR6278164'... 2020-06-21T11:13:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:14 prefetch.2.10.7: 'SRR6278164' is valid 2020-06-21T11:15:14 prefetch.2.10.7: 1) 'SRR6278164' was downloaded successfully Read 12007729 spots for SRR6278164/SRR6278164.sra Written 12007729 spots for SRR6278164/SRR6278164.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: 00:03:16 12007729 reads; of these: 12007729 (100.00%) were unpaired; of these: 494932 (4.12%) aligned 0 times 8581316 (71.46%) aligned exactly 1 time 2931481 (24.41%) aligned >1 times 95.88% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 2527766 / 11512797 = 0.2196 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 20:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.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 20:22:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:18: 1000000 INFO @ Sun, 21 Jun 2020 20:22:24: 2000000 INFO @ Sun, 21 Jun 2020 20:22:30: 3000000 INFO @ Sun, 21 Jun 2020 20:22:36: 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 20:22:42: 5000000 INFO @ Sun, 21 Jun 2020 20:22:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.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 20:22:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:49: 6000000 INFO @ Sun, 21 Jun 2020 20:22:49: 1000000 INFO @ Sun, 21 Jun 2020 20:22:55: 7000000 INFO @ Sun, 21 Jun 2020 20:22:55: 2000000 INFO @ Sun, 21 Jun 2020 20:23:02: 8000000 INFO @ Sun, 21 Jun 2020 20:23:02: 3000000 INFO @ Sun, 21 Jun 2020 20:23:09: 4000000 INFO @ Sun, 21 Jun 2020 20:23:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:23:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:23:09: #1 total tags in treatment: 8985031 INFO @ Sun, 21 Jun 2020 20:23:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:09: #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 20:23:10: #1 tags after filtering in treatment: 8984870 INFO @ Sun, 21 Jun 2020 20:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:10: #2 looking for paired plus/minus strand peaks... 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 20:23:11: #2 number of paired peaks: 8683 INFO @ Sun, 21 Jun 2020 20:23:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:11: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:23:11: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.05_model.r INFO @ Sun, 21 Jun 2020 20:23:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.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 20:23:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:15: 5000000 INFO @ Sun, 21 Jun 2020 20:23:19: 1000000 INFO @ Sun, 21 Jun 2020 20:23:22: 6000000 INFO @ Sun, 21 Jun 2020 20:23:26: 2000000 INFO @ Sun, 21 Jun 2020 20:23:29: 7000000 INFO @ Sun, 21 Jun 2020 20:23:33: 3000000 INFO @ Sun, 21 Jun 2020 20:23:36: 8000000 INFO @ Sun, 21 Jun 2020 20:23:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:39: 4000000 INFO @ Sun, 21 Jun 2020 20:23:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:23:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:23:42: #1 total tags in treatment: 8985031 INFO @ Sun, 21 Jun 2020 20:23:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:42: #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 20:23:43: #1 tags after filtering in treatment: 8984870 INFO @ Sun, 21 Jun 2020 20:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:44: #2 number of paired peaks: 8683 INFO @ Sun, 21 Jun 2020 20:23:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:44: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:23:44: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.10_model.r INFO @ Sun, 21 Jun 2020 20:23:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:46: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:50: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (10119 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:52: 6000000 INFO @ Sun, 21 Jun 2020 20:23:58: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:24:04: 8000000 INFO @ Sun, 21 Jun 2020 20:24:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:24:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:24:11: #1 total tags in treatment: 8985031 INFO @ Sun, 21 Jun 2020 20:24:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:11: #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 20:24:11: #1 tags after filtering in treatment: 8984870 INFO @ Sun, 21 Jun 2020 20:24:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:12: #2 number of paired peaks: 8683 INFO @ Sun, 21 Jun 2020 20:24:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:12: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:24:12: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:24:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.20_model.r INFO @ Sun, 21 Jun 2020 20:24:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.10_summits.bed INFO @ Sun, 21 Jun 2020 20:24:21: Done! pass1 - making usageList (416 chroms): 2 millis pass2 - checking and writing primary data (7526 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:24:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380801/SRX3380801.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:50: Done! pass1 - making usageList (210 chroms): 1 millis pass2 - checking and writing primary data (4217 records, 4 fields): 20 millis CompletedMACS2peakCalling