Job ID = 6459783 SRX = SRX826333 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:36:29 prefetch.2.10.7: 1) Downloading 'SRR1737833'... 2020-06-21T13:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:38:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:38:59 prefetch.2.10.7: 'SRR1737833' is valid 2020-06-21T13:38:59 prefetch.2.10.7: 1) 'SRR1737833' was downloaded successfully Read 19577660 spots for SRR1737833/SRR1737833.sra Written 19577660 spots for SRR1737833/SRR1737833.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: 00:02:47 19577660 reads; of these: 19577660 (100.00%) were unpaired; of these: 8895113 (45.44%) aligned 0 times 9337860 (47.70%) aligned exactly 1 time 1344687 (6.87%) aligned >1 times 54.56% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 4399884 / 10682547 = 0.4119 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 22:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.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 22:45:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:45:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:45:40: 1000000 INFO @ Sun, 21 Jun 2020 22:45:45: 2000000 INFO @ Sun, 21 Jun 2020 22:45:50: 3000000 INFO @ Sun, 21 Jun 2020 22:45:55: 4000000 INFO @ Sun, 21 Jun 2020 22:46:00: 5000000 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 22:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.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 22:46:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:46:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:46:06: 6000000 INFO @ Sun, 21 Jun 2020 22:46:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:46:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:46:08: #1 total tags in treatment: 6282663 INFO @ Sun, 21 Jun 2020 22:46:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:46:08: #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 22:46:08: #1 tags after filtering in treatment: 6282459 INFO @ Sun, 21 Jun 2020 22:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:46:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:46:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:46:09: #2 number of paired peaks: 2265 INFO @ Sun, 21 Jun 2020 22:46:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:46:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:46:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:46:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:46:09: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 22:46:09: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 22:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.05_model.r INFO @ Sun, 21 Jun 2020 22:46:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:46:10: 1000000 INFO @ Sun, 21 Jun 2020 22:46:15: 2000000 INFO @ Sun, 21 Jun 2020 22:46:20: 3000000 INFO @ Sun, 21 Jun 2020 22:46:25: 4000000 INFO @ Sun, 21 Jun 2020 22:46:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:46:30: 5000000 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 22:46:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.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 22:46:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:46:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.05_summits.bed INFO @ Sun, 21 Jun 2020 22:46:35: Done! pass1 - making usageList (104 chroms): 1 millis pass2 - checking and writing primary data (5177 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:46:36: 6000000 INFO @ Sun, 21 Jun 2020 22:46:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:46:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:46:37: #1 total tags in treatment: 6282663 INFO @ Sun, 21 Jun 2020 22:46:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:46:37: #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 22:46:38: #1 tags after filtering in treatment: 6282459 INFO @ Sun, 21 Jun 2020 22:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:46:38: #1 finished! INFO @ Sun, 21 Jun 2020 22:46:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:46:38: #2 number of paired peaks: 2265 INFO @ Sun, 21 Jun 2020 22:46:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:46:38: start X-correlation... INFO @ Sun, 21 Jun 2020 22:46:38: end of X-cor INFO @ Sun, 21 Jun 2020 22:46:38: #2 finished! INFO @ Sun, 21 Jun 2020 22:46:38: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 22:46:38: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 22:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.10_model.r INFO @ Sun, 21 Jun 2020 22:46:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:46:41: 1000000 INFO @ Sun, 21 Jun 2020 22:46:46: 2000000 INFO @ Sun, 21 Jun 2020 22:46:52: 3000000 INFO @ Sun, 21 Jun 2020 22:46:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:46:57: 4000000 INFO @ Sun, 21 Jun 2020 22:47:02: 5000000 INFO @ Sun, 21 Jun 2020 22:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.10_summits.bed BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:47:04: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (3955 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:47:08: 6000000 INFO @ Sun, 21 Jun 2020 22:47:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:47:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:47:10: #1 total tags in treatment: 6282663 INFO @ Sun, 21 Jun 2020 22:47:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:47:10: #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 22:47:10: #1 tags after filtering in treatment: 6282459 INFO @ Sun, 21 Jun 2020 22:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:47:10: #1 finished! INFO @ Sun, 21 Jun 2020 22:47:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:47:11: #2 number of paired peaks: 2265 INFO @ Sun, 21 Jun 2020 22:47:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:47:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:47:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:47:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:47:11: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 22:47:11: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 22:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.20_model.r INFO @ Sun, 21 Jun 2020 22:47:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:47:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:47:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX826333/SRX826333.20_summits.bed INFO @ Sun, 21 Jun 2020 22:47:34: Done! pass1 - making usageList (90 chroms): 2 millis pass2 - checking and writing primary data (2656 records, 4 fields): 7 millis CompletedMACS2peakCalling