Job ID = 6454028 SRX = SRX1794215 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:47:18 prefetch.2.10.7: 1) Downloading 'SRR3575246'... 2020-06-21T08:47:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:48:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:48:17 prefetch.2.10.7: 'SRR3575246' is valid 2020-06-21T08:48:17 prefetch.2.10.7: 1) 'SRR3575246' was downloaded successfully Read 9989575 spots for SRR3575246/SRR3575246.sra Written 9989575 spots for SRR3575246/SRR3575246.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: 00:02:25 9989575 reads; of these: 9989575 (100.00%) were unpaired; of these: 626597 (6.27%) aligned 0 times 7465812 (74.74%) aligned exactly 1 time 1897166 (18.99%) aligned >1 times 93.73% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 1237437 / 9362978 = 0.1322 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 17:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.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 17:54:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:17: 1000000 INFO @ Sun, 21 Jun 2020 17:54:23: 2000000 INFO @ Sun, 21 Jun 2020 17:54:28: 3000000 INFO @ Sun, 21 Jun 2020 17:54:34: 4000000 INFO @ Sun, 21 Jun 2020 17:54:39: 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 17:54:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.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 17:54:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:45: 6000000 INFO @ Sun, 21 Jun 2020 17:54:50: 1000000 INFO @ Sun, 21 Jun 2020 17:54:51: 7000000 INFO @ Sun, 21 Jun 2020 17:54:57: 2000000 INFO @ Sun, 21 Jun 2020 17:54:58: 8000000 INFO @ Sun, 21 Jun 2020 17:54:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:54:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:54:59: #1 total tags in treatment: 8125541 INFO @ Sun, 21 Jun 2020 17:54:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:59: #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 17:54:59: #1 tags after filtering in treatment: 8125386 INFO @ Sun, 21 Jun 2020 17:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:00: #2 number of paired peaks: 5381 INFO @ Sun, 21 Jun 2020 17:55:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:00: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 17:55:00: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 17:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.05_model.r INFO @ Sun, 21 Jun 2020 17:55:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:04: 3000000 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 17:55:10: 4000000 INFO @ Sun, 21 Jun 2020 17:55:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.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 17:55:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:17: 5000000 INFO @ Sun, 21 Jun 2020 17:55:18: 1000000 INFO @ Sun, 21 Jun 2020 17:55:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:24: 6000000 INFO @ Sun, 21 Jun 2020 17:55:24: 2000000 INFO @ Sun, 21 Jun 2020 17:55:30: 3000000 INFO @ Sun, 21 Jun 2020 17:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.05_summits.bed INFO @ Sun, 21 Jun 2020 17:55:31: Done! INFO @ Sun, 21 Jun 2020 17:55:31: 7000000 pass1 - making usageList (340 chroms): 2 millis pass2 - checking and writing primary data (9848 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:55:36: 4000000 INFO @ Sun, 21 Jun 2020 17:55:38: 8000000 INFO @ Sun, 21 Jun 2020 17:55:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:55:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:55:39: #1 total tags in treatment: 8125541 INFO @ Sun, 21 Jun 2020 17:55:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:39: #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 17:55:39: #1 tags after filtering in treatment: 8125386 INFO @ Sun, 21 Jun 2020 17:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:40: #2 number of paired peaks: 5381 INFO @ Sun, 21 Jun 2020 17:55:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:40: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 17:55:40: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 17:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.10_model.r INFO @ Sun, 21 Jun 2020 17:55:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:42: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:55:48: 6000000 INFO @ Sun, 21 Jun 2020 17:55:54: 7000000 INFO @ Sun, 21 Jun 2020 17:55:59: 8000000 INFO @ Sun, 21 Jun 2020 17:56:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:56:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:56:00: #1 total tags in treatment: 8125541 INFO @ Sun, 21 Jun 2020 17:56:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:00: #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 17:56:00: #1 tags after filtering in treatment: 8125386 INFO @ Sun, 21 Jun 2020 17:56:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:01: #2 number of paired peaks: 5381 INFO @ Sun, 21 Jun 2020 17:56:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:01: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 17:56:01: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 17:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.20_model.r INFO @ Sun, 21 Jun 2020 17:56:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:12: Done! pass1 - making usageList (213 chroms): 2 millis pass2 - checking and writing primary data (6254 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794215/SRX1794215.20_summits.bed INFO @ Sun, 21 Jun 2020 17:56:33: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (2932 records, 4 fields): 9 millis CompletedMACS2peakCalling