Job ID = 6453961 SRX = SRX1715673 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:41:17 prefetch.2.10.7: 1) Downloading 'SRR3405214'... 2020-06-21T08:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:53:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:53:01 prefetch.2.10.7: 1) 'SRR3405214' was downloaded successfully Read 55708155 spots for SRR3405214/SRR3405214.sra Written 55708155 spots for SRR3405214/SRR3405214.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:29 55708155 reads; of these: 55708155 (100.00%) were unpaired; of these: 1111513 (2.00%) aligned 0 times 48672049 (87.37%) aligned exactly 1 time 5924593 (10.64%) aligned >1 times 98.00% overall alignment rate Time searching: 00:12:30 Overall time: 00:12:30 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 24 files... [bam_rmdupse_core] 36480893 / 54596642 = 0.6682 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 18:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.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 18:17:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:16: 1000000 INFO @ Sun, 21 Jun 2020 18:17:21: 2000000 INFO @ Sun, 21 Jun 2020 18:17:26: 3000000 INFO @ Sun, 21 Jun 2020 18:17:30: 4000000 INFO @ Sun, 21 Jun 2020 18:17:35: 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 18:17:40: 6000000 INFO @ Sun, 21 Jun 2020 18:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.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 18:17:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:45: 7000000 INFO @ Sun, 21 Jun 2020 18:17:47: 1000000 INFO @ Sun, 21 Jun 2020 18:17:50: 8000000 INFO @ Sun, 21 Jun 2020 18:17:53: 2000000 INFO @ Sun, 21 Jun 2020 18:17:54: 9000000 INFO @ Sun, 21 Jun 2020 18:17:58: 3000000 INFO @ Sun, 21 Jun 2020 18:17:59: 10000000 INFO @ Sun, 21 Jun 2020 18:18:04: 4000000 INFO @ Sun, 21 Jun 2020 18:18:04: 11000000 INFO @ Sun, 21 Jun 2020 18:18:09: 12000000 INFO @ Sun, 21 Jun 2020 18:18:09: 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 18:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.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 18:18:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:14: 13000000 INFO @ Sun, 21 Jun 2020 18:18:14: 6000000 INFO @ Sun, 21 Jun 2020 18:18:17: 1000000 INFO @ Sun, 21 Jun 2020 18:18:19: 14000000 INFO @ Sun, 21 Jun 2020 18:18:20: 7000000 INFO @ Sun, 21 Jun 2020 18:18:22: 2000000 INFO @ Sun, 21 Jun 2020 18:18:24: 15000000 INFO @ Sun, 21 Jun 2020 18:18:25: 8000000 INFO @ Sun, 21 Jun 2020 18:18:28: 3000000 INFO @ Sun, 21 Jun 2020 18:18:29: 16000000 INFO @ Sun, 21 Jun 2020 18:18:31: 9000000 INFO @ Sun, 21 Jun 2020 18:18:33: 4000000 INFO @ Sun, 21 Jun 2020 18:18:34: 17000000 INFO @ Sun, 21 Jun 2020 18:18:36: 10000000 INFO @ Sun, 21 Jun 2020 18:18:39: 5000000 INFO @ Sun, 21 Jun 2020 18:18:39: 18000000 INFO @ Sun, 21 Jun 2020 18:18:40: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:18:40: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:18:40: #1 total tags in treatment: 18115749 INFO @ Sun, 21 Jun 2020 18:18:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:40: #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 18:18:40: #1 tags after filtering in treatment: 18115749 INFO @ Sun, 21 Jun 2020 18:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:42: 11000000 INFO @ Sun, 21 Jun 2020 18:18:42: #2 number of paired peaks: 3318 INFO @ Sun, 21 Jun 2020 18:18:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:42: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:18:42: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sun, 21 Jun 2020 18:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.05_model.r INFO @ Sun, 21 Jun 2020 18:18:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:44: 6000000 INFO @ Sun, 21 Jun 2020 18:18:47: 12000000 INFO @ Sun, 21 Jun 2020 18:18:49: 7000000 INFO @ Sun, 21 Jun 2020 18:18:52: 13000000 INFO @ Sun, 21 Jun 2020 18:18:55: 8000000 INFO @ Sun, 21 Jun 2020 18:18:58: 14000000 INFO @ Sun, 21 Jun 2020 18:19:00: 9000000 INFO @ Sun, 21 Jun 2020 18:19:04: 15000000 INFO @ Sun, 21 Jun 2020 18:19:05: 10000000 INFO @ Sun, 21 Jun 2020 18:19:09: 16000000 INFO @ Sun, 21 Jun 2020 18:19:11: 11000000 INFO @ Sun, 21 Jun 2020 18:19:15: 17000000 INFO @ Sun, 21 Jun 2020 18:19:16: 12000000 INFO @ Sun, 21 Jun 2020 18:19:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:21: 18000000 INFO @ Sun, 21 Jun 2020 18:19:21: 13000000 INFO @ Sun, 21 Jun 2020 18:19:22: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:19:22: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:19:22: #1 total tags in treatment: 18115749 INFO @ Sun, 21 Jun 2020 18:19:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:22: #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 18:19:22: #1 tags after filtering in treatment: 18115749 INFO @ Sun, 21 Jun 2020 18:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:24: #2 number of paired peaks: 3318 INFO @ Sun, 21 Jun 2020 18:19:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:24: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:19:24: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sun, 21 Jun 2020 18:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.10_model.r INFO @ Sun, 21 Jun 2020 18:19:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:27: 14000000 INFO @ Sun, 21 Jun 2020 18:19:32: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:38: 16000000 INFO @ Sun, 21 Jun 2020 18:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.05_summits.bed INFO @ Sun, 21 Jun 2020 18:19:41: Done! pass1 - making usageList (471 chroms): 2 millis pass2 - checking and writing primary data (8355 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:19:43: 17000000 INFO @ Sun, 21 Jun 2020 18:19:49: 18000000 INFO @ Sun, 21 Jun 2020 18:19:50: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:19:50: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:19:50: #1 total tags in treatment: 18115749 INFO @ Sun, 21 Jun 2020 18:19:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:50: #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 18:19:51: #1 tags after filtering in treatment: 18115749 INFO @ Sun, 21 Jun 2020 18:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:52: #2 number of paired peaks: 3318 INFO @ Sun, 21 Jun 2020 18:19:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:52: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:19:52: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sun, 21 Jun 2020 18:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.20_model.r INFO @ Sun, 21 Jun 2020 18:19:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.10_summits.bed INFO @ Sun, 21 Jun 2020 18:20:22: Done! pass1 - making usageList (257 chroms): 2 millis pass2 - checking and writing primary data (6047 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715673/SRX1715673.20_summits.bed INFO @ Sun, 21 Jun 2020 18:20:49: Done! pass1 - making usageList (110 chroms): 2 millis pass2 - checking and writing primary data (3140 records, 4 fields): 7 millis CompletedMACS2peakCalling