Job ID = 6454146 SRX = SRX1840067 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:34 prefetch.2.10.7: 1) Downloading 'SRR3661293'... 2020-06-21T09:00:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:05:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:05:02 prefetch.2.10.7: 1) 'SRR3661293' was downloaded successfully Read 20514613 spots for SRR3661293/SRR3661293.sra Written 20514613 spots for SRR3661293/SRR3661293.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: 00:08:48 20514613 reads; of these: 20514613 (100.00%) were unpaired; of these: 5026372 (24.50%) aligned 0 times 12018129 (58.58%) aligned exactly 1 time 3470112 (16.92%) aligned >1 times 75.50% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 12141957 / 15488241 = 0.7839 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 18:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.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 18:19:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:40: 1000000 INFO @ Sun, 21 Jun 2020 18:19:48: 2000000 INFO @ Sun, 21 Jun 2020 18:19:56: 3000000 INFO @ Sun, 21 Jun 2020 18:19:58: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:19:58: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:19:58: #1 total tags in treatment: 3346284 INFO @ Sun, 21 Jun 2020 18:19:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:58: #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 18:19:59: #1 tags after filtering in treatment: 3346236 INFO @ Sun, 21 Jun 2020 18:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:59: #2 number of paired peaks: 2486 INFO @ Sun, 21 Jun 2020 18:19:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:59: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 18:19:59: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 18:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.05_model.r INFO @ Sun, 21 Jun 2020 18:19:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:59: #3 Pre-compute pvalue-qvalue table... 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 18:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.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 18:20:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:10: 1000000 INFO @ Sun, 21 Jun 2020 18:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:11: Done! pass1 - making usageList (726 chroms): 1 millis pass2 - checking and writing primary data (3499 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:18: 2000000 INFO @ Sun, 21 Jun 2020 18:20:25: 3000000 INFO @ Sun, 21 Jun 2020 18:20:28: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:20:28: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:20:28: #1 total tags in treatment: 3346284 INFO @ Sun, 21 Jun 2020 18:20:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:28: #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 18:20:29: #1 tags after filtering in treatment: 3346236 INFO @ Sun, 21 Jun 2020 18:20:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:29: #2 number of paired peaks: 2486 INFO @ Sun, 21 Jun 2020 18:20:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:29: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 18:20:29: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 18:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.10_model.r INFO @ Sun, 21 Jun 2020 18:20:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:29: #3 Pre-compute pvalue-qvalue table... 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 18:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.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 18:20:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:40: 1000000 INFO @ Sun, 21 Jun 2020 18:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.10_summits.bed INFO @ Sun, 21 Jun 2020 18:20:42: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:47: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:55: 3000000 INFO @ Sun, 21 Jun 2020 18:20:58: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:20:58: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:20:58: #1 total tags in treatment: 3346284 INFO @ Sun, 21 Jun 2020 18:20:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:58: #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 18:20:58: #1 tags after filtering in treatment: 3346236 INFO @ Sun, 21 Jun 2020 18:20:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:59: #2 number of paired peaks: 2486 INFO @ Sun, 21 Jun 2020 18:20:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:59: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 18:20:59: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 18:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.20_model.r INFO @ Sun, 21 Jun 2020 18:20:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840067/SRX1840067.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:11: Done! pass1 - making usageList (440 chroms): 2 millis pass2 - checking and writing primary data (1205 records, 4 fields): 13 millis CompletedMACS2peakCalling