Job ID = 6455534 SRX = SRX287864 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:04:10 prefetch.2.10.7: 1) Downloading 'SRR870053'... 2020-06-21T10:04:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:39 prefetch.2.10.7: 'SRR870053' is valid 2020-06-21T10:05:39 prefetch.2.10.7: 1) 'SRR870053' was downloaded successfully Read 14919889 spots for SRR870053/SRR870053.sra Written 14919889 spots for SRR870053/SRR870053.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: 00:03:26 14919889 reads; of these: 14919889 (100.00%) were unpaired; of these: 633310 (4.24%) aligned 0 times 12321147 (82.58%) aligned exactly 1 time 1965432 (13.17%) aligned >1 times 95.76% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 2014284 / 14286579 = 0.1410 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 19:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.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 19:13:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:41: 1000000 INFO @ Sun, 21 Jun 2020 19:13:46: 2000000 INFO @ Sun, 21 Jun 2020 19:13:51: 3000000 INFO @ Sun, 21 Jun 2020 19:13:56: 4000000 INFO @ Sun, 21 Jun 2020 19:14:01: 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 19:14:05: 6000000 INFO @ Sun, 21 Jun 2020 19:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.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 19:14:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:10: 7000000 INFO @ Sun, 21 Jun 2020 19:14:16: 1000000 INFO @ Sun, 21 Jun 2020 19:14:16: 8000000 INFO @ Sun, 21 Jun 2020 19:14:21: 2000000 INFO @ Sun, 21 Jun 2020 19:14:21: 9000000 INFO @ Sun, 21 Jun 2020 19:14:26: 3000000 INFO @ Sun, 21 Jun 2020 19:14:26: 10000000 INFO @ Sun, 21 Jun 2020 19:14:31: 4000000 INFO @ Sun, 21 Jun 2020 19:14:31: 11000000 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 19:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.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 19:14:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:37: 12000000 INFO @ Sun, 21 Jun 2020 19:14:37: 5000000 INFO @ Sun, 21 Jun 2020 19:14:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:38: #1 total tags in treatment: 12272295 INFO @ Sun, 21 Jun 2020 19:14:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:38: #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 19:14:39: #1 tags after filtering in treatment: 12272290 INFO @ Sun, 21 Jun 2020 19:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:40: #2 number of paired peaks: 3118 INFO @ Sun, 21 Jun 2020 19:14:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:40: #2 predicted fragment length is 214 bps INFO @ Sun, 21 Jun 2020 19:14:40: #2 alternative fragment length(s) may be 3,214 bps INFO @ Sun, 21 Jun 2020 19:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.05_model.r INFO @ Sun, 21 Jun 2020 19:14:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:42: 6000000 INFO @ Sun, 21 Jun 2020 19:14:42: 1000000 INFO @ Sun, 21 Jun 2020 19:14:47: 7000000 INFO @ Sun, 21 Jun 2020 19:14:48: 2000000 INFO @ Sun, 21 Jun 2020 19:14:53: 8000000 INFO @ Sun, 21 Jun 2020 19:14:54: 3000000 INFO @ Sun, 21 Jun 2020 19:14:59: 9000000 INFO @ Sun, 21 Jun 2020 19:15:01: 4000000 INFO @ Sun, 21 Jun 2020 19:15:04: 10000000 INFO @ Sun, 21 Jun 2020 19:15:07: 5000000 INFO @ Sun, 21 Jun 2020 19:15:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:09: 11000000 INFO @ Sun, 21 Jun 2020 19:15:13: 6000000 INFO @ Sun, 21 Jun 2020 19:15:15: 12000000 INFO @ Sun, 21 Jun 2020 19:15:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:16: #1 total tags in treatment: 12272295 INFO @ Sun, 21 Jun 2020 19:15:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:16: #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 19:15:17: #1 tags after filtering in treatment: 12272290 INFO @ Sun, 21 Jun 2020 19:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:18: #2 number of paired peaks: 3118 INFO @ Sun, 21 Jun 2020 19:15:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:18: #2 predicted fragment length is 214 bps INFO @ Sun, 21 Jun 2020 19:15:18: #2 alternative fragment length(s) may be 3,214 bps INFO @ Sun, 21 Jun 2020 19:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.10_model.r INFO @ Sun, 21 Jun 2020 19:15:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:19: 7000000 INFO @ Sun, 21 Jun 2020 19:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:22: Done! pass1 - making usageList (259 chroms): 2 millis pass2 - checking and writing primary data (5614 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:25: 8000000 INFO @ Sun, 21 Jun 2020 19:15:31: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:37: 10000000 INFO @ Sun, 21 Jun 2020 19:15:43: 11000000 INFO @ Sun, 21 Jun 2020 19:15:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:49: 12000000 INFO @ Sun, 21 Jun 2020 19:15:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:51: #1 total tags in treatment: 12272295 INFO @ Sun, 21 Jun 2020 19:15:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:51: #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 19:15:51: #1 tags after filtering in treatment: 12272290 INFO @ Sun, 21 Jun 2020 19:15:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:52: #2 number of paired peaks: 3118 INFO @ Sun, 21 Jun 2020 19:15:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:52: #2 predicted fragment length is 214 bps INFO @ Sun, 21 Jun 2020 19:15:52: #2 alternative fragment length(s) may be 3,214 bps INFO @ Sun, 21 Jun 2020 19:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.20_model.r INFO @ Sun, 21 Jun 2020 19:15:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:01: Done! pass1 - making usageList (141 chroms): 2 millis pass2 - checking and writing primary data (2948 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287864/SRX287864.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:36: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 5 millis CompletedMACS2peakCalling