Job ID = 6459493 SRX = SRX6827674 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:35:46 prefetch.2.10.7: 1) Downloading 'SRR10095454'... 2020-06-21T13:35:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:38:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:38:20 prefetch.2.10.7: 1) 'SRR10095454' was downloaded successfully Read 25043509 spots for SRR10095454/SRR10095454.sra Written 25043509 spots for SRR10095454/SRR10095454.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: 00:07:43 25043509 reads; of these: 25043509 (100.00%) were unpaired; of these: 1255193 (5.01%) aligned 0 times 16271417 (64.97%) aligned exactly 1 time 7516899 (30.02%) aligned >1 times 94.99% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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 12 files... [bam_rmdupse_core] 5584423 / 23788316 = 0.2348 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 22:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.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 22:51:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:51:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:52:03: 1000000 INFO @ Sun, 21 Jun 2020 22:52:09: 2000000 INFO @ Sun, 21 Jun 2020 22:52:15: 3000000 INFO @ Sun, 21 Jun 2020 22:52:20: 4000000 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 22:52:26: 5000000 INFO @ Sun, 21 Jun 2020 22:52:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.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 22:52:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:52:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:52:32: 6000000 INFO @ Sun, 21 Jun 2020 22:52:34: 1000000 INFO @ Sun, 21 Jun 2020 22:52:39: 7000000 INFO @ Sun, 21 Jun 2020 22:52:41: 2000000 INFO @ Sun, 21 Jun 2020 22:52:45: 8000000 INFO @ Sun, 21 Jun 2020 22:52:48: 3000000 INFO @ Sun, 21 Jun 2020 22:52:52: 9000000 INFO @ Sun, 21 Jun 2020 22:52:54: 4000000 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 22:52:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.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 22:52:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:52:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:52:59: 10000000 INFO @ Sun, 21 Jun 2020 22:53:01: 5000000 INFO @ Sun, 21 Jun 2020 22:53:05: 1000000 INFO @ Sun, 21 Jun 2020 22:53:06: 11000000 INFO @ Sun, 21 Jun 2020 22:53:08: 6000000 INFO @ Sun, 21 Jun 2020 22:53:12: 2000000 INFO @ Sun, 21 Jun 2020 22:53:13: 12000000 INFO @ Sun, 21 Jun 2020 22:53:15: 7000000 INFO @ Sun, 21 Jun 2020 22:53:19: 3000000 INFO @ Sun, 21 Jun 2020 22:53:20: 13000000 INFO @ Sun, 21 Jun 2020 22:53:23: 8000000 INFO @ Sun, 21 Jun 2020 22:53:27: 4000000 INFO @ Sun, 21 Jun 2020 22:53:28: 14000000 INFO @ Sun, 21 Jun 2020 22:53:30: 9000000 INFO @ Sun, 21 Jun 2020 22:53:35: 5000000 INFO @ Sun, 21 Jun 2020 22:53:35: 15000000 INFO @ Sun, 21 Jun 2020 22:53:38: 10000000 INFO @ Sun, 21 Jun 2020 22:53:42: 6000000 INFO @ Sun, 21 Jun 2020 22:53:43: 16000000 INFO @ Sun, 21 Jun 2020 22:53:45: 11000000 INFO @ Sun, 21 Jun 2020 22:53:49: 7000000 INFO @ Sun, 21 Jun 2020 22:53:50: 17000000 INFO @ Sun, 21 Jun 2020 22:53:52: 12000000 INFO @ Sun, 21 Jun 2020 22:53:56: 8000000 INFO @ Sun, 21 Jun 2020 22:53:57: 18000000 INFO @ Sun, 21 Jun 2020 22:53:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:53:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:53:59: #1 total tags in treatment: 18203893 INFO @ Sun, 21 Jun 2020 22:53:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:53:59: #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 22:53:59: 13000000 INFO @ Sun, 21 Jun 2020 22:53:59: #1 tags after filtering in treatment: 18203835 INFO @ Sun, 21 Jun 2020 22:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:53:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:53:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:54:01: #2 number of paired peaks: 1171 INFO @ Sun, 21 Jun 2020 22:54:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:54:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:54:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:54:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:54:01: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:54:01: #2 alternative fragment length(s) may be 3,111 bps INFO @ Sun, 21 Jun 2020 22:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.05_model.r INFO @ Sun, 21 Jun 2020 22:54:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:54:03: 9000000 INFO @ Sun, 21 Jun 2020 22:54:06: 14000000 INFO @ Sun, 21 Jun 2020 22:54:10: 10000000 INFO @ Sun, 21 Jun 2020 22:54:13: 15000000 INFO @ Sun, 21 Jun 2020 22:54:17: 11000000 INFO @ Sun, 21 Jun 2020 22:54:21: 16000000 INFO @ Sun, 21 Jun 2020 22:54:24: 12000000 INFO @ Sun, 21 Jun 2020 22:54:28: 17000000 INFO @ Sun, 21 Jun 2020 22:54:31: 13000000 INFO @ Sun, 21 Jun 2020 22:54:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:54:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:54:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:54:36: #1 total tags in treatment: 18203893 INFO @ Sun, 21 Jun 2020 22:54:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:54:36: #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 22:54:37: #1 tags after filtering in treatment: 18203835 INFO @ Sun, 21 Jun 2020 22:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:54:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:54:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:54:38: 14000000 INFO @ Sun, 21 Jun 2020 22:54:38: #2 number of paired peaks: 1171 INFO @ Sun, 21 Jun 2020 22:54:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:54:39: start X-correlation... INFO @ Sun, 21 Jun 2020 22:54:39: end of X-cor INFO @ Sun, 21 Jun 2020 22:54:39: #2 finished! INFO @ Sun, 21 Jun 2020 22:54:39: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:54:39: #2 alternative fragment length(s) may be 3,111 bps INFO @ Sun, 21 Jun 2020 22:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.10_model.r INFO @ Sun, 21 Jun 2020 22:54:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:54:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:54:44: 15000000 INFO @ Sun, 21 Jun 2020 22:54:51: 16000000 INFO @ Sun, 21 Jun 2020 22:54:57: 17000000 INFO @ Sun, 21 Jun 2020 22:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.05_summits.bed INFO @ Sun, 21 Jun 2020 22:55:00: Done! pass1 - making usageList (687 chroms): 1 millis pass2 - checking and writing primary data (3331 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:55:03: 18000000 INFO @ Sun, 21 Jun 2020 22:55:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:55:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:55:04: #1 total tags in treatment: 18203893 INFO @ Sun, 21 Jun 2020 22:55:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:55:04: #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 22:55:05: #1 tags after filtering in treatment: 18203835 INFO @ Sun, 21 Jun 2020 22:55:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:55:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:55:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:55:06: #2 number of paired peaks: 1171 INFO @ Sun, 21 Jun 2020 22:55:06: start model_add_line... INFO @ Sun, 21 Jun 2020 22:55:06: start X-correlation... INFO @ Sun, 21 Jun 2020 22:55:06: end of X-cor INFO @ Sun, 21 Jun 2020 22:55:06: #2 finished! INFO @ Sun, 21 Jun 2020 22:55:06: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 22:55:06: #2 alternative fragment length(s) may be 3,111 bps INFO @ Sun, 21 Jun 2020 22:55:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.20_model.r INFO @ Sun, 21 Jun 2020 22:55:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:55:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:55:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.10_summits.bed INFO @ Sun, 21 Jun 2020 22:55:34: Done! pass1 - making usageList (574 chroms): 1 millis pass2 - checking and writing primary data (2120 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:55:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827674/SRX6827674.20_summits.bed INFO @ Sun, 21 Jun 2020 22:56:03: Done! pass1 - making usageList (467 chroms): 1 millis pass2 - checking and writing primary data (1439 records, 4 fields): 14 millis CompletedMACS2peakCalling