Job ID = 6452972 SRX = SRX084579 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:06:39 prefetch.2.10.7: 1) Downloading 'SRR315119'... 2020-06-21T08:06:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:09:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:09:07 prefetch.2.10.7: 1) 'SRR315119' was downloaded successfully Read 42129254 spots for SRR315119/SRR315119.sra Written 42129254 spots for SRR315119/SRR315119.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: 00:08:23 42129254 reads; of these: 42129254 (100.00%) were unpaired; of these: 12154043 (28.85%) aligned 0 times 21685856 (51.47%) aligned exactly 1 time 8289355 (19.68%) aligned >1 times 71.15% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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] 15530852 / 29975211 = 0.5181 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 17:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.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 17:25:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:30: 1000000 INFO @ Sun, 21 Jun 2020 17:25:36: 2000000 INFO @ Sun, 21 Jun 2020 17:25:41: 3000000 INFO @ Sun, 21 Jun 2020 17:25:46: 4000000 INFO @ Sun, 21 Jun 2020 17:25:52: 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 17:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.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 17:25:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:58: 6000000 INFO @ Sun, 21 Jun 2020 17:26:02: 1000000 INFO @ Sun, 21 Jun 2020 17:26:04: 7000000 INFO @ Sun, 21 Jun 2020 17:26:09: 2000000 INFO @ Sun, 21 Jun 2020 17:26:11: 8000000 INFO @ Sun, 21 Jun 2020 17:26:17: 3000000 INFO @ Sun, 21 Jun 2020 17:26:17: 9000000 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 17:26:24: 4000000 INFO @ Sun, 21 Jun 2020 17:26:24: 10000000 INFO @ Sun, 21 Jun 2020 17:26:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.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 17:26:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:26:31: 11000000 INFO @ Sun, 21 Jun 2020 17:26:31: 5000000 INFO @ Sun, 21 Jun 2020 17:26:31: 1000000 INFO @ Sun, 21 Jun 2020 17:26:38: 12000000 INFO @ Sun, 21 Jun 2020 17:26:38: 2000000 INFO @ Sun, 21 Jun 2020 17:26:38: 6000000 INFO @ Sun, 21 Jun 2020 17:26:44: 13000000 INFO @ Sun, 21 Jun 2020 17:26:45: 3000000 INFO @ Sun, 21 Jun 2020 17:26:45: 7000000 INFO @ Sun, 21 Jun 2020 17:26:51: 14000000 INFO @ Sun, 21 Jun 2020 17:26:51: 4000000 INFO @ Sun, 21 Jun 2020 17:26:53: 8000000 INFO @ Sun, 21 Jun 2020 17:26:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:26:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:26:54: #1 total tags in treatment: 14444359 INFO @ Sun, 21 Jun 2020 17:26:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:54: #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 17:26:54: #1 tags after filtering in treatment: 14444301 INFO @ Sun, 21 Jun 2020 17:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:56: #2 number of paired peaks: 3740 INFO @ Sun, 21 Jun 2020 17:26:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:56: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 17:26:56: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 17:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.05_model.r INFO @ Sun, 21 Jun 2020 17:26:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:26:58: 5000000 INFO @ Sun, 21 Jun 2020 17:27:00: 9000000 INFO @ Sun, 21 Jun 2020 17:27:05: 6000000 INFO @ Sun, 21 Jun 2020 17:27:08: 10000000 INFO @ Sun, 21 Jun 2020 17:27:11: 7000000 INFO @ Sun, 21 Jun 2020 17:27:15: 11000000 INFO @ Sun, 21 Jun 2020 17:27:18: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:27:23: 12000000 INFO @ Sun, 21 Jun 2020 17:27:25: 9000000 INFO @ Sun, 21 Jun 2020 17:27:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:30: 13000000 INFO @ Sun, 21 Jun 2020 17:27:31: 10000000 INFO @ Sun, 21 Jun 2020 17:27:38: 11000000 INFO @ Sun, 21 Jun 2020 17:27:38: 14000000 INFO @ Sun, 21 Jun 2020 17:27:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:27:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:27:41: #1 total tags in treatment: 14444359 INFO @ Sun, 21 Jun 2020 17:27:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:41: #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 17:27:42: #1 tags after filtering in treatment: 14444301 INFO @ Sun, 21 Jun 2020 17:27:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:27:43: #2 number of paired peaks: 3740 INFO @ Sun, 21 Jun 2020 17:27:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:43: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 17:27:43: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 17:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.10_model.r INFO @ Sun, 21 Jun 2020 17:27:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:27:45: 12000000 INFO @ Sun, 21 Jun 2020 17:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.05_summits.bed INFO @ Sun, 21 Jun 2020 17:27:45: Done! pass1 - making usageList (752 chroms): 2 millis pass2 - checking and writing primary data (13687 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:27:50: 13000000 INFO @ Sun, 21 Jun 2020 17:27:56: 14000000 INFO @ Sun, 21 Jun 2020 17:27:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:27:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:27:59: #1 total tags in treatment: 14444359 INFO @ Sun, 21 Jun 2020 17:27:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:59: #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 17:27:59: #1 tags after filtering in treatment: 14444301 INFO @ Sun, 21 Jun 2020 17:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:01: #2 number of paired peaks: 3740 INFO @ Sun, 21 Jun 2020 17:28:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:01: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 17:28:01: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 17:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.20_model.r INFO @ Sun, 21 Jun 2020 17:28:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.10_summits.bed INFO @ Sun, 21 Jun 2020 17:28:38: Done! pass1 - making usageList (646 chroms): 3 millis pass2 - checking and writing primary data (10404 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:28:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084579/SRX084579.20_summits.bed INFO @ Sun, 21 Jun 2020 17:28:52: Done! pass1 - making usageList (511 chroms): 2 millis pass2 - checking and writing primary data (7572 records, 4 fields): 24 millis CompletedMACS2peakCalling