Job ID = 6457911 SRX = SRX485216 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:07:06 prefetch.2.10.7: 1) Downloading 'SRR1187974'... 2020-06-21T12:07:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:10:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:10:18 prefetch.2.10.7: 1) 'SRR1187974' was downloaded successfully 2020-06-21T12:10:18 prefetch.2.10.7: 'SRR1187974' has 0 unresolved dependencies Read 22256853 spots for SRR1187974/SRR1187974.sra Written 22256853 spots for SRR1187974/SRR1187974.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: 00:06:46 22256853 reads; of these: 22256853 (100.00%) were unpaired; of these: 1174799 (5.28%) aligned 0 times 12653959 (56.85%) aligned exactly 1 time 8428095 (37.87%) aligned >1 times 94.72% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 6671605 / 21082054 = 0.3165 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 21:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.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 21:23:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:31: 1000000 INFO @ Sun, 21 Jun 2020 21:23:36: 2000000 INFO @ Sun, 21 Jun 2020 21:23:41: 3000000 INFO @ Sun, 21 Jun 2020 21:23:46: 4000000 INFO @ Sun, 21 Jun 2020 21:23:51: 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 21:23:56: 6000000 INFO @ Sun, 21 Jun 2020 21:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.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 21:23:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:02: 7000000 INFO @ Sun, 21 Jun 2020 21:24:02: 1000000 INFO @ Sun, 21 Jun 2020 21:24:07: 8000000 INFO @ Sun, 21 Jun 2020 21:24:08: 2000000 INFO @ Sun, 21 Jun 2020 21:24:13: 9000000 INFO @ Sun, 21 Jun 2020 21:24:14: 3000000 INFO @ Sun, 21 Jun 2020 21:24:18: 10000000 INFO @ Sun, 21 Jun 2020 21:24:20: 4000000 INFO @ Sun, 21 Jun 2020 21:24:24: 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 21:24:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.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 21:24:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:26: 5000000 INFO @ Sun, 21 Jun 2020 21:24:30: 12000000 INFO @ Sun, 21 Jun 2020 21:24:32: 1000000 INFO @ Sun, 21 Jun 2020 21:24:32: 6000000 INFO @ Sun, 21 Jun 2020 21:24:35: 13000000 INFO @ Sun, 21 Jun 2020 21:24:37: 2000000 INFO @ Sun, 21 Jun 2020 21:24:38: 7000000 INFO @ Sun, 21 Jun 2020 21:24:41: 14000000 INFO @ Sun, 21 Jun 2020 21:24:43: 3000000 INFO @ Sun, 21 Jun 2020 21:24:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:24:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:24:43: #1 total tags in treatment: 14410449 INFO @ Sun, 21 Jun 2020 21:24:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:43: #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 21:24:44: #1 tags after filtering in treatment: 14410427 INFO @ Sun, 21 Jun 2020 21:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:44: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:44: 8000000 INFO @ Sun, 21 Jun 2020 21:24:45: #2 number of paired peaks: 2609 INFO @ Sun, 21 Jun 2020 21:24:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:45: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 21:24:45: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 21:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.05_model.r INFO @ Sun, 21 Jun 2020 21:24:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:24:48: 4000000 INFO @ Sun, 21 Jun 2020 21:24:50: 9000000 INFO @ Sun, 21 Jun 2020 21:24:54: 5000000 INFO @ Sun, 21 Jun 2020 21:24:56: 10000000 INFO @ Sun, 21 Jun 2020 21:24:59: 6000000 INFO @ Sun, 21 Jun 2020 21:25:02: 11000000 INFO @ Sun, 21 Jun 2020 21:25:05: 7000000 INFO @ Sun, 21 Jun 2020 21:25:09: 12000000 INFO @ Sun, 21 Jun 2020 21:25:10: 8000000 INFO @ Sun, 21 Jun 2020 21:25:15: 13000000 INFO @ Sun, 21 Jun 2020 21:25:16: 9000000 INFO @ Sun, 21 Jun 2020 21:25:21: 14000000 INFO @ Sun, 21 Jun 2020 21:25:21: 10000000 INFO @ Sun, 21 Jun 2020 21:25:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:25:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:25:24: #1 total tags in treatment: 14410449 INFO @ Sun, 21 Jun 2020 21:25:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:24: #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 21:25:24: #1 tags after filtering in treatment: 14410427 INFO @ Sun, 21 Jun 2020 21:25:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:25: #2 number of paired peaks: 2609 INFO @ Sun, 21 Jun 2020 21:25:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:25: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 21:25:25: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 21:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.10_model.r INFO @ Sun, 21 Jun 2020 21:25:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:27: 11000000 INFO @ Sun, 21 Jun 2020 21:25:32: 12000000 INFO @ Sun, 21 Jun 2020 21:25:37: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:38: Done! pass1 - making usageList (911 chroms): 3 millis pass2 - checking and writing primary data (11480 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:42: 14000000 INFO @ Sun, 21 Jun 2020 21:25:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:25:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:25:45: #1 total tags in treatment: 14410449 INFO @ Sun, 21 Jun 2020 21:25:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:45: #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 21:25:45: #1 tags after filtering in treatment: 14410427 INFO @ Sun, 21 Jun 2020 21:25:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:46: #2 number of paired peaks: 2609 INFO @ Sun, 21 Jun 2020 21:25:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:46: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 21:25:46: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 21:25:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.20_model.r INFO @ Sun, 21 Jun 2020 21:25:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.10_summits.bed INFO @ Sun, 21 Jun 2020 21:26:17: Done! pass1 - making usageList (724 chroms): 2 millis pass2 - checking and writing primary data (6709 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:26:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485216/SRX485216.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:38: Done! pass1 - making usageList (421 chroms): 4 millis pass2 - checking and writing primary data (2882 records, 4 fields): 14 millis CompletedMACS2peakCalling