Job ID = 6456180 SRX = SRX3279766 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:29:36 prefetch.2.10.7: 1) Downloading 'SRR6168916'... 2020-06-21T10:29:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:35:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:35:42 prefetch.2.10.7: 1) 'SRR6168916' was downloaded successfully 2020-06-21T10:35:42 prefetch.2.10.7: 'SRR6168916' has 0 unresolved dependencies Read 36078793 spots for SRR6168916/SRR6168916.sra Written 36078793 spots for SRR6168916/SRR6168916.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: 00:07:22 36078793 reads; of these: 36078793 (100.00%) were unpaired; of these: 1038326 (2.88%) aligned 0 times 33370835 (92.49%) aligned exactly 1 time 1669632 (4.63%) aligned >1 times 97.12% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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 16 files... [bam_rmdupse_core] 16872711 / 35040467 = 0.4815 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 19:52:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.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 19:52:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:28: 1000000 INFO @ Sun, 21 Jun 2020 19:52:35: 2000000 INFO @ Sun, 21 Jun 2020 19:52:41: 3000000 INFO @ Sun, 21 Jun 2020 19:52:47: 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 19:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.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 19:52:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:54: 5000000 INFO @ Sun, 21 Jun 2020 19:52:58: 1000000 INFO @ Sun, 21 Jun 2020 19:53:01: 6000000 INFO @ Sun, 21 Jun 2020 19:53:05: 2000000 INFO @ Sun, 21 Jun 2020 19:53:08: 7000000 INFO @ Sun, 21 Jun 2020 19:53:11: 3000000 INFO @ Sun, 21 Jun 2020 19:53:14: 8000000 INFO @ Sun, 21 Jun 2020 19:53:17: 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 19:53:21: 9000000 INFO @ Sun, 21 Jun 2020 19:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.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 19:53:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:23: 5000000 INFO @ Sun, 21 Jun 2020 19:53:28: 10000000 INFO @ Sun, 21 Jun 2020 19:53:29: 1000000 INFO @ Sun, 21 Jun 2020 19:53:30: 6000000 INFO @ Sun, 21 Jun 2020 19:53:35: 2000000 INFO @ Sun, 21 Jun 2020 19:53:35: 11000000 INFO @ Sun, 21 Jun 2020 19:53:36: 7000000 INFO @ Sun, 21 Jun 2020 19:53:41: 3000000 INFO @ Sun, 21 Jun 2020 19:53:42: 12000000 INFO @ Sun, 21 Jun 2020 19:53:43: 8000000 INFO @ Sun, 21 Jun 2020 19:53:48: 4000000 INFO @ Sun, 21 Jun 2020 19:53:49: 9000000 INFO @ Sun, 21 Jun 2020 19:53:49: 13000000 INFO @ Sun, 21 Jun 2020 19:53:54: 5000000 INFO @ Sun, 21 Jun 2020 19:53:56: 10000000 INFO @ Sun, 21 Jun 2020 19:53:56: 14000000 INFO @ Sun, 21 Jun 2020 19:54:01: 6000000 INFO @ Sun, 21 Jun 2020 19:54:02: 11000000 INFO @ Sun, 21 Jun 2020 19:54:04: 15000000 INFO @ Sun, 21 Jun 2020 19:54:07: 7000000 INFO @ Sun, 21 Jun 2020 19:54:09: 12000000 INFO @ Sun, 21 Jun 2020 19:54:11: 16000000 INFO @ Sun, 21 Jun 2020 19:54:14: 8000000 INFO @ Sun, 21 Jun 2020 19:54:15: 13000000 INFO @ Sun, 21 Jun 2020 19:54:19: 17000000 INFO @ Sun, 21 Jun 2020 19:54:20: 9000000 INFO @ Sun, 21 Jun 2020 19:54:22: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:54:26: 18000000 INFO @ Sun, 21 Jun 2020 19:54:26: 10000000 INFO @ Sun, 21 Jun 2020 19:54:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:54:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:54:27: #1 total tags in treatment: 18167756 INFO @ Sun, 21 Jun 2020 19:54:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:27: #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 19:54:28: #1 tags after filtering in treatment: 18167520 INFO @ Sun, 21 Jun 2020 19:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:29: 15000000 INFO @ Sun, 21 Jun 2020 19:54:30: #2 number of paired peaks: 17062 INFO @ Sun, 21 Jun 2020 19:54:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:31: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:54:31: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.05_model.r INFO @ Sun, 21 Jun 2020 19:54:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:33: 11000000 INFO @ Sun, 21 Jun 2020 19:54:36: 16000000 INFO @ Sun, 21 Jun 2020 19:54:39: 12000000 INFO @ Sun, 21 Jun 2020 19:54:43: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:54:45: 13000000 INFO @ Sun, 21 Jun 2020 19:54:49: 18000000 INFO @ Sun, 21 Jun 2020 19:54:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:54:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:54:50: #1 total tags in treatment: 18167756 INFO @ Sun, 21 Jun 2020 19:54:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:50: #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 19:54:51: #1 tags after filtering in treatment: 18167520 INFO @ Sun, 21 Jun 2020 19:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:52: 14000000 INFO @ Sun, 21 Jun 2020 19:54:54: #2 number of paired peaks: 17062 INFO @ Sun, 21 Jun 2020 19:54:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:54: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:54:54: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:54:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.10_model.r INFO @ Sun, 21 Jun 2020 19:54:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:58: 15000000 INFO @ Sun, 21 Jun 2020 19:55:03: 16000000 INFO @ Sun, 21 Jun 2020 19:55:08: 17000000 INFO @ Sun, 21 Jun 2020 19:55:14: 18000000 INFO @ Sun, 21 Jun 2020 19:55:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:55:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:55:15: #1 total tags in treatment: 18167756 INFO @ Sun, 21 Jun 2020 19:55:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:15: #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 19:55:16: #1 tags after filtering in treatment: 18167520 INFO @ Sun, 21 Jun 2020 19:55:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:18: #2 number of paired peaks: 17062 INFO @ Sun, 21 Jun 2020 19:55:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:19: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:55:19: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:55:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.20_model.r INFO @ Sun, 21 Jun 2020 19:55:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.05_summits.bed INFO @ Sun, 21 Jun 2020 19:55:40: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (8702 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:01: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (8197 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279766/SRX3279766.20_summits.bed INFO @ Sun, 21 Jun 2020 19:56:23: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (7555 records, 4 fields): 9 millis CompletedMACS2peakCalling