Job ID = 6455886 SRX = SRX3020550 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:20:21 prefetch.2.10.7: 1) Downloading 'SRR5850460'... 2020-06-21T10:20:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:06 prefetch.2.10.7: 'SRR5850460' is valid 2020-06-21T10:21:06 prefetch.2.10.7: 1) 'SRR5850460' was downloaded successfully 2020-06-21T10:21:06 prefetch.2.10.7: 'SRR5850460' has 0 unresolved dependencies Read 7035503 spots for SRR5850460/SRR5850460.sra Written 7035503 spots for SRR5850460/SRR5850460.sra 2020-06-21T10:21:40 prefetch.2.10.7: 1) Downloading 'SRR5850461'... 2020-06-21T10:21:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:47 prefetch.2.10.7: 'SRR5850461' is valid 2020-06-21T10:22:47 prefetch.2.10.7: 1) 'SRR5850461' was downloaded successfully 2020-06-21T10:22:47 prefetch.2.10.7: 'SRR5850461' has 0 unresolved dependencies Read 7007123 spots for SRR5850461/SRR5850461.sra Written 7007123 spots for SRR5850461/SRR5850461.sra 2020-06-21T10:23:20 prefetch.2.10.7: 1) Downloading 'SRR5850462'... 2020-06-21T10:23:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:13 prefetch.2.10.7: 'SRR5850462' is valid 2020-06-21T10:24:13 prefetch.2.10.7: 1) 'SRR5850462' was downloaded successfully 2020-06-21T10:24:13 prefetch.2.10.7: 'SRR5850462' has 0 unresolved dependencies Read 7036734 spots for SRR5850462/SRR5850462.sra Written 7036734 spots for SRR5850462/SRR5850462.sra 2020-06-21T10:24:52 prefetch.2.10.7: 1) Downloading 'SRR5850463'... 2020-06-21T10:24:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:50 prefetch.2.10.7: 'SRR5850463' is valid 2020-06-21T10:25:50 prefetch.2.10.7: 1) 'SRR5850463' was downloaded successfully 2020-06-21T10:25:50 prefetch.2.10.7: 'SRR5850463' has 0 unresolved dependencies Read 6970032 spots for SRR5850463/SRR5850463.sra Written 6970032 spots for SRR5850463/SRR5850463.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: 00:05:54 28049392 reads; of these: 28049392 (100.00%) were unpaired; of these: 6092502 (21.72%) aligned 0 times 18115266 (64.58%) aligned exactly 1 time 3841624 (13.70%) aligned >1 times 78.28% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 8527788 / 21956890 = 0.3884 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 19:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.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 19:36:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:57: 1000000 INFO @ Sun, 21 Jun 2020 19:37:03: 2000000 INFO @ Sun, 21 Jun 2020 19:37:09: 3000000 INFO @ Sun, 21 Jun 2020 19:37:15: 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 19:37:21: 5000000 INFO @ Sun, 21 Jun 2020 19:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.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 19:37:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:27: 6000000 INFO @ Sun, 21 Jun 2020 19:37:28: 1000000 INFO @ Sun, 21 Jun 2020 19:37:34: 7000000 INFO @ Sun, 21 Jun 2020 19:37:34: 2000000 INFO @ Sun, 21 Jun 2020 19:37:41: 8000000 INFO @ Sun, 21 Jun 2020 19:37:41: 3000000 INFO @ Sun, 21 Jun 2020 19:37:47: 9000000 INFO @ Sun, 21 Jun 2020 19:37:47: 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 19:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.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 19:37:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:54: 5000000 INFO @ Sun, 21 Jun 2020 19:37:54: 10000000 INFO @ Sun, 21 Jun 2020 19:37:58: 1000000 INFO @ Sun, 21 Jun 2020 19:38:00: 6000000 INFO @ Sun, 21 Jun 2020 19:38:00: 11000000 INFO @ Sun, 21 Jun 2020 19:38:04: 2000000 INFO @ Sun, 21 Jun 2020 19:38:07: 7000000 INFO @ Sun, 21 Jun 2020 19:38:07: 12000000 INFO @ Sun, 21 Jun 2020 19:38:11: 3000000 INFO @ Sun, 21 Jun 2020 19:38:13: 8000000 INFO @ Sun, 21 Jun 2020 19:38:14: 13000000 INFO @ Sun, 21 Jun 2020 19:38:17: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:38:17: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:38:17: #1 total tags in treatment: 13429102 INFO @ Sun, 21 Jun 2020 19:38:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:17: #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 19:38:17: #1 tags after filtering in treatment: 13428990 INFO @ Sun, 21 Jun 2020 19:38:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:17: 4000000 INFO @ Sun, 21 Jun 2020 19:38:19: #2 number of paired peaks: 11412 INFO @ Sun, 21 Jun 2020 19:38:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:19: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:38:19: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:38:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.05_model.r INFO @ Sun, 21 Jun 2020 19:38:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:20: 9000000 INFO @ Sun, 21 Jun 2020 19:38:24: 5000000 INFO @ Sun, 21 Jun 2020 19:38:27: 10000000 INFO @ Sun, 21 Jun 2020 19:38:31: 6000000 INFO @ Sun, 21 Jun 2020 19:38:33: 11000000 INFO @ Sun, 21 Jun 2020 19:38:37: 7000000 INFO @ Sun, 21 Jun 2020 19:38:40: 12000000 INFO @ Sun, 21 Jun 2020 19:38:44: 8000000 INFO @ Sun, 21 Jun 2020 19:38:47: 13000000 INFO @ Sun, 21 Jun 2020 19:38:50: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:38:50: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:38:50: #1 total tags in treatment: 13429102 INFO @ Sun, 21 Jun 2020 19:38:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:50: #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 19:38:50: 9000000 INFO @ Sun, 21 Jun 2020 19:38:50: #1 tags after filtering in treatment: 13428990 INFO @ Sun, 21 Jun 2020 19:38:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:50: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:38:52: #2 number of paired peaks: 11412 INFO @ Sun, 21 Jun 2020 19:38:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:52: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:38:52: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.10_model.r INFO @ Sun, 21 Jun 2020 19:38:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:56: 10000000 INFO @ Sun, 21 Jun 2020 19:38:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:01: 11000000 INFO @ Sun, 21 Jun 2020 19:39:07: 12000000 INFO @ Sun, 21 Jun 2020 19:39:13: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.05_summits.bed INFO @ Sun, 21 Jun 2020 19:39:15: Done! pass1 - making usageList (397 chroms): 3 millis pass2 - checking and writing primary data (9387 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:16: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:39:16: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:39:16: #1 total tags in treatment: 13429102 INFO @ Sun, 21 Jun 2020 19:39:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:16: #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 19:39:16: #1 tags after filtering in treatment: 13428990 INFO @ Sun, 21 Jun 2020 19:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:18: #2 number of paired peaks: 11412 INFO @ Sun, 21 Jun 2020 19:39:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:18: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:39:18: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:39:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.20_model.r INFO @ Sun, 21 Jun 2020 19:39:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.10_summits.bed INFO @ Sun, 21 Jun 2020 19:39:46: Done! pass1 - making usageList (244 chroms): 2 millis pass2 - checking and writing primary data (8619 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020550/SRX3020550.20_summits.bed INFO @ Sun, 21 Jun 2020 19:40:09: Done! pass1 - making usageList (156 chroms): 2 millis pass2 - checking and writing primary data (7915 records, 4 fields): 13 millis CompletedMACS2peakCalling