Job ID = 6497694 SRX = SRX1021228 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:26:12 prefetch.2.10.7: 1) Downloading 'SRR2013425'... 2020-06-25T22:26:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:34:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:34:51 prefetch.2.10.7: 1) 'SRR2013425' was downloaded successfully Read 23190712 spots for SRR2013425/SRR2013425.sra Written 23190712 spots for SRR2013425/SRR2013425.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: 00:40:26 23190712 reads; of these: 23190712 (100.00%) were paired; of these: 5321293 (22.95%) aligned concordantly 0 times 13105117 (56.51%) aligned concordantly exactly 1 time 4764302 (20.54%) aligned concordantly >1 times ---- 5321293 pairs aligned concordantly 0 times; of these: 8537 (0.16%) aligned discordantly 1 time ---- 5312756 pairs aligned 0 times concordantly or discordantly; of these: 10625512 mates make up the pairs; of these: 10089304 (94.95%) aligned 0 times 394743 (3.72%) aligned exactly 1 time 141465 (1.33%) aligned >1 times 78.25% overall alignment rate Time searching: 00:40:26 Overall time: 00:40:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7727928 / 17863477 = 0.4326 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 @ Fri, 26 Jun 2020 08:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.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 @ Fri, 26 Jun 2020 08:28:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:28:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:28:08: 1000000 INFO @ Fri, 26 Jun 2020 08:28:14: 2000000 INFO @ Fri, 26 Jun 2020 08:28:20: 3000000 INFO @ Fri, 26 Jun 2020 08:28:27: 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 @ Fri, 26 Jun 2020 08:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.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 @ Fri, 26 Jun 2020 08:28:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:28:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:28:33: 5000000 INFO @ Fri, 26 Jun 2020 08:28:38: 1000000 INFO @ Fri, 26 Jun 2020 08:28:39: 6000000 INFO @ Fri, 26 Jun 2020 08:28:45: 2000000 INFO @ Fri, 26 Jun 2020 08:28:45: 7000000 INFO @ Fri, 26 Jun 2020 08:28:51: 3000000 INFO @ Fri, 26 Jun 2020 08:28:51: 8000000 INFO @ Fri, 26 Jun 2020 08:28:58: 9000000 INFO @ Fri, 26 Jun 2020 08:28:58: 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 @ Fri, 26 Jun 2020 08:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.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 @ Fri, 26 Jun 2020 08:29:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:29:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:29:04: 10000000 INFO @ Fri, 26 Jun 2020 08:29:04: 5000000 INFO @ Fri, 26 Jun 2020 08:29:08: 1000000 INFO @ Fri, 26 Jun 2020 08:29:10: 11000000 INFO @ Fri, 26 Jun 2020 08:29:10: 6000000 INFO @ Fri, 26 Jun 2020 08:29:13: 2000000 INFO @ Fri, 26 Jun 2020 08:29:16: 12000000 INFO @ Fri, 26 Jun 2020 08:29:17: 7000000 INFO @ Fri, 26 Jun 2020 08:29:19: 3000000 INFO @ Fri, 26 Jun 2020 08:29:22: 13000000 INFO @ Fri, 26 Jun 2020 08:29:23: 8000000 INFO @ Fri, 26 Jun 2020 08:29:25: 4000000 INFO @ Fri, 26 Jun 2020 08:29:29: 14000000 INFO @ Fri, 26 Jun 2020 08:29:30: 9000000 INFO @ Fri, 26 Jun 2020 08:29:30: 5000000 INFO @ Fri, 26 Jun 2020 08:29:35: 15000000 INFO @ Fri, 26 Jun 2020 08:29:36: 6000000 INFO @ Fri, 26 Jun 2020 08:29:36: 10000000 INFO @ Fri, 26 Jun 2020 08:29:42: 7000000 INFO @ Fri, 26 Jun 2020 08:29:42: 16000000 INFO @ Fri, 26 Jun 2020 08:29:42: 11000000 INFO @ Fri, 26 Jun 2020 08:29:47: 8000000 INFO @ Fri, 26 Jun 2020 08:29:48: 17000000 INFO @ Fri, 26 Jun 2020 08:29:49: 12000000 INFO @ Fri, 26 Jun 2020 08:29:53: 9000000 INFO @ Fri, 26 Jun 2020 08:29:54: 18000000 INFO @ Fri, 26 Jun 2020 08:29:55: 13000000 INFO @ Fri, 26 Jun 2020 08:29:59: 10000000 INFO @ Fri, 26 Jun 2020 08:30:00: 19000000 INFO @ Fri, 26 Jun 2020 08:30:02: 14000000 INFO @ Fri, 26 Jun 2020 08:30:04: 11000000 INFO @ Fri, 26 Jun 2020 08:30:07: 20000000 INFO @ Fri, 26 Jun 2020 08:30:09: 15000000 INFO @ Fri, 26 Jun 2020 08:30:10: 12000000 INFO @ Fri, 26 Jun 2020 08:30:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:30:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:30:12: #1 total tags in treatment: 10143472 INFO @ Fri, 26 Jun 2020 08:30:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:30:12: #1 tags after filtering in treatment: 9320869 INFO @ Fri, 26 Jun 2020 08:30:12: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:30:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:30:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:30:13: #2 number of paired peaks: 1104 INFO @ Fri, 26 Jun 2020 08:30:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:30:13: start X-correlation... INFO @ Fri, 26 Jun 2020 08:30:13: end of X-cor INFO @ Fri, 26 Jun 2020 08:30:13: #2 finished! INFO @ Fri, 26 Jun 2020 08:30:13: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 08:30:13: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 08:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.05_model.r INFO @ Fri, 26 Jun 2020 08:30:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:15: 16000000 INFO @ Fri, 26 Jun 2020 08:30:16: 13000000 INFO @ Fri, 26 Jun 2020 08:30:21: 14000000 INFO @ Fri, 26 Jun 2020 08:30:22: 17000000 INFO @ Fri, 26 Jun 2020 08:30:27: 15000000 INFO @ Fri, 26 Jun 2020 08:30:28: 18000000 INFO @ Fri, 26 Jun 2020 08:30:33: 16000000 INFO @ Fri, 26 Jun 2020 08:30:34: 19000000 INFO @ Fri, 26 Jun 2020 08:30:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:39: 17000000 INFO @ Fri, 26 Jun 2020 08:30:41: 20000000 INFO @ Fri, 26 Jun 2020 08:30:45: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:30:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:30:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:30:46: #1 total tags in treatment: 10143472 INFO @ Fri, 26 Jun 2020 08:30:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:30:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:30:46: #1 tags after filtering in treatment: 9320869 INFO @ Fri, 26 Jun 2020 08:30:46: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:30:46: #1 finished! INFO @ Fri, 26 Jun 2020 08:30:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:30:47: #2 number of paired peaks: 1104 INFO @ Fri, 26 Jun 2020 08:30:47: start model_add_line... INFO @ Fri, 26 Jun 2020 08:30:47: start X-correlation... INFO @ Fri, 26 Jun 2020 08:30:47: end of X-cor INFO @ Fri, 26 Jun 2020 08:30:47: #2 finished! INFO @ Fri, 26 Jun 2020 08:30:47: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 08:30:47: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 08:30:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.10_model.r INFO @ Fri, 26 Jun 2020 08:30:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:30:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.05_summits.bed INFO @ Fri, 26 Jun 2020 08:30:50: Done! INFO @ Fri, 26 Jun 2020 08:30:50: 19000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6224 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:30:56: 20000000 INFO @ Fri, 26 Jun 2020 08:31:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:31:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:31:00: #1 total tags in treatment: 10143472 INFO @ Fri, 26 Jun 2020 08:31:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:31:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:31:01: #1 tags after filtering in treatment: 9320869 INFO @ Fri, 26 Jun 2020 08:31:01: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:31:01: #1 finished! INFO @ Fri, 26 Jun 2020 08:31:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:31:01: #2 number of paired peaks: 1104 INFO @ Fri, 26 Jun 2020 08:31:01: start model_add_line... INFO @ Fri, 26 Jun 2020 08:31:02: start X-correlation... INFO @ Fri, 26 Jun 2020 08:31:02: end of X-cor INFO @ Fri, 26 Jun 2020 08:31:02: #2 finished! INFO @ Fri, 26 Jun 2020 08:31:02: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 08:31:02: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 08:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.20_model.r INFO @ Fri, 26 Jun 2020 08:31:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:31:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:31:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:31:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:31:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.10_summits.bed INFO @ Fri, 26 Jun 2020 08:31:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3180 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:31:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021228/SRX1021228.20_summits.bed INFO @ Fri, 26 Jun 2020 08:31:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1259 records, 4 fields): 4 millis CompletedMACS2peakCalling