Job ID = 6498719 SRX = SRX749038 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:55:59 prefetch.2.10.7: 1) Downloading 'SRR1636766'... 2020-06-25T23:55:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:03:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:03:39 prefetch.2.10.7: 1) 'SRR1636766' was downloaded successfully Read 38301738 spots for SRR1636766/SRR1636766.sra Written 38301738 spots for SRR1636766/SRR1636766.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: 00:40:45 38301738 reads; of these: 38301738 (100.00%) were paired; of these: 6354912 (16.59%) aligned concordantly 0 times 27802586 (72.59%) aligned concordantly exactly 1 time 4144240 (10.82%) aligned concordantly >1 times ---- 6354912 pairs aligned concordantly 0 times; of these: 104894 (1.65%) aligned discordantly 1 time ---- 6250018 pairs aligned 0 times concordantly or discordantly; of these: 12500036 mates make up the pairs; of these: 11270589 (90.16%) aligned 0 times 1013917 (8.11%) aligned exactly 1 time 215530 (1.72%) aligned >1 times 85.29% overall alignment rate Time searching: 00:40:45 Overall time: 00:40:45 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 28 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] 24808876 / 32022776 = 0.7747 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 09:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.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 09:59:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:59:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:59:37: 1000000 INFO @ Fri, 26 Jun 2020 09:59:42: 2000000 INFO @ Fri, 26 Jun 2020 09:59:48: 3000000 INFO @ Fri, 26 Jun 2020 09:59:53: 4000000 INFO @ Fri, 26 Jun 2020 09:59:59: 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 @ Fri, 26 Jun 2020 10:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.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 10:00:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:00:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:00:04: 6000000 INFO @ Fri, 26 Jun 2020 10:00:07: 1000000 INFO @ Fri, 26 Jun 2020 10:00:10: 7000000 INFO @ Fri, 26 Jun 2020 10:00:13: 2000000 INFO @ Fri, 26 Jun 2020 10:00:16: 8000000 INFO @ Fri, 26 Jun 2020 10:00:19: 3000000 INFO @ Fri, 26 Jun 2020 10:00:21: 9000000 INFO @ Fri, 26 Jun 2020 10:00:25: 4000000 INFO @ Fri, 26 Jun 2020 10:00:27: 10000000 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 10:00:31: 5000000 INFO @ Fri, 26 Jun 2020 10:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.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 10:00:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:00:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:00:33: 11000000 INFO @ Fri, 26 Jun 2020 10:00:37: 6000000 INFO @ Fri, 26 Jun 2020 10:00:37: 1000000 INFO @ Fri, 26 Jun 2020 10:00:39: 12000000 INFO @ Fri, 26 Jun 2020 10:00:42: 2000000 INFO @ Fri, 26 Jun 2020 10:00:43: 7000000 INFO @ Fri, 26 Jun 2020 10:00:45: 13000000 INFO @ Fri, 26 Jun 2020 10:00:47: 3000000 INFO @ Fri, 26 Jun 2020 10:00:49: 8000000 INFO @ Fri, 26 Jun 2020 10:00:51: 14000000 INFO @ Fri, 26 Jun 2020 10:00:53: 4000000 INFO @ Fri, 26 Jun 2020 10:00:54: 9000000 INFO @ Fri, 26 Jun 2020 10:00:57: 15000000 INFO @ Fri, 26 Jun 2020 10:00:58: 5000000 INFO @ Fri, 26 Jun 2020 10:01:00: 10000000 INFO @ Fri, 26 Jun 2020 10:01:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:01:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:01:02: #1 total tags in treatment: 7204186 INFO @ Fri, 26 Jun 2020 10:01:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:01:02: #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 10:01:02: #1 tags after filtering in treatment: 4762462 INFO @ Fri, 26 Jun 2020 10:01:02: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 26 Jun 2020 10:01:02: #1 finished! INFO @ Fri, 26 Jun 2020 10:01:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:01:02: #2 number of paired peaks: 6039 INFO @ Fri, 26 Jun 2020 10:01:02: start model_add_line... INFO @ Fri, 26 Jun 2020 10:01:02: start X-correlation... INFO @ Fri, 26 Jun 2020 10:01:02: end of X-cor INFO @ Fri, 26 Jun 2020 10:01:02: #2 finished! INFO @ Fri, 26 Jun 2020 10:01:02: #2 predicted fragment length is 141 bps INFO @ Fri, 26 Jun 2020 10:01:02: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 26 Jun 2020 10:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.05_model.r INFO @ Fri, 26 Jun 2020 10:01:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:01:03: 6000000 INFO @ Fri, 26 Jun 2020 10:01:06: 11000000 INFO @ Fri, 26 Jun 2020 10:01:08: 7000000 INFO @ Fri, 26 Jun 2020 10:01:12: 12000000 INFO @ Fri, 26 Jun 2020 10:01:14: 8000000 INFO @ Fri, 26 Jun 2020 10:01:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:01:18: 13000000 INFO @ Fri, 26 Jun 2020 10:01:19: 9000000 INFO @ Fri, 26 Jun 2020 10:01:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:01:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:01:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.05_summits.bed INFO @ Fri, 26 Jun 2020 10:01:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12206 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:01:24: 14000000 INFO @ Fri, 26 Jun 2020 10:01:24: 10000000 INFO @ Fri, 26 Jun 2020 10:01:29: 11000000 INFO @ Fri, 26 Jun 2020 10:01:30: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:01:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:01:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:01:34: #1 total tags in treatment: 7204186 INFO @ Fri, 26 Jun 2020 10:01:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:01:34: #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 10:01:34: #1 tags after filtering in treatment: 4762462 INFO @ Fri, 26 Jun 2020 10:01:34: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 26 Jun 2020 10:01:34: #1 finished! INFO @ Fri, 26 Jun 2020 10:01:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:01:34: 12000000 INFO @ Fri, 26 Jun 2020 10:01:35: #2 number of paired peaks: 6039 INFO @ Fri, 26 Jun 2020 10:01:35: start model_add_line... INFO @ Fri, 26 Jun 2020 10:01:35: start X-correlation... INFO @ Fri, 26 Jun 2020 10:01:35: end of X-cor INFO @ Fri, 26 Jun 2020 10:01:35: #2 finished! INFO @ Fri, 26 Jun 2020 10:01:35: #2 predicted fragment length is 141 bps INFO @ Fri, 26 Jun 2020 10:01:35: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 26 Jun 2020 10:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.10_model.r INFO @ Fri, 26 Jun 2020 10:01:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:01:40: 13000000 INFO @ Fri, 26 Jun 2020 10:01:44: 14000000 INFO @ Fri, 26 Jun 2020 10:01:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:01:49: 15000000 INFO @ Fri, 26 Jun 2020 10:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.10_summits.bed INFO @ Fri, 26 Jun 2020 10:01:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9088 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:01:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:01:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:01:53: #1 total tags in treatment: 7204186 INFO @ Fri, 26 Jun 2020 10:01:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:01:53: #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 10:01:53: #1 tags after filtering in treatment: 4762462 INFO @ Fri, 26 Jun 2020 10:01:53: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 26 Jun 2020 10:01:53: #1 finished! INFO @ Fri, 26 Jun 2020 10:01:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:01:54: #2 number of paired peaks: 6039 INFO @ Fri, 26 Jun 2020 10:01:54: start model_add_line... INFO @ Fri, 26 Jun 2020 10:01:54: start X-correlation... INFO @ Fri, 26 Jun 2020 10:01:54: end of X-cor INFO @ Fri, 26 Jun 2020 10:01:54: #2 finished! INFO @ Fri, 26 Jun 2020 10:01:54: #2 predicted fragment length is 141 bps INFO @ Fri, 26 Jun 2020 10:01:54: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 26 Jun 2020 10:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.20_model.r INFO @ Fri, 26 Jun 2020 10:01:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:02:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749038/SRX749038.20_summits.bed INFO @ Fri, 26 Jun 2020 10:02:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6376 records, 4 fields): 8 millis CompletedMACS2peakCalling