Job ID = 6497811 SRX = SRX1728713 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:45:00 prefetch.2.10.7: 1) Downloading 'SRR3452730'... 2020-06-25T22:45:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:47:23 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:47:24 prefetch.2.10.7: 'SRR3452730' is valid 2020-06-25T22:47:24 prefetch.2.10.7: 1) 'SRR3452730' was downloaded successfully 2020-06-25T22:47:24 prefetch.2.10.7: 'SRR3452730' has 0 unresolved dependencies Read 11755087 spots for SRR3452730/SRR3452730.sra Written 11755087 spots for SRR3452730/SRR3452730.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: 00:28:04 11755087 reads; of these: 11755087 (100.00%) were paired; of these: 1366027 (11.62%) aligned concordantly 0 times 6357881 (54.09%) aligned concordantly exactly 1 time 4031179 (34.29%) aligned concordantly >1 times ---- 1366027 pairs aligned concordantly 0 times; of these: 404259 (29.59%) aligned discordantly 1 time ---- 961768 pairs aligned 0 times concordantly or discordantly; of these: 1923536 mates make up the pairs; of these: 1206193 (62.71%) aligned 0 times 248910 (12.94%) aligned exactly 1 time 468433 (24.35%) aligned >1 times 94.87% overall alignment rate Time searching: 00:28:04 Overall time: 00:28:04 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 12 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] 1118999 / 10719436 = 0.1044 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 08:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.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 08:21:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:21:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:21:41: 1000000 INFO @ Fri, 26 Jun 2020 08:21:47: 2000000 INFO @ Fri, 26 Jun 2020 08:21:52: 3000000 INFO @ Fri, 26 Jun 2020 08:21:57: 4000000 INFO @ Fri, 26 Jun 2020 08:22:03: 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 08:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.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 08:22:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:08: 6000000 INFO @ Fri, 26 Jun 2020 08:22:13: 1000000 INFO @ Fri, 26 Jun 2020 08:22:15: 7000000 INFO @ Fri, 26 Jun 2020 08:22:19: 2000000 INFO @ Fri, 26 Jun 2020 08:22:21: 8000000 INFO @ Fri, 26 Jun 2020 08:22:25: 3000000 INFO @ Fri, 26 Jun 2020 08:22:27: 9000000 INFO @ Fri, 26 Jun 2020 08:22:31: 4000000 INFO @ Fri, 26 Jun 2020 08:22:33: 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 08:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.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 08:22:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:38: 5000000 INFO @ Fri, 26 Jun 2020 08:22:40: 11000000 INFO @ Fri, 26 Jun 2020 08:22:43: 1000000 INFO @ Fri, 26 Jun 2020 08:22:45: 6000000 INFO @ Fri, 26 Jun 2020 08:22:47: 12000000 INFO @ Fri, 26 Jun 2020 08:22:50: 2000000 INFO @ Fri, 26 Jun 2020 08:22:52: 7000000 INFO @ Fri, 26 Jun 2020 08:22:54: 13000000 INFO @ Fri, 26 Jun 2020 08:22:58: 3000000 INFO @ Fri, 26 Jun 2020 08:22:59: 8000000 INFO @ Fri, 26 Jun 2020 08:23:01: 14000000 INFO @ Fri, 26 Jun 2020 08:23:06: 9000000 INFO @ Fri, 26 Jun 2020 08:23:06: 4000000 INFO @ Fri, 26 Jun 2020 08:23:08: 15000000 INFO @ Fri, 26 Jun 2020 08:23:13: 10000000 INFO @ Fri, 26 Jun 2020 08:23:14: 5000000 INFO @ Fri, 26 Jun 2020 08:23:15: 16000000 INFO @ Fri, 26 Jun 2020 08:23:20: 11000000 INFO @ Fri, 26 Jun 2020 08:23:23: 17000000 INFO @ Fri, 26 Jun 2020 08:23:23: 6000000 INFO @ Fri, 26 Jun 2020 08:23:27: 12000000 INFO @ Fri, 26 Jun 2020 08:23:30: 18000000 INFO @ Fri, 26 Jun 2020 08:23:31: 7000000 INFO @ Fri, 26 Jun 2020 08:23:35: 13000000 INFO @ Fri, 26 Jun 2020 08:23:37: 19000000 INFO @ Fri, 26 Jun 2020 08:23:39: 8000000 INFO @ Fri, 26 Jun 2020 08:23:42: 14000000 INFO @ Fri, 26 Jun 2020 08:23:44: 20000000 INFO @ Fri, 26 Jun 2020 08:23:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:44: #1 total tags in treatment: 9287844 INFO @ Fri, 26 Jun 2020 08:23:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:44: #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 08:23:45: #1 tags after filtering in treatment: 8187980 INFO @ Fri, 26 Jun 2020 08:23:45: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 08:23:45: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:45: #2 number of paired peaks: 227 WARNING @ Fri, 26 Jun 2020 08:23:45: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Fri, 26 Jun 2020 08:23:45: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:45: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:45: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:45: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:45: #2 predicted fragment length is 109 bps INFO @ Fri, 26 Jun 2020 08:23:45: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 26 Jun 2020 08:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.05_model.r INFO @ Fri, 26 Jun 2020 08:23:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:47: 9000000 INFO @ Fri, 26 Jun 2020 08:23:49: 15000000 INFO @ Fri, 26 Jun 2020 08:23:55: 10000000 INFO @ Fri, 26 Jun 2020 08:23:56: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:24:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:24:03: 11000000 INFO @ Fri, 26 Jun 2020 08:24:03: 17000000 INFO @ Fri, 26 Jun 2020 08:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.05_summits.bed INFO @ Fri, 26 Jun 2020 08:24:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1794 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:24:10: 18000000 INFO @ Fri, 26 Jun 2020 08:24:11: 12000000 INFO @ Fri, 26 Jun 2020 08:24:17: 19000000 INFO @ Fri, 26 Jun 2020 08:24:19: 13000000 INFO @ Fri, 26 Jun 2020 08:24:24: 20000000 INFO @ Fri, 26 Jun 2020 08:24:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:24:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:24:25: #1 total tags in treatment: 9287844 INFO @ Fri, 26 Jun 2020 08:24:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:24:25: #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 08:24:25: #1 tags after filtering in treatment: 8187980 INFO @ Fri, 26 Jun 2020 08:24:25: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 08:24:25: #1 finished! INFO @ Fri, 26 Jun 2020 08:24:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:24:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:24:25: #2 number of paired peaks: 227 WARNING @ Fri, 26 Jun 2020 08:24:25: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Fri, 26 Jun 2020 08:24:26: start model_add_line... INFO @ Fri, 26 Jun 2020 08:24:26: start X-correlation... INFO @ Fri, 26 Jun 2020 08:24:26: end of X-cor INFO @ Fri, 26 Jun 2020 08:24:26: #2 finished! INFO @ Fri, 26 Jun 2020 08:24:26: #2 predicted fragment length is 109 bps INFO @ Fri, 26 Jun 2020 08:24:26: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 26 Jun 2020 08:24:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.10_model.r INFO @ Fri, 26 Jun 2020 08:24:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:24:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:24:27: 14000000 INFO @ Fri, 26 Jun 2020 08:24:35: 15000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:24:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:24:42: 16000000 INFO @ Fri, 26 Jun 2020 08:24:49: 17000000 INFO @ Fri, 26 Jun 2020 08:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.10_summits.bed INFO @ Fri, 26 Jun 2020 08:24:50: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:24:57: 18000000 INFO @ Fri, 26 Jun 2020 08:25:04: 19000000 INFO @ Fri, 26 Jun 2020 08:25:11: 20000000 INFO @ Fri, 26 Jun 2020 08:25:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:25:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:25:12: #1 total tags in treatment: 9287844 INFO @ Fri, 26 Jun 2020 08:25:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:25:12: #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 08:25:12: #1 tags after filtering in treatment: 8187980 INFO @ Fri, 26 Jun 2020 08:25:12: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 08:25:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:25:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:25:12: #2 number of paired peaks: 227 WARNING @ Fri, 26 Jun 2020 08:25:12: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Fri, 26 Jun 2020 08:25:12: start model_add_line... INFO @ Fri, 26 Jun 2020 08:25:12: start X-correlation... INFO @ Fri, 26 Jun 2020 08:25:12: end of X-cor INFO @ Fri, 26 Jun 2020 08:25:12: #2 finished! INFO @ Fri, 26 Jun 2020 08:25:12: #2 predicted fragment length is 109 bps INFO @ Fri, 26 Jun 2020 08:25:12: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 26 Jun 2020 08:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.20_model.r INFO @ Fri, 26 Jun 2020 08:25:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:25:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728713/SRX1728713.20_summits.bed INFO @ Fri, 26 Jun 2020 08:25:37: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 1 millis CompletedMACS2peakCalling