Job ID = 6497695 SRX = SRX1021230 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:27:57 prefetch.2.10.7: 1) Downloading 'SRR2013427'... 2020-06-25T22:27:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:30:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:30:58 prefetch.2.10.7: 1) 'SRR2013427' was downloaded successfully Read 19369199 spots for SRR2013427/SRR2013427.sra Written 19369199 spots for SRR2013427/SRR2013427.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: 00:42:06 19369199 reads; of these: 19369199 (100.00%) were paired; of these: 3024910 (15.62%) aligned concordantly 0 times 12174223 (62.85%) aligned concordantly exactly 1 time 4170066 (21.53%) aligned concordantly >1 times ---- 3024910 pairs aligned concordantly 0 times; of these: 9876 (0.33%) aligned discordantly 1 time ---- 3015034 pairs aligned 0 times concordantly or discordantly; of these: 6030068 mates make up the pairs; of these: 5637716 (93.49%) aligned 0 times 280642 (4.65%) aligned exactly 1 time 111710 (1.85%) aligned >1 times 85.45% overall alignment rate Time searching: 00:42:06 Overall time: 00:42:06 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] 1360624 / 16341968 = 0.0833 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 08:26:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.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 08:26:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:26:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:26:07: 1000000 INFO @ Fri, 26 Jun 2020 08:26:12: 2000000 INFO @ Fri, 26 Jun 2020 08:26:17: 3000000 INFO @ Fri, 26 Jun 2020 08:26:22: 4000000 INFO @ Fri, 26 Jun 2020 08:26:27: 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 08:26:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.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 08:26:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:26:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:26:33: 6000000 INFO @ Fri, 26 Jun 2020 08:26:38: 1000000 INFO @ Fri, 26 Jun 2020 08:26:39: 7000000 INFO @ Fri, 26 Jun 2020 08:26:44: 2000000 INFO @ Fri, 26 Jun 2020 08:26:45: 8000000 INFO @ Fri, 26 Jun 2020 08:26:50: 3000000 INFO @ Fri, 26 Jun 2020 08:26:51: 9000000 INFO @ Fri, 26 Jun 2020 08:26:56: 4000000 INFO @ Fri, 26 Jun 2020 08:26:57: 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 08:27:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.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 08:27:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:27:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:27:02: 5000000 INFO @ Fri, 26 Jun 2020 08:27:03: 11000000 INFO @ Fri, 26 Jun 2020 08:27:07: 1000000 INFO @ Fri, 26 Jun 2020 08:27:08: 6000000 INFO @ Fri, 26 Jun 2020 08:27:09: 12000000 INFO @ Fri, 26 Jun 2020 08:27:12: 2000000 INFO @ Fri, 26 Jun 2020 08:27:14: 7000000 INFO @ Fri, 26 Jun 2020 08:27:15: 13000000 INFO @ Fri, 26 Jun 2020 08:27:17: 3000000 INFO @ Fri, 26 Jun 2020 08:27:20: 8000000 INFO @ Fri, 26 Jun 2020 08:27:21: 14000000 INFO @ Fri, 26 Jun 2020 08:27:22: 4000000 INFO @ Fri, 26 Jun 2020 08:27:26: 9000000 INFO @ Fri, 26 Jun 2020 08:27:27: 15000000 INFO @ Fri, 26 Jun 2020 08:27:27: 5000000 INFO @ Fri, 26 Jun 2020 08:27:32: 10000000 INFO @ Fri, 26 Jun 2020 08:27:32: 6000000 INFO @ Fri, 26 Jun 2020 08:27:33: 16000000 INFO @ Fri, 26 Jun 2020 08:27:38: 7000000 INFO @ Fri, 26 Jun 2020 08:27:38: 11000000 INFO @ Fri, 26 Jun 2020 08:27:39: 17000000 INFO @ Fri, 26 Jun 2020 08:27:43: 8000000 INFO @ Fri, 26 Jun 2020 08:27:44: 12000000 INFO @ Fri, 26 Jun 2020 08:27:45: 18000000 INFO @ Fri, 26 Jun 2020 08:27:48: 9000000 INFO @ Fri, 26 Jun 2020 08:27:51: 13000000 INFO @ Fri, 26 Jun 2020 08:27:51: 19000000 INFO @ Fri, 26 Jun 2020 08:27:53: 10000000 INFO @ Fri, 26 Jun 2020 08:27:57: 14000000 INFO @ Fri, 26 Jun 2020 08:27:57: 20000000 INFO @ Fri, 26 Jun 2020 08:27:58: 11000000 INFO @ Fri, 26 Jun 2020 08:28:03: 15000000 INFO @ Fri, 26 Jun 2020 08:28:03: 12000000 INFO @ Fri, 26 Jun 2020 08:28:04: 21000000 INFO @ Fri, 26 Jun 2020 08:28:08: 13000000 INFO @ Fri, 26 Jun 2020 08:28:09: 16000000 INFO @ Fri, 26 Jun 2020 08:28:10: 22000000 INFO @ Fri, 26 Jun 2020 08:28:14: 14000000 INFO @ Fri, 26 Jun 2020 08:28:15: 17000000 INFO @ Fri, 26 Jun 2020 08:28:16: 23000000 INFO @ Fri, 26 Jun 2020 08:28:19: 15000000 INFO @ Fri, 26 Jun 2020 08:28:21: 18000000 INFO @ Fri, 26 Jun 2020 08:28:22: 24000000 INFO @ Fri, 26 Jun 2020 08:28:24: 16000000 INFO @ Fri, 26 Jun 2020 08:28:27: 19000000 INFO @ Fri, 26 Jun 2020 08:28:27: 25000000 INFO @ Fri, 26 Jun 2020 08:28:29: 17000000 INFO @ Fri, 26 Jun 2020 08:28:33: 20000000 INFO @ Fri, 26 Jun 2020 08:28:33: 26000000 INFO @ Fri, 26 Jun 2020 08:28:34: 18000000 INFO @ Fri, 26 Jun 2020 08:28:39: 21000000 INFO @ Fri, 26 Jun 2020 08:28:39: 19000000 INFO @ Fri, 26 Jun 2020 08:28:39: 27000000 INFO @ Fri, 26 Jun 2020 08:28:44: 20000000 INFO @ Fri, 26 Jun 2020 08:28:45: 22000000 INFO @ Fri, 26 Jun 2020 08:28:45: 28000000 INFO @ Fri, 26 Jun 2020 08:28:49: 21000000 INFO @ Fri, 26 Jun 2020 08:28:51: 23000000 INFO @ Fri, 26 Jun 2020 08:28:51: 29000000 INFO @ Fri, 26 Jun 2020 08:28:55: 22000000 INFO @ Fri, 26 Jun 2020 08:28:57: 30000000 INFO @ Fri, 26 Jun 2020 08:28:57: 24000000 INFO @ Fri, 26 Jun 2020 08:28:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:28:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:28:59: #1 total tags in treatment: 14984063 INFO @ Fri, 26 Jun 2020 08:28:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:28:59: #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 08:28:59: #1 tags after filtering in treatment: 13816859 INFO @ Fri, 26 Jun 2020 08:28:59: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:28:59: #1 finished! INFO @ Fri, 26 Jun 2020 08:28:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:00: #2 number of paired peaks: 509 WARNING @ Fri, 26 Jun 2020 08:29:00: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Fri, 26 Jun 2020 08:29:00: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:00: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:00: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:00: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:00: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 08:29:00: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 08:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.05_model.r INFO @ Fri, 26 Jun 2020 08:29:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:29:01: 23000000 INFO @ Fri, 26 Jun 2020 08:29:04: 25000000 INFO @ Fri, 26 Jun 2020 08:29:07: 24000000 INFO @ Fri, 26 Jun 2020 08:29:10: 26000000 INFO @ Fri, 26 Jun 2020 08:29:13: 25000000 INFO @ Fri, 26 Jun 2020 08:29:16: 27000000 INFO @ Fri, 26 Jun 2020 08:29:19: 26000000 INFO @ Fri, 26 Jun 2020 08:29:23: 28000000 INFO @ Fri, 26 Jun 2020 08:29:24: 27000000 INFO @ Fri, 26 Jun 2020 08:29:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:29:30: 28000000 INFO @ Fri, 26 Jun 2020 08:29:31: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:29:36: 29000000 INFO @ Fri, 26 Jun 2020 08:29:37: 30000000 INFO @ Fri, 26 Jun 2020 08:29:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:29:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:29:40: #1 total tags in treatment: 14984063 INFO @ Fri, 26 Jun 2020 08:29:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:29:40: #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 08:29:40: #1 tags after filtering in treatment: 13816859 INFO @ Fri, 26 Jun 2020 08:29:40: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:29:40: #1 finished! INFO @ Fri, 26 Jun 2020 08:29:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:41: #2 number of paired peaks: 509 WARNING @ Fri, 26 Jun 2020 08:29:41: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Fri, 26 Jun 2020 08:29:41: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:41: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:41: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:41: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:41: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 08:29:41: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 08:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.10_model.r INFO @ Fri, 26 Jun 2020 08:29:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:29:42: 30000000 INFO @ Fri, 26 Jun 2020 08:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.05_summits.bed INFO @ Fri, 26 Jun 2020 08:29:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8912 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:29:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:29:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:29:44: #1 total tags in treatment: 14984063 INFO @ Fri, 26 Jun 2020 08:29:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:29:44: #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 08:29:44: #1 tags after filtering in treatment: 13816859 INFO @ Fri, 26 Jun 2020 08:29:44: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 08:29:44: #1 finished! INFO @ Fri, 26 Jun 2020 08:29:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:45: #2 number of paired peaks: 509 WARNING @ Fri, 26 Jun 2020 08:29:45: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Fri, 26 Jun 2020 08:29:45: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:45: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:45: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:45: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:45: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 08:29:45: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 08:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.20_model.r INFO @ Fri, 26 Jun 2020 08:29:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.10_summits.bed INFO @ Fri, 26 Jun 2020 08:30:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5594 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021230/SRX1021230.20_summits.bed INFO @ Fri, 26 Jun 2020 08:30:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2950 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。