Job ID = 6497814 SRX = SRX1728717 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:36:49 prefetch.2.10.7: 1) Downloading 'SRR3452734'... 2020-06-25T22:36:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:39:30 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:39:30 prefetch.2.10.7: 1) 'SRR3452734' was downloaded successfully 2020-06-25T22:39:30 prefetch.2.10.7: 'SRR3452734' has 0 unresolved dependencies Read 23404572 spots for SRR3452734/SRR3452734.sra Written 23404572 spots for SRR3452734/SRR3452734.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: 00:56:06 23404572 reads; of these: 23404572 (100.00%) were paired; of these: 2529832 (10.81%) aligned concordantly 0 times 15159511 (64.77%) aligned concordantly exactly 1 time 5715229 (24.42%) aligned concordantly >1 times ---- 2529832 pairs aligned concordantly 0 times; of these: 223009 (8.82%) aligned discordantly 1 time ---- 2306823 pairs aligned 0 times concordantly or discordantly; of these: 4613646 mates make up the pairs; of these: 3571522 (77.41%) aligned 0 times 693133 (15.02%) aligned exactly 1 time 348991 (7.56%) aligned >1 times 92.37% overall alignment rate Time searching: 00:56:06 Overall time: 00:56:06 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 20 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] 3586136 / 21075961 = 0.1702 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 08:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.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 08:49:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:49:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:49:38: 1000000 INFO @ Fri, 26 Jun 2020 08:49:43: 2000000 INFO @ Fri, 26 Jun 2020 08:49:47: 3000000 INFO @ Fri, 26 Jun 2020 08:49:52: 4000000 INFO @ Fri, 26 Jun 2020 08:49:57: 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 08:50:01: 6000000 INFO @ Fri, 26 Jun 2020 08:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.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 08:50:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:06: 7000000 INFO @ Fri, 26 Jun 2020 08:50:08: 1000000 INFO @ Fri, 26 Jun 2020 08:50:11: 8000000 INFO @ Fri, 26 Jun 2020 08:50:12: 2000000 INFO @ Fri, 26 Jun 2020 08:50:16: 9000000 INFO @ Fri, 26 Jun 2020 08:50:17: 3000000 INFO @ Fri, 26 Jun 2020 08:50:21: 10000000 INFO @ Fri, 26 Jun 2020 08:50:22: 4000000 INFO @ Fri, 26 Jun 2020 08:50:26: 11000000 INFO @ Fri, 26 Jun 2020 08:50:27: 5000000 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 08:50:31: 12000000 INFO @ Fri, 26 Jun 2020 08:50:31: 6000000 INFO @ Fri, 26 Jun 2020 08:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.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 08:50:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:36: 13000000 INFO @ Fri, 26 Jun 2020 08:50:36: 7000000 INFO @ Fri, 26 Jun 2020 08:50:38: 1000000 INFO @ Fri, 26 Jun 2020 08:50:40: 14000000 INFO @ Fri, 26 Jun 2020 08:50:41: 8000000 INFO @ Fri, 26 Jun 2020 08:50:43: 2000000 INFO @ Fri, 26 Jun 2020 08:50:45: 15000000 INFO @ Fri, 26 Jun 2020 08:50:46: 9000000 INFO @ Fri, 26 Jun 2020 08:50:48: 3000000 INFO @ Fri, 26 Jun 2020 08:50:50: 16000000 INFO @ Fri, 26 Jun 2020 08:50:51: 10000000 INFO @ Fri, 26 Jun 2020 08:50:53: 4000000 INFO @ Fri, 26 Jun 2020 08:50:55: 17000000 INFO @ Fri, 26 Jun 2020 08:50:56: 11000000 INFO @ Fri, 26 Jun 2020 08:50:58: 5000000 INFO @ Fri, 26 Jun 2020 08:51:00: 18000000 INFO @ Fri, 26 Jun 2020 08:51:01: 12000000 INFO @ Fri, 26 Jun 2020 08:51:03: 6000000 INFO @ Fri, 26 Jun 2020 08:51:05: 19000000 INFO @ Fri, 26 Jun 2020 08:51:06: 13000000 INFO @ Fri, 26 Jun 2020 08:51:08: 7000000 INFO @ Fri, 26 Jun 2020 08:51:09: 20000000 INFO @ Fri, 26 Jun 2020 08:51:11: 14000000 INFO @ Fri, 26 Jun 2020 08:51:13: 8000000 INFO @ Fri, 26 Jun 2020 08:51:14: 21000000 INFO @ Fri, 26 Jun 2020 08:51:16: 15000000 INFO @ Fri, 26 Jun 2020 08:51:18: 9000000 INFO @ Fri, 26 Jun 2020 08:51:19: 22000000 INFO @ Fri, 26 Jun 2020 08:51:21: 16000000 INFO @ Fri, 26 Jun 2020 08:51:23: 10000000 INFO @ Fri, 26 Jun 2020 08:51:25: 23000000 INFO @ Fri, 26 Jun 2020 08:51:26: 17000000 INFO @ Fri, 26 Jun 2020 08:51:28: 11000000 INFO @ Fri, 26 Jun 2020 08:51:30: 24000000 INFO @ Fri, 26 Jun 2020 08:51:31: 18000000 INFO @ Fri, 26 Jun 2020 08:51:33: 12000000 INFO @ Fri, 26 Jun 2020 08:51:35: 25000000 INFO @ Fri, 26 Jun 2020 08:51:37: 19000000 INFO @ Fri, 26 Jun 2020 08:51:38: 13000000 INFO @ Fri, 26 Jun 2020 08:51:40: 26000000 INFO @ Fri, 26 Jun 2020 08:51:42: 20000000 INFO @ Fri, 26 Jun 2020 08:51:43: 14000000 INFO @ Fri, 26 Jun 2020 08:51:45: 27000000 INFO @ Fri, 26 Jun 2020 08:51:46: 21000000 INFO @ Fri, 26 Jun 2020 08:51:48: 15000000 INFO @ Fri, 26 Jun 2020 08:51:50: 28000000 INFO @ Fri, 26 Jun 2020 08:51:51: 22000000 INFO @ Fri, 26 Jun 2020 08:51:53: 16000000 INFO @ Fri, 26 Jun 2020 08:51:54: 29000000 INFO @ Fri, 26 Jun 2020 08:51:56: 23000000 INFO @ Fri, 26 Jun 2020 08:51:57: 17000000 INFO @ Fri, 26 Jun 2020 08:51:59: 30000000 INFO @ Fri, 26 Jun 2020 08:52:01: 24000000 INFO @ Fri, 26 Jun 2020 08:52:03: 18000000 INFO @ Fri, 26 Jun 2020 08:52:04: 31000000 INFO @ Fri, 26 Jun 2020 08:52:06: 25000000 INFO @ Fri, 26 Jun 2020 08:52:08: 19000000 INFO @ Fri, 26 Jun 2020 08:52:09: 32000000 INFO @ Fri, 26 Jun 2020 08:52:11: 26000000 INFO @ Fri, 26 Jun 2020 08:52:12: 20000000 INFO @ Fri, 26 Jun 2020 08:52:13: 33000000 INFO @ Fri, 26 Jun 2020 08:52:15: 27000000 INFO @ Fri, 26 Jun 2020 08:52:17: 21000000 INFO @ Fri, 26 Jun 2020 08:52:18: 34000000 INFO @ Fri, 26 Jun 2020 08:52:20: 28000000 INFO @ Fri, 26 Jun 2020 08:52:22: 22000000 INFO @ Fri, 26 Jun 2020 08:52:23: 35000000 INFO @ Fri, 26 Jun 2020 08:52:25: 29000000 INFO @ Fri, 26 Jun 2020 08:52:27: 23000000 INFO @ Fri, 26 Jun 2020 08:52:28: 36000000 INFO @ Fri, 26 Jun 2020 08:52:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:52:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:52:29: #1 total tags in treatment: 17304411 INFO @ Fri, 26 Jun 2020 08:52:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:29: #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 08:52:29: #1 tags after filtering in treatment: 13972146 INFO @ Fri, 26 Jun 2020 08:52:29: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 26 Jun 2020 08:52:29: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:30: #2 number of paired peaks: 2041 INFO @ Fri, 26 Jun 2020 08:52:30: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:30: 30000000 INFO @ Fri, 26 Jun 2020 08:52:30: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:30: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:30: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:30: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 08:52:30: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 08:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.05_model.r INFO @ Fri, 26 Jun 2020 08:52:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:32: 24000000 INFO @ Fri, 26 Jun 2020 08:52:35: 31000000 INFO @ Fri, 26 Jun 2020 08:52:37: 25000000 INFO @ Fri, 26 Jun 2020 08:52:40: 32000000 INFO @ Fri, 26 Jun 2020 08:52:42: 26000000 INFO @ Fri, 26 Jun 2020 08:52:45: 33000000 INFO @ Fri, 26 Jun 2020 08:52:46: 27000000 INFO @ Fri, 26 Jun 2020 08:52:49: 34000000 INFO @ Fri, 26 Jun 2020 08:52:51: 28000000 INFO @ Fri, 26 Jun 2020 08:52:54: 35000000 INFO @ Fri, 26 Jun 2020 08:52:56: 29000000 INFO @ Fri, 26 Jun 2020 08:52:59: 36000000 INFO @ Fri, 26 Jun 2020 08:53:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:53:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:53:00: #1 total tags in treatment: 17304411 INFO @ Fri, 26 Jun 2020 08:53:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:53:00: #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 08:53:00: #1 tags after filtering in treatment: 13972146 INFO @ Fri, 26 Jun 2020 08:53:00: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 26 Jun 2020 08:53:00: #1 finished! INFO @ Fri, 26 Jun 2020 08:53:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:53:01: 30000000 INFO @ Fri, 26 Jun 2020 08:53:01: #2 number of paired peaks: 2041 INFO @ Fri, 26 Jun 2020 08:53:01: start model_add_line... INFO @ Fri, 26 Jun 2020 08:53:01: start X-correlation... INFO @ Fri, 26 Jun 2020 08:53:01: end of X-cor INFO @ Fri, 26 Jun 2020 08:53:01: #2 finished! INFO @ Fri, 26 Jun 2020 08:53:01: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 08:53:01: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 08:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.10_model.r INFO @ Fri, 26 Jun 2020 08:53:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:53:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:53:05: 31000000 INFO @ Fri, 26 Jun 2020 08:53:10: 32000000 INFO @ Fri, 26 Jun 2020 08:53:14: 33000000 INFO @ Fri, 26 Jun 2020 08:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.05_summits.bed INFO @ Fri, 26 Jun 2020 08:53:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5429 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:53:18: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:53:23: 35000000 INFO @ Fri, 26 Jun 2020 08:53:27: 36000000 INFO @ Fri, 26 Jun 2020 08:53:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:53:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:53:28: #1 total tags in treatment: 17304411 INFO @ Fri, 26 Jun 2020 08:53:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:53:28: #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 08:53:28: #1 tags after filtering in treatment: 13972146 INFO @ Fri, 26 Jun 2020 08:53:28: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 26 Jun 2020 08:53:28: #1 finished! INFO @ Fri, 26 Jun 2020 08:53:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:53:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:53:29: #2 number of paired peaks: 2041 INFO @ Fri, 26 Jun 2020 08:53:29: start model_add_line... INFO @ Fri, 26 Jun 2020 08:53:29: start X-correlation... INFO @ Fri, 26 Jun 2020 08:53:29: end of X-cor INFO @ Fri, 26 Jun 2020 08:53:29: #2 finished! INFO @ Fri, 26 Jun 2020 08:53:29: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 08:53:29: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 08:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.20_model.r INFO @ Fri, 26 Jun 2020 08:53:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:53:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.10_summits.bed INFO @ Fri, 26 Jun 2020 08:53:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3612 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:54:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728717/SRX1728717.20_summits.bed INFO @ Fri, 26 Jun 2020 08:54:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2429 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。