Job ID = 6627010 SRX = SRX8325342 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14001733 spots for SRR11772148/SRR11772148.sra Written 14001733 spots for SRR11772148/SRR11772148.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627506 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:41:47 14001733 reads; of these: 14001733 (100.00%) were paired; of these: 3471510 (24.79%) aligned concordantly 0 times 1578979 (11.28%) aligned concordantly exactly 1 time 8951244 (63.93%) aligned concordantly >1 times ---- 3471510 pairs aligned concordantly 0 times; of these: 318641 (9.18%) aligned discordantly 1 time ---- 3152869 pairs aligned 0 times concordantly or discordantly; of these: 6305738 mates make up the pairs; of these: 2966905 (47.05%) aligned 0 times 1061461 (16.83%) aligned exactly 1 time 2277372 (36.12%) aligned >1 times 89.41% overall alignment rate Time searching: 01:41:47 Overall time: 01:41:47 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] 2749077 / 9976124 = 0.2756 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 @ Tue, 14 Jul 2020 11:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.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 @ Tue, 14 Jul 2020 11:13:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:13:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:14:01: 1000000 INFO @ Tue, 14 Jul 2020 11:14:08: 2000000 INFO @ Tue, 14 Jul 2020 11:14:16: 3000000 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 @ Tue, 14 Jul 2020 11:14:23: 4000000 INFO @ Tue, 14 Jul 2020 11:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.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 @ Tue, 14 Jul 2020 11:14:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:14:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:14:31: 5000000 INFO @ Tue, 14 Jul 2020 11:14:31: 1000000 INFO @ Tue, 14 Jul 2020 11:14:38: 6000000 INFO @ Tue, 14 Jul 2020 11:14:39: 2000000 INFO @ Tue, 14 Jul 2020 11:14:45: 7000000 INFO @ Tue, 14 Jul 2020 11:14:47: 3000000 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 @ Tue, 14 Jul 2020 11:14:53: 8000000 INFO @ Tue, 14 Jul 2020 11:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.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 @ Tue, 14 Jul 2020 11:14:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:14:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:14:55: 4000000 INFO @ Tue, 14 Jul 2020 11:15:03: 9000000 INFO @ Tue, 14 Jul 2020 11:15:03: 1000000 INFO @ Tue, 14 Jul 2020 11:15:04: 5000000 INFO @ Tue, 14 Jul 2020 11:15:12: 10000000 INFO @ Tue, 14 Jul 2020 11:15:13: 6000000 INFO @ Tue, 14 Jul 2020 11:15:14: 2000000 INFO @ Tue, 14 Jul 2020 11:15:21: 11000000 INFO @ Tue, 14 Jul 2020 11:15:22: 7000000 INFO @ Tue, 14 Jul 2020 11:15:24: 3000000 INFO @ Tue, 14 Jul 2020 11:15:30: 12000000 INFO @ Tue, 14 Jul 2020 11:15:31: 8000000 INFO @ Tue, 14 Jul 2020 11:15:35: 4000000 INFO @ Tue, 14 Jul 2020 11:15:39: 13000000 INFO @ Tue, 14 Jul 2020 11:15:41: 9000000 INFO @ Tue, 14 Jul 2020 11:15:45: 5000000 INFO @ Tue, 14 Jul 2020 11:15:48: 14000000 INFO @ Tue, 14 Jul 2020 11:15:51: 10000000 INFO @ Tue, 14 Jul 2020 11:15:55: 6000000 INFO @ Tue, 14 Jul 2020 11:15:57: 15000000 INFO @ Tue, 14 Jul 2020 11:16:02: 11000000 INFO @ Tue, 14 Jul 2020 11:16:04: 7000000 INFO @ Tue, 14 Jul 2020 11:16:07: 16000000 INFO @ Tue, 14 Jul 2020 11:16:11: 12000000 INFO @ Tue, 14 Jul 2020 11:16:14: 8000000 INFO @ Tue, 14 Jul 2020 11:16:16: 17000000 INFO @ Tue, 14 Jul 2020 11:16:20: 13000000 INFO @ Tue, 14 Jul 2020 11:16:23: 9000000 INFO @ Tue, 14 Jul 2020 11:16:25: 18000000 INFO @ Tue, 14 Jul 2020 11:16:29: 14000000 INFO @ Tue, 14 Jul 2020 11:16:33: 10000000 INFO @ Tue, 14 Jul 2020 11:16:34: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:16:38: 15000000 INFO @ Tue, 14 Jul 2020 11:16:39: #1 tag size is determined as 114 bps INFO @ Tue, 14 Jul 2020 11:16:39: #1 tag size = 114 INFO @ Tue, 14 Jul 2020 11:16:39: #1 total tags in treatment: 7797872 INFO @ Tue, 14 Jul 2020 11:16:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:16:39: #1 tags after filtering in treatment: 4967050 INFO @ Tue, 14 Jul 2020 11:16:39: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 14 Jul 2020 11:16:39: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:40: #2 number of paired peaks: 7920 INFO @ Tue, 14 Jul 2020 11:16:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:40: #2 predicted fragment length is 235 bps INFO @ Tue, 14 Jul 2020 11:16:40: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 14 Jul 2020 11:16:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.05_model.r INFO @ Tue, 14 Jul 2020 11:16:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:16:43: 11000000 INFO @ Tue, 14 Jul 2020 11:16:47: 16000000 INFO @ Tue, 14 Jul 2020 11:16:53: 12000000 INFO @ Tue, 14 Jul 2020 11:16:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:16:56: 17000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.05_summits.bed INFO @ Tue, 14 Jul 2020 11:17:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9101 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:03: 13000000 INFO @ Tue, 14 Jul 2020 11:17:05: 18000000 INFO @ Tue, 14 Jul 2020 11:17:13: 14000000 INFO @ Tue, 14 Jul 2020 11:17:15: 19000000 INFO @ Tue, 14 Jul 2020 11:17:20: #1 tag size is determined as 114 bps INFO @ Tue, 14 Jul 2020 11:17:20: #1 tag size = 114 INFO @ Tue, 14 Jul 2020 11:17:20: #1 total tags in treatment: 7797872 INFO @ Tue, 14 Jul 2020 11:17:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:17:20: #1 tags after filtering in treatment: 4967050 INFO @ Tue, 14 Jul 2020 11:17:20: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 14 Jul 2020 11:17:20: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:21: #2 number of paired peaks: 7920 INFO @ Tue, 14 Jul 2020 11:17:21: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:21: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:21: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:21: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:21: #2 predicted fragment length is 235 bps INFO @ Tue, 14 Jul 2020 11:17:21: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 14 Jul 2020 11:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.10_model.r INFO @ Tue, 14 Jul 2020 11:17:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:23: 15000000 INFO @ Tue, 14 Jul 2020 11:17:33: 16000000 INFO @ Tue, 14 Jul 2020 11:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.10_summits.bed INFO @ Tue, 14 Jul 2020 11:17:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7312 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:42: 17000000 INFO @ Tue, 14 Jul 2020 11:17:52: 18000000 INFO @ Tue, 14 Jul 2020 11:18:02: 19000000 INFO @ Tue, 14 Jul 2020 11:18:07: #1 tag size is determined as 114 bps INFO @ Tue, 14 Jul 2020 11:18:07: #1 tag size = 114 INFO @ Tue, 14 Jul 2020 11:18:07: #1 total tags in treatment: 7797872 INFO @ Tue, 14 Jul 2020 11:18:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:18:07: #1 tags after filtering in treatment: 4967050 INFO @ Tue, 14 Jul 2020 11:18:07: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 14 Jul 2020 11:18:07: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:08: #2 number of paired peaks: 7920 INFO @ Tue, 14 Jul 2020 11:18:08: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:08: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:08: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:08: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:08: #2 predicted fragment length is 235 bps INFO @ Tue, 14 Jul 2020 11:18:08: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 14 Jul 2020 11:18:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.20_model.r INFO @ Tue, 14 Jul 2020 11:18:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:18:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325342/SRX8325342.20_summits.bed INFO @ Tue, 14 Jul 2020 11:18:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5456 records, 4 fields): 7 millis CompletedMACS2peakCalling