Job ID = 14168826 SRX = ERX3978892 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31668681 spots for ERR3975961/ERR3975961.sra Written 31668681 spots for ERR3975961/ERR3975961.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170071 ("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: 02:21:49 31668681 reads; of these: 31668681 (100.00%) were paired; of these: 10949330 (34.57%) aligned concordantly 0 times 15655784 (49.44%) aligned concordantly exactly 1 time 5063567 (15.99%) aligned concordantly >1 times ---- 10949330 pairs aligned concordantly 0 times; of these: 927192 (8.47%) aligned discordantly 1 time ---- 10022138 pairs aligned 0 times concordantly or discordantly; of these: 20044276 mates make up the pairs; of these: 9386632 (46.83%) aligned 0 times 6090866 (30.39%) aligned exactly 1 time 4566778 (22.78%) aligned >1 times 85.18% overall alignment rate Time searching: 02:21:49 Overall time: 02:21:49 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 24 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] 17246540 / 21288763 = 0.8101 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 23:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.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, 10 Dec 2021 23:27:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:27:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:27:15: 1000000 INFO @ Fri, 10 Dec 2021 23:27:20: 2000000 INFO @ Fri, 10 Dec 2021 23:27:25: 3000000 INFO @ Fri, 10 Dec 2021 23:27:30: 4000000 INFO @ Fri, 10 Dec 2021 23:27:35: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 23:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.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, 10 Dec 2021 23:27:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:27:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:27:41: 6000000 INFO @ Fri, 10 Dec 2021 23:27:47: 7000000 INFO @ Fri, 10 Dec 2021 23:27:47: 1000000 INFO @ Fri, 10 Dec 2021 23:27:53: 8000000 INFO @ Fri, 10 Dec 2021 23:27:56: 2000000 INFO @ Fri, 10 Dec 2021 23:27:59: 9000000 INFO @ Fri, 10 Dec 2021 23:28:06: 10000000 INFO @ Fri, 10 Dec 2021 23:28:06: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 23:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.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, 10 Dec 2021 23:28:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:28:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:28:12: 11000000 INFO @ Fri, 10 Dec 2021 23:28:15: 1000000 INFO @ Fri, 10 Dec 2021 23:28:16: 4000000 INFO @ Fri, 10 Dec 2021 23:28:18: 12000000 INFO @ Fri, 10 Dec 2021 23:28:22: 2000000 INFO @ Fri, 10 Dec 2021 23:28:25: 13000000 INFO @ Fri, 10 Dec 2021 23:28:26: 5000000 INFO @ Fri, 10 Dec 2021 23:28:28: 3000000 INFO @ Fri, 10 Dec 2021 23:28:32: 14000000 INFO @ Fri, 10 Dec 2021 23:28:35: 4000000 INFO @ Fri, 10 Dec 2021 23:28:36: 6000000 INFO @ Fri, 10 Dec 2021 23:28:38: 15000000 INFO @ Fri, 10 Dec 2021 23:28:41: 5000000 INFO @ Fri, 10 Dec 2021 23:28:45: 7000000 INFO @ Fri, 10 Dec 2021 23:28:45: 16000000 INFO @ Fri, 10 Dec 2021 23:28:48: 6000000 INFO @ Fri, 10 Dec 2021 23:28:52: 17000000 INFO @ Fri, 10 Dec 2021 23:28:53: 8000000 INFO @ Fri, 10 Dec 2021 23:28:54: 7000000 INFO @ Fri, 10 Dec 2021 23:28:58: 18000000 INFO @ Fri, 10 Dec 2021 23:29:01: 8000000 INFO @ Fri, 10 Dec 2021 23:29:01: 9000000 INFO @ Fri, 10 Dec 2021 23:29:05: 19000000 INFO @ Fri, 10 Dec 2021 23:29:07: 9000000 INFO @ Fri, 10 Dec 2021 23:29:08: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:29:08: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:29:08: #1 total tags in treatment: 4029744 INFO @ Fri, 10 Dec 2021 23:29:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:29:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:29:08: #1 tags after filtering in treatment: 3394824 INFO @ Fri, 10 Dec 2021 23:29:08: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 23:29:08: #1 finished! INFO @ Fri, 10 Dec 2021 23:29:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:29:08: #2 number of paired peaks: 4786 INFO @ Fri, 10 Dec 2021 23:29:08: start model_add_line... INFO @ Fri, 10 Dec 2021 23:29:08: start X-correlation... INFO @ Fri, 10 Dec 2021 23:29:08: end of X-cor INFO @ Fri, 10 Dec 2021 23:29:08: #2 finished! INFO @ Fri, 10 Dec 2021 23:29:08: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 23:29:08: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 23:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.05_model.r INFO @ Fri, 10 Dec 2021 23:29:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:29:10: 10000000 INFO @ Fri, 10 Dec 2021 23:29:13: 10000000 INFO @ Fri, 10 Dec 2021 23:29:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:29:19: 11000000 INFO @ Fri, 10 Dec 2021 23:29:20: 11000000 INFO @ Fri, 10 Dec 2021 23:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.05_summits.bed INFO @ Fri, 10 Dec 2021 23:29:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9507 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:29:28: 12000000 INFO @ Fri, 10 Dec 2021 23:29:28: 12000000 INFO @ Fri, 10 Dec 2021 23:29:36: 13000000 INFO @ Fri, 10 Dec 2021 23:29:37: 13000000 INFO @ Fri, 10 Dec 2021 23:29:42: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:29:46: 14000000 INFO @ Fri, 10 Dec 2021 23:29:49: 15000000 INFO @ Fri, 10 Dec 2021 23:29:55: 15000000 INFO @ Fri, 10 Dec 2021 23:29:56: 16000000 INFO @ Fri, 10 Dec 2021 23:30:02: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:30:05: 16000000 INFO @ Fri, 10 Dec 2021 23:30:09: 18000000 INFO @ Fri, 10 Dec 2021 23:30:13: 17000000 INFO @ Fri, 10 Dec 2021 23:30:16: 19000000 INFO @ Fri, 10 Dec 2021 23:30:18: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:30:18: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:30:18: #1 total tags in treatment: 4029744 INFO @ Fri, 10 Dec 2021 23:30:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:30:19: #1 tags after filtering in treatment: 3394824 INFO @ Fri, 10 Dec 2021 23:30:19: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 23:30:19: #1 finished! INFO @ Fri, 10 Dec 2021 23:30:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:30:19: #2 number of paired peaks: 4786 INFO @ Fri, 10 Dec 2021 23:30:19: start model_add_line... INFO @ Fri, 10 Dec 2021 23:30:19: start X-correlation... INFO @ Fri, 10 Dec 2021 23:30:19: end of X-cor INFO @ Fri, 10 Dec 2021 23:30:19: #2 finished! INFO @ Fri, 10 Dec 2021 23:30:19: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 23:30:19: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 23:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.20_model.r INFO @ Fri, 10 Dec 2021 23:30:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:30:22: 18000000 INFO @ Fri, 10 Dec 2021 23:30:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:30:30: 19000000 INFO @ Fri, 10 Dec 2021 23:30:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:30:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:30:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.20_summits.bed INFO @ Fri, 10 Dec 2021 23:30:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1851 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:30:34: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:30:34: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:30:34: #1 total tags in treatment: 4029744 INFO @ Fri, 10 Dec 2021 23:30:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:30:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:30:34: #1 tags after filtering in treatment: 3394824 INFO @ Fri, 10 Dec 2021 23:30:34: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 23:30:34: #1 finished! INFO @ Fri, 10 Dec 2021 23:30:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:30:35: #2 number of paired peaks: 4786 INFO @ Fri, 10 Dec 2021 23:30:35: start model_add_line... INFO @ Fri, 10 Dec 2021 23:30:35: start X-correlation... INFO @ Fri, 10 Dec 2021 23:30:35: end of X-cor INFO @ Fri, 10 Dec 2021 23:30:35: #2 finished! INFO @ Fri, 10 Dec 2021 23:30:35: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 23:30:35: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 23:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.10_model.r INFO @ Fri, 10 Dec 2021 23:30:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:30:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:30:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:30:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:30:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978892/ERX3978892.10_summits.bed INFO @ Fri, 10 Dec 2021 23:30:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5752 records, 4 fields): 7 millis CompletedMACS2peakCalling