Job ID = 14167230 SRX = SRX8973513 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22972851 spots for SRR12901793/SRR12901793.sra Written 22972851 spots for SRR12901793/SRR12901793.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167907 ("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: 00:28:39 22972851 reads; of these: 22972851 (100.00%) were paired; of these: 9848412 (42.87%) aligned concordantly 0 times 9275206 (40.37%) aligned concordantly exactly 1 time 3849233 (16.76%) aligned concordantly >1 times ---- 9848412 pairs aligned concordantly 0 times; of these: 204414 (2.08%) aligned discordantly 1 time ---- 9643998 pairs aligned 0 times concordantly or discordantly; of these: 19287996 mates make up the pairs; of these: 17939853 (93.01%) aligned 0 times 837951 (4.34%) aligned exactly 1 time 510192 (2.65%) aligned >1 times 60.95% overall alignment rate Time searching: 00:28:39 Overall time: 00:28:39 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] 473472 / 13317825 = 0.0356 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 11:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.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 11:45:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:45:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:45:23: 1000000 INFO @ Fri, 10 Dec 2021 11:45:29: 2000000 INFO @ Fri, 10 Dec 2021 11:45:35: 3000000 INFO @ Fri, 10 Dec 2021 11:45:41: 4000000 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 11:45:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.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 11:45:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:45:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:45:47: 5000000 INFO @ Fri, 10 Dec 2021 11:45:53: 1000000 INFO @ Fri, 10 Dec 2021 11:45:54: 6000000 INFO @ Fri, 10 Dec 2021 11:45:59: 2000000 INFO @ Fri, 10 Dec 2021 11:46:00: 7000000 INFO @ Fri, 10 Dec 2021 11:46:05: 3000000 INFO @ Fri, 10 Dec 2021 11:46:07: 8000000 INFO @ Fri, 10 Dec 2021 11:46:11: 4000000 INFO @ Fri, 10 Dec 2021 11:46:14: 9000000 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 11:46:17: 5000000 INFO @ Fri, 10 Dec 2021 11:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.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 11:46:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:46:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:46:20: 10000000 INFO @ Fri, 10 Dec 2021 11:46:23: 6000000 INFO @ Fri, 10 Dec 2021 11:46:24: 1000000 INFO @ Fri, 10 Dec 2021 11:46:27: 11000000 INFO @ Fri, 10 Dec 2021 11:46:29: 7000000 INFO @ Fri, 10 Dec 2021 11:46:31: 2000000 INFO @ Fri, 10 Dec 2021 11:46:34: 12000000 INFO @ Fri, 10 Dec 2021 11:46:35: 8000000 INFO @ Fri, 10 Dec 2021 11:46:38: 3000000 INFO @ Fri, 10 Dec 2021 11:46:40: 13000000 INFO @ Fri, 10 Dec 2021 11:46:41: 9000000 INFO @ Fri, 10 Dec 2021 11:46:45: 4000000 INFO @ Fri, 10 Dec 2021 11:46:47: 14000000 INFO @ Fri, 10 Dec 2021 11:46:47: 10000000 INFO @ Fri, 10 Dec 2021 11:46:52: 5000000 INFO @ Fri, 10 Dec 2021 11:46:53: 11000000 INFO @ Fri, 10 Dec 2021 11:46:53: 15000000 INFO @ Fri, 10 Dec 2021 11:46:59: 6000000 INFO @ Fri, 10 Dec 2021 11:46:59: 12000000 INFO @ Fri, 10 Dec 2021 11:47:00: 16000000 INFO @ Fri, 10 Dec 2021 11:47:05: 13000000 INFO @ Fri, 10 Dec 2021 11:47:06: 7000000 INFO @ Fri, 10 Dec 2021 11:47:07: 17000000 INFO @ Fri, 10 Dec 2021 11:47:11: 14000000 INFO @ Fri, 10 Dec 2021 11:47:12: 8000000 INFO @ Fri, 10 Dec 2021 11:47:13: 18000000 INFO @ Fri, 10 Dec 2021 11:47:18: 15000000 INFO @ Fri, 10 Dec 2021 11:47:19: 9000000 INFO @ Fri, 10 Dec 2021 11:47:20: 19000000 INFO @ Fri, 10 Dec 2021 11:47:24: 16000000 INFO @ Fri, 10 Dec 2021 11:47:26: 10000000 INFO @ Fri, 10 Dec 2021 11:47:27: 20000000 INFO @ Fri, 10 Dec 2021 11:47:30: 17000000 INFO @ Fri, 10 Dec 2021 11:47:33: 11000000 INFO @ Fri, 10 Dec 2021 11:47:33: 21000000 INFO @ Fri, 10 Dec 2021 11:47:36: 18000000 INFO @ Fri, 10 Dec 2021 11:47:40: 12000000 INFO @ Fri, 10 Dec 2021 11:47:40: 22000000 INFO @ Fri, 10 Dec 2021 11:47:42: 19000000 INFO @ Fri, 10 Dec 2021 11:47:47: 13000000 INFO @ Fri, 10 Dec 2021 11:47:47: 23000000 INFO @ Fri, 10 Dec 2021 11:47:48: 20000000 INFO @ Fri, 10 Dec 2021 11:47:54: 24000000 INFO @ Fri, 10 Dec 2021 11:47:54: 14000000 INFO @ Fri, 10 Dec 2021 11:47:54: 21000000 INFO @ Fri, 10 Dec 2021 11:48:00: 22000000 INFO @ Fri, 10 Dec 2021 11:48:00: 25000000 INFO @ Fri, 10 Dec 2021 11:48:00: 15000000 INFO @ Fri, 10 Dec 2021 11:48:06: 23000000 INFO @ Fri, 10 Dec 2021 11:48:07: 26000000 INFO @ Fri, 10 Dec 2021 11:48:07: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:48:12: 24000000 INFO @ Fri, 10 Dec 2021 11:48:13: 27000000 INFO @ Fri, 10 Dec 2021 11:48:14: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:48:14: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:48:14: #1 total tags in treatment: 12653406 INFO @ Fri, 10 Dec 2021 11:48:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:48:14: #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 11:48:14: #1 tags after filtering in treatment: 12091102 INFO @ Fri, 10 Dec 2021 11:48:14: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:48:14: #1 finished! INFO @ Fri, 10 Dec 2021 11:48:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:48:14: 17000000 INFO @ Fri, 10 Dec 2021 11:48:15: #2 number of paired peaks: 176 WARNING @ Fri, 10 Dec 2021 11:48:15: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 10 Dec 2021 11:48:15: start model_add_line... INFO @ Fri, 10 Dec 2021 11:48:15: start X-correlation... INFO @ Fri, 10 Dec 2021 11:48:15: end of X-cor INFO @ Fri, 10 Dec 2021 11:48:15: #2 finished! INFO @ Fri, 10 Dec 2021 11:48:15: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 11:48:15: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 11:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.05_model.r INFO @ Fri, 10 Dec 2021 11:48:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:48:18: 25000000 INFO @ Fri, 10 Dec 2021 11:48:21: 18000000 INFO @ Fri, 10 Dec 2021 11:48:24: 26000000 INFO @ Fri, 10 Dec 2021 11:48:28: 19000000 INFO @ Fri, 10 Dec 2021 11:48:30: 27000000 INFO @ Fri, 10 Dec 2021 11:48:30: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:48:30: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:48:30: #1 total tags in treatment: 12653406 INFO @ Fri, 10 Dec 2021 11:48:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:48:30: #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 11:48:31: #1 tags after filtering in treatment: 12091102 INFO @ Fri, 10 Dec 2021 11:48:31: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:48:31: #1 finished! INFO @ Fri, 10 Dec 2021 11:48:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:48:31: #2 number of paired peaks: 176 WARNING @ Fri, 10 Dec 2021 11:48:31: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 10 Dec 2021 11:48:31: start model_add_line... INFO @ Fri, 10 Dec 2021 11:48:31: start X-correlation... INFO @ Fri, 10 Dec 2021 11:48:31: end of X-cor INFO @ Fri, 10 Dec 2021 11:48:31: #2 finished! INFO @ Fri, 10 Dec 2021 11:48:31: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 11:48:31: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 11:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.10_model.r INFO @ Fri, 10 Dec 2021 11:48:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:48:34: 20000000 INFO @ Fri, 10 Dec 2021 11:48:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:48:41: 21000000 INFO @ Fri, 10 Dec 2021 11:48:47: 22000000 INFO @ Fri, 10 Dec 2021 11:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.05_summits.bed INFO @ Fri, 10 Dec 2021 11:48:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1158 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:48:53: 23000000 INFO @ Fri, 10 Dec 2021 11:48:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:49:00: 24000000 INFO @ Fri, 10 Dec 2021 11:49:06: 25000000 INFO @ Fri, 10 Dec 2021 11:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.10_summits.bed INFO @ Fri, 10 Dec 2021 11:49:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:49:12: 26000000 INFO @ Fri, 10 Dec 2021 11:49:18: 27000000 INFO @ Fri, 10 Dec 2021 11:49:18: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:49:18: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:49:18: #1 total tags in treatment: 12653406 INFO @ Fri, 10 Dec 2021 11:49:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:49:18: #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 11:49:19: #1 tags after filtering in treatment: 12091102 INFO @ Fri, 10 Dec 2021 11:49:19: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:49:19: #1 finished! INFO @ Fri, 10 Dec 2021 11:49:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:49:19: #2 number of paired peaks: 176 WARNING @ Fri, 10 Dec 2021 11:49:19: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 10 Dec 2021 11:49:19: start model_add_line... INFO @ Fri, 10 Dec 2021 11:49:19: start X-correlation... INFO @ Fri, 10 Dec 2021 11:49:19: end of X-cor INFO @ Fri, 10 Dec 2021 11:49:19: #2 finished! INFO @ Fri, 10 Dec 2021 11:49:19: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 11:49:19: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 11:49:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.20_model.r INFO @ Fri, 10 Dec 2021 11:49:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:49:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:49:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973513/SRX8973513.20_summits.bed INFO @ Fri, 10 Dec 2021 11:49:55: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (547 records, 4 fields): 2 millis CompletedMACS2peakCalling