Job ID = 14171484 SRX = SRX10971117 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:47:53 prefetch.2.10.7: 1) Downloading 'SRR14631241'... 2021-12-11T02:47:53 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:48:56 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:48:56 prefetch.2.10.7: 1) 'SRR14631241' was downloaded successfully 2021-12-11T02:48:56 prefetch.2.10.7: 'SRR14631241' has 0 unresolved dependencies Read 16195141 spots for SRR14631241/SRR14631241.sra Written 16195141 spots for SRR14631241/SRR14631241.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172161 ("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: 00:52:59 16195141 reads; of these: 16195141 (100.00%) were paired; of these: 2197012 (13.57%) aligned concordantly 0 times 11929681 (73.66%) aligned concordantly exactly 1 time 2068448 (12.77%) aligned concordantly >1 times ---- 2197012 pairs aligned concordantly 0 times; of these: 313679 (14.28%) aligned discordantly 1 time ---- 1883333 pairs aligned 0 times concordantly or discordantly; of these: 3766666 mates make up the pairs; of these: 2502042 (66.43%) aligned 0 times 566082 (15.03%) aligned exactly 1 time 698542 (18.55%) aligned >1 times 92.28% overall alignment rate Time searching: 00:52:59 Overall time: 00:52:59 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] 1402950 / 14149827 = 0.0991 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 @ Sat, 11 Dec 2021 12:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.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 @ Sat, 11 Dec 2021 12:52:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:52:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:52:55: 1000000 INFO @ Sat, 11 Dec 2021 12:53:00: 2000000 INFO @ Sat, 11 Dec 2021 12:53:05: 3000000 INFO @ Sat, 11 Dec 2021 12:53:10: 4000000 INFO @ Sat, 11 Dec 2021 12:53:15: 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 @ Sat, 11 Dec 2021 12:53:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.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 @ Sat, 11 Dec 2021 12:53:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:53:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:53:20: 6000000 INFO @ Sat, 11 Dec 2021 12:53:25: 1000000 INFO @ Sat, 11 Dec 2021 12:53:25: 7000000 INFO @ Sat, 11 Dec 2021 12:53:30: 2000000 INFO @ Sat, 11 Dec 2021 12:53:30: 8000000 INFO @ Sat, 11 Dec 2021 12:53:35: 3000000 INFO @ Sat, 11 Dec 2021 12:53:35: 9000000 INFO @ Sat, 11 Dec 2021 12:53:40: 4000000 INFO @ Sat, 11 Dec 2021 12:53:40: 10000000 INFO @ Sat, 11 Dec 2021 12:53:46: 5000000 INFO @ Sat, 11 Dec 2021 12:53:46: 11000000 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 @ Sat, 11 Dec 2021 12:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.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 @ Sat, 11 Dec 2021 12:53:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:53:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:53:51: 6000000 INFO @ Sat, 11 Dec 2021 12:53:51: 12000000 INFO @ Sat, 11 Dec 2021 12:53:55: 1000000 INFO @ Sat, 11 Dec 2021 12:53:56: 7000000 INFO @ Sat, 11 Dec 2021 12:53:56: 13000000 INFO @ Sat, 11 Dec 2021 12:54:00: 2000000 INFO @ Sat, 11 Dec 2021 12:54:01: 14000000 INFO @ Sat, 11 Dec 2021 12:54:01: 8000000 INFO @ Sat, 11 Dec 2021 12:54:05: 3000000 INFO @ Sat, 11 Dec 2021 12:54:06: 9000000 INFO @ Sat, 11 Dec 2021 12:54:07: 15000000 INFO @ Sat, 11 Dec 2021 12:54:10: 4000000 INFO @ Sat, 11 Dec 2021 12:54:11: 10000000 INFO @ Sat, 11 Dec 2021 12:54:12: 16000000 INFO @ Sat, 11 Dec 2021 12:54:16: 5000000 INFO @ Sat, 11 Dec 2021 12:54:17: 11000000 INFO @ Sat, 11 Dec 2021 12:54:17: 17000000 INFO @ Sat, 11 Dec 2021 12:54:21: 6000000 INFO @ Sat, 11 Dec 2021 12:54:22: 12000000 INFO @ Sat, 11 Dec 2021 12:54:22: 18000000 INFO @ Sat, 11 Dec 2021 12:54:26: 7000000 INFO @ Sat, 11 Dec 2021 12:54:27: 13000000 INFO @ Sat, 11 Dec 2021 12:54:27: 19000000 INFO @ Sat, 11 Dec 2021 12:54:31: 8000000 INFO @ Sat, 11 Dec 2021 12:54:32: 14000000 INFO @ Sat, 11 Dec 2021 12:54:32: 20000000 INFO @ Sat, 11 Dec 2021 12:54:36: 9000000 INFO @ Sat, 11 Dec 2021 12:54:38: 21000000 INFO @ Sat, 11 Dec 2021 12:54:38: 15000000 INFO @ Sat, 11 Dec 2021 12:54:41: 10000000 INFO @ Sat, 11 Dec 2021 12:54:43: 22000000 INFO @ Sat, 11 Dec 2021 12:54:43: 16000000 INFO @ Sat, 11 Dec 2021 12:54:46: 11000000 INFO @ Sat, 11 Dec 2021 12:54:48: 23000000 INFO @ Sat, 11 Dec 2021 12:54:48: 17000000 INFO @ Sat, 11 Dec 2021 12:54:52: 12000000 INFO @ Sat, 11 Dec 2021 12:54:53: 24000000 INFO @ Sat, 11 Dec 2021 12:54:53: 18000000 INFO @ Sat, 11 Dec 2021 12:54:57: 13000000 INFO @ Sat, 11 Dec 2021 12:54:58: 25000000 INFO @ Sat, 11 Dec 2021 12:54:58: 19000000 INFO @ Sat, 11 Dec 2021 12:55:02: 14000000 INFO @ Sat, 11 Dec 2021 12:55:03: 26000000 INFO @ Sat, 11 Dec 2021 12:55:03: 20000000 INFO @ Sat, 11 Dec 2021 12:55:07: 15000000 INFO @ Sat, 11 Dec 2021 12:55:09: 27000000 INFO @ Sat, 11 Dec 2021 12:55:09: 21000000 INFO @ Sat, 11 Dec 2021 12:55:09: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:55:09: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:55:09: #1 total tags in treatment: 12609968 INFO @ Sat, 11 Dec 2021 12:55:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:55:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:55:09: #1 tags after filtering in treatment: 11785773 INFO @ Sat, 11 Dec 2021 12:55:09: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 12:55:09: #1 finished! INFO @ Sat, 11 Dec 2021 12:55:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:55:10: #2 number of paired peaks: 843 WARNING @ Sat, 11 Dec 2021 12:55:10: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sat, 11 Dec 2021 12:55:10: start model_add_line... INFO @ Sat, 11 Dec 2021 12:55:10: start X-correlation... INFO @ Sat, 11 Dec 2021 12:55:10: end of X-cor INFO @ Sat, 11 Dec 2021 12:55:10: #2 finished! INFO @ Sat, 11 Dec 2021 12:55:10: #2 predicted fragment length is 241 bps INFO @ Sat, 11 Dec 2021 12:55:10: #2 alternative fragment length(s) may be 241 bps INFO @ Sat, 11 Dec 2021 12:55:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.05_model.r INFO @ Sat, 11 Dec 2021 12:55:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:55:13: 16000000 INFO @ Sat, 11 Dec 2021 12:55:14: 22000000 INFO @ Sat, 11 Dec 2021 12:55:18: 17000000 INFO @ Sat, 11 Dec 2021 12:55:19: 23000000 INFO @ Sat, 11 Dec 2021 12:55:23: 18000000 INFO @ Sat, 11 Dec 2021 12:55:24: 24000000 INFO @ Sat, 11 Dec 2021 12:55:28: 19000000 INFO @ Sat, 11 Dec 2021 12:55:29: 25000000 INFO @ Sat, 11 Dec 2021 12:55:33: 20000000 INFO @ Sat, 11 Dec 2021 12:55:34: 26000000 INFO @ Sat, 11 Dec 2021 12:55:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:55:38: 21000000 INFO @ Sat, 11 Dec 2021 12:55:40: 27000000 INFO @ Sat, 11 Dec 2021 12:55:40: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:55:40: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:55:40: #1 total tags in treatment: 12609968 INFO @ Sat, 11 Dec 2021 12:55:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:55:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:55:41: #1 tags after filtering in treatment: 11785773 INFO @ Sat, 11 Dec 2021 12:55:41: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 12:55:41: #1 finished! INFO @ Sat, 11 Dec 2021 12:55:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:55:41: #2 number of paired peaks: 843 WARNING @ Sat, 11 Dec 2021 12:55:41: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sat, 11 Dec 2021 12:55:41: start model_add_line... INFO @ Sat, 11 Dec 2021 12:55:42: start X-correlation... INFO @ Sat, 11 Dec 2021 12:55:42: end of X-cor INFO @ Sat, 11 Dec 2021 12:55:42: #2 finished! INFO @ Sat, 11 Dec 2021 12:55:42: #2 predicted fragment length is 241 bps INFO @ Sat, 11 Dec 2021 12:55:42: #2 alternative fragment length(s) may be 241 bps INFO @ Sat, 11 Dec 2021 12:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.10_model.r INFO @ Sat, 11 Dec 2021 12:55:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:55:43: 22000000 INFO @ Sat, 11 Dec 2021 12:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.05_summits.bed INFO @ Sat, 11 Dec 2021 12:55:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2863 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:55:48: 23000000 INFO @ Sat, 11 Dec 2021 12:55:53: 24000000 INFO @ Sat, 11 Dec 2021 12:55:58: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:56:03: 26000000 INFO @ Sat, 11 Dec 2021 12:56:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:56:09: 27000000 INFO @ Sat, 11 Dec 2021 12:56:09: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:56:09: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:56:09: #1 total tags in treatment: 12609968 INFO @ Sat, 11 Dec 2021 12:56:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:56:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:56:10: #1 tags after filtering in treatment: 11785773 INFO @ Sat, 11 Dec 2021 12:56:10: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 12:56:10: #1 finished! INFO @ Sat, 11 Dec 2021 12:56:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:56:10: #2 number of paired peaks: 843 WARNING @ Sat, 11 Dec 2021 12:56:10: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sat, 11 Dec 2021 12:56:10: start model_add_line... INFO @ Sat, 11 Dec 2021 12:56:11: start X-correlation... INFO @ Sat, 11 Dec 2021 12:56:11: end of X-cor INFO @ Sat, 11 Dec 2021 12:56:11: #2 finished! INFO @ Sat, 11 Dec 2021 12:56:11: #2 predicted fragment length is 241 bps INFO @ Sat, 11 Dec 2021 12:56:11: #2 alternative fragment length(s) may be 241 bps INFO @ Sat, 11 Dec 2021 12:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.20_model.r INFO @ Sat, 11 Dec 2021 12:56:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.10_summits.bed INFO @ Sat, 11 Dec 2021 12:56:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2099 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:56:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:56:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971117/SRX10971117.20_summits.bed INFO @ Sat, 11 Dec 2021 12:56:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1516 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。