Job ID = 6458343 SRX = SRX5011089 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:33:07 prefetch.2.10.7: 1) Downloading 'SRR8191538'... 2020-06-21T12:33:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:38 prefetch.2.10.7: 1) 'SRR8191538' was downloaded successfully Read 21996208 spots for SRR8191538/SRR8191538.sra Written 21996208 spots for SRR8191538/SRR8191538.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:01 21996208 reads; of these: 21996208 (100.00%) were unpaired; of these: 3363557 (15.29%) aligned 0 times 14174012 (64.44%) aligned exactly 1 time 4458639 (20.27%) aligned >1 times 84.71% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5126738 / 18632651 = 0.2751 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 @ Sun, 21 Jun 2020 21:45:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.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 @ Sun, 21 Jun 2020 21:45:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:53: 1000000 INFO @ Sun, 21 Jun 2020 21:45:59: 2000000 INFO @ Sun, 21 Jun 2020 21:46:06: 3000000 INFO @ Sun, 21 Jun 2020 21:46:12: 4000000 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 @ Sun, 21 Jun 2020 21:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.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 @ Sun, 21 Jun 2020 21:46:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:18: 5000000 INFO @ Sun, 21 Jun 2020 21:46:23: 1000000 INFO @ Sun, 21 Jun 2020 21:46:25: 6000000 INFO @ Sun, 21 Jun 2020 21:46:30: 2000000 INFO @ Sun, 21 Jun 2020 21:46:31: 7000000 INFO @ Sun, 21 Jun 2020 21:46:37: 3000000 INFO @ Sun, 21 Jun 2020 21:46:38: 8000000 INFO @ Sun, 21 Jun 2020 21:46:44: 4000000 INFO @ Sun, 21 Jun 2020 21:46:45: 9000000 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 @ Sun, 21 Jun 2020 21:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.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 @ Sun, 21 Jun 2020 21:46:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:51: 5000000 INFO @ Sun, 21 Jun 2020 21:46:51: 10000000 INFO @ Sun, 21 Jun 2020 21:46:54: 1000000 INFO @ Sun, 21 Jun 2020 21:46:57: 6000000 INFO @ Sun, 21 Jun 2020 21:46:58: 11000000 INFO @ Sun, 21 Jun 2020 21:47:00: 2000000 INFO @ Sun, 21 Jun 2020 21:47:04: 7000000 INFO @ Sun, 21 Jun 2020 21:47:05: 12000000 INFO @ Sun, 21 Jun 2020 21:47:07: 3000000 INFO @ Sun, 21 Jun 2020 21:47:11: 8000000 INFO @ Sun, 21 Jun 2020 21:47:12: 13000000 INFO @ Sun, 21 Jun 2020 21:47:14: 4000000 INFO @ Sun, 21 Jun 2020 21:47:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:16: #1 total tags in treatment: 13505913 INFO @ Sun, 21 Jun 2020 21:47:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:47:16: #1 tags after filtering in treatment: 13505809 INFO @ Sun, 21 Jun 2020 21:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:17: #2 number of paired peaks: 986 WARNING @ Sun, 21 Jun 2020 21:47:17: Fewer paired peaks (986) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 986 pairs to build model! INFO @ Sun, 21 Jun 2020 21:47:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:17: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 21:47:17: #2 alternative fragment length(s) may be 4,116 bps INFO @ Sun, 21 Jun 2020 21:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.05_model.r INFO @ Sun, 21 Jun 2020 21:47:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:17: 9000000 INFO @ Sun, 21 Jun 2020 21:47:21: 5000000 INFO @ Sun, 21 Jun 2020 21:47:24: 10000000 INFO @ Sun, 21 Jun 2020 21:47:27: 6000000 INFO @ Sun, 21 Jun 2020 21:47:31: 11000000 INFO @ Sun, 21 Jun 2020 21:47:34: 7000000 INFO @ Sun, 21 Jun 2020 21:47:38: 12000000 INFO @ Sun, 21 Jun 2020 21:47:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:45: 13000000 INFO @ Sun, 21 Jun 2020 21:47:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:47: 9000000 INFO @ Sun, 21 Jun 2020 21:47:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:49: #1 total tags in treatment: 13505913 INFO @ Sun, 21 Jun 2020 21:47:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:47:49: #1 tags after filtering in treatment: 13505809 INFO @ Sun, 21 Jun 2020 21:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:50: #2 number of paired peaks: 986 WARNING @ Sun, 21 Jun 2020 21:47:50: Fewer paired peaks (986) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 986 pairs to build model! INFO @ Sun, 21 Jun 2020 21:47:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:50: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 21:47:50: #2 alternative fragment length(s) may be 4,116 bps INFO @ Sun, 21 Jun 2020 21:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.10_model.r INFO @ Sun, 21 Jun 2020 21:47:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:53: 10000000 INFO @ Sun, 21 Jun 2020 21:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:59: Done! pass1 - making usageList (598 chroms): 1 millis pass2 - checking and writing primary data (3046 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:00: 11000000 INFO @ Sun, 21 Jun 2020 21:48:06: 12000000 INFO @ Sun, 21 Jun 2020 21:48:12: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:48:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:16: #1 total tags in treatment: 13505913 INFO @ Sun, 21 Jun 2020 21:48:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:48:16: #1 tags after filtering in treatment: 13505809 INFO @ Sun, 21 Jun 2020 21:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:17: #2 number of paired peaks: 986 WARNING @ Sun, 21 Jun 2020 21:48:17: Fewer paired peaks (986) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 986 pairs to build model! INFO @ Sun, 21 Jun 2020 21:48:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:17: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 21:48:17: #2 alternative fragment length(s) may be 4,116 bps INFO @ Sun, 21 Jun 2020 21:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.20_model.r INFO @ Sun, 21 Jun 2020 21:48:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:33: Done! pass1 - making usageList (438 chroms): 1 millis pass2 - checking and writing primary data (1828 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011089/SRX5011089.20_summits.bed INFO @ Sun, 21 Jun 2020 21:49:02: Done! pass1 - making usageList (295 chroms): 1 millis pass2 - checking and writing primary data (1017 records, 4 fields): 11 millis CompletedMACS2peakCalling