Job ID = 6455499 SRX = SRX287835 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:03:59 prefetch.2.10.7: 1) Downloading 'SRR870024'... 2020-06-21T10:03:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:41 prefetch.2.10.7: 'SRR870024' is valid 2020-06-21T10:05:41 prefetch.2.10.7: 1) 'SRR870024' was downloaded successfully Read 16333147 spots for SRR870024/SRR870024.sra Written 16333147 spots for SRR870024/SRR870024.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:53 16333147 reads; of these: 16333147 (100.00%) were unpaired; of these: 703783 (4.31%) aligned 0 times 13834614 (84.70%) aligned exactly 1 time 1794750 (10.99%) aligned >1 times 95.69% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1671615 / 15629364 = 0.1070 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 19:14:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.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 19:14:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:38: 1000000 INFO @ Sun, 21 Jun 2020 19:14:44: 2000000 INFO @ Sun, 21 Jun 2020 19:14:49: 3000000 INFO @ Sun, 21 Jun 2020 19:14:54: 4000000 INFO @ Sun, 21 Jun 2020 19:15:00: 5000000 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 19:15:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.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 19:15:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:06: 6000000 INFO @ Sun, 21 Jun 2020 19:15:10: 1000000 INFO @ Sun, 21 Jun 2020 19:15:12: 7000000 INFO @ Sun, 21 Jun 2020 19:15:17: 2000000 INFO @ Sun, 21 Jun 2020 19:15:18: 8000000 INFO @ Sun, 21 Jun 2020 19:15:25: 9000000 INFO @ Sun, 21 Jun 2020 19:15:25: 3000000 INFO @ Sun, 21 Jun 2020 19:15:31: 10000000 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 19:15:32: 4000000 INFO @ Sun, 21 Jun 2020 19:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.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 19:15:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:37: 11000000 INFO @ Sun, 21 Jun 2020 19:15:39: 5000000 INFO @ Sun, 21 Jun 2020 19:15:40: 1000000 INFO @ Sun, 21 Jun 2020 19:15:44: 12000000 INFO @ Sun, 21 Jun 2020 19:15:46: 6000000 INFO @ Sun, 21 Jun 2020 19:15:48: 2000000 INFO @ Sun, 21 Jun 2020 19:15:51: 13000000 INFO @ Sun, 21 Jun 2020 19:15:53: 7000000 INFO @ Sun, 21 Jun 2020 19:15:55: 3000000 INFO @ Sun, 21 Jun 2020 19:15:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:58: #1 total tags in treatment: 13957749 INFO @ Sun, 21 Jun 2020 19:15:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:58: #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 19:15:58: #1 tags after filtering in treatment: 13957720 INFO @ Sun, 21 Jun 2020 19:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:59: #2 number of paired peaks: 695 WARNING @ Sun, 21 Jun 2020 19:15:59: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:59: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:15:59: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 19:15:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.05_model.r INFO @ Sun, 21 Jun 2020 19:15:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:01: 8000000 INFO @ Sun, 21 Jun 2020 19:16:03: 4000000 INFO @ Sun, 21 Jun 2020 19:16:08: 9000000 INFO @ Sun, 21 Jun 2020 19:16:10: 5000000 INFO @ Sun, 21 Jun 2020 19:16:15: 10000000 INFO @ Sun, 21 Jun 2020 19:16:17: 6000000 INFO @ Sun, 21 Jun 2020 19:16:22: 11000000 INFO @ Sun, 21 Jun 2020 19:16:24: 7000000 INFO @ Sun, 21 Jun 2020 19:16:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:30: 12000000 INFO @ Sun, 21 Jun 2020 19:16:31: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:16:37: 13000000 INFO @ Sun, 21 Jun 2020 19:16:39: 9000000 INFO @ Sun, 21 Jun 2020 19:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.05_summits.bed INFO @ Sun, 21 Jun 2020 19:16:43: Done! pass1 - making usageList (133 chroms): 2 millis pass2 - checking and writing primary data (6355 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:44: #1 total tags in treatment: 13957749 INFO @ Sun, 21 Jun 2020 19:16:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:44: #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 19:16:45: #1 tags after filtering in treatment: 13957720 INFO @ Sun, 21 Jun 2020 19:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:46: 10000000 INFO @ Sun, 21 Jun 2020 19:16:46: #2 number of paired peaks: 695 WARNING @ Sun, 21 Jun 2020 19:16:46: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:46: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:16:46: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 19:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.10_model.r INFO @ Sun, 21 Jun 2020 19:16:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:52: 11000000 INFO @ Sun, 21 Jun 2020 19:16:59: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:17:06: 13000000 INFO @ Sun, 21 Jun 2020 19:17:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:12: #1 total tags in treatment: 13957749 INFO @ Sun, 21 Jun 2020 19:17:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:12: #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 19:17:13: #1 tags after filtering in treatment: 13957720 INFO @ Sun, 21 Jun 2020 19:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:14: #2 number of paired peaks: 695 WARNING @ Sun, 21 Jun 2020 19:17:14: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:14: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:17:14: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 19:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.20_model.r INFO @ Sun, 21 Jun 2020 19:17:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.10_summits.bed INFO @ Sun, 21 Jun 2020 19:17:34: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (4508 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287835/SRX287835.20_summits.bed INFO @ Sun, 21 Jun 2020 19:17:58: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (2752 records, 4 fields): 7 millis CompletedMACS2peakCalling