Job ID = 6459288 SRX = SRX661064 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:05:46 prefetch.2.10.7: 1) Downloading 'SRR1524299'... 2020-06-21T13:05:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:08:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:08:39 prefetch.2.10.7: 1) 'SRR1524299' was downloaded successfully Read 16838774 spots for SRR1524299/SRR1524299.sra Written 16838774 spots for SRR1524299/SRR1524299.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: 00:04:11 16838774 reads; of these: 16838774 (100.00%) were unpaired; of these: 3865780 (22.96%) aligned 0 times 9752536 (57.92%) aligned exactly 1 time 3220458 (19.13%) aligned >1 times 77.04% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 1936940 / 12972994 = 0.1493 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 22:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.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 22:17:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:37: 1000000 INFO @ Sun, 21 Jun 2020 22:17:42: 2000000 INFO @ Sun, 21 Jun 2020 22:17:48: 3000000 INFO @ Sun, 21 Jun 2020 22:17:54: 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 22:18:00: 5000000 INFO @ Sun, 21 Jun 2020 22:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.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 22:18:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:06: 6000000 INFO @ Sun, 21 Jun 2020 22:18:08: 1000000 INFO @ Sun, 21 Jun 2020 22:18:13: 7000000 INFO @ Sun, 21 Jun 2020 22:18:15: 2000000 INFO @ Sun, 21 Jun 2020 22:18:19: 8000000 INFO @ Sun, 21 Jun 2020 22:18:22: 3000000 INFO @ Sun, 21 Jun 2020 22:18:26: 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 22:18:30: 4000000 INFO @ Sun, 21 Jun 2020 22:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.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 22:18:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:33: 10000000 INFO @ Sun, 21 Jun 2020 22:18:37: 5000000 INFO @ Sun, 21 Jun 2020 22:18:38: 1000000 INFO @ Sun, 21 Jun 2020 22:18:40: 11000000 INFO @ Sun, 21 Jun 2020 22:18:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:18:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:18:41: #1 total tags in treatment: 11036054 INFO @ Sun, 21 Jun 2020 22:18:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:41: #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 22:18:41: #1 tags after filtering in treatment: 11036050 INFO @ Sun, 21 Jun 2020 22:18:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:42: #2 number of paired peaks: 646 WARNING @ Sun, 21 Jun 2020 22:18:42: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Sun, 21 Jun 2020 22:18:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:42: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 22:18:42: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 22:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.05_model.r INFO @ Sun, 21 Jun 2020 22:18:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:45: 6000000 INFO @ Sun, 21 Jun 2020 22:18:46: 2000000 INFO @ Sun, 21 Jun 2020 22:18:52: 7000000 INFO @ Sun, 21 Jun 2020 22:18:53: 3000000 INFO @ Sun, 21 Jun 2020 22:18:59: 8000000 INFO @ Sun, 21 Jun 2020 22:19:01: 4000000 INFO @ Sun, 21 Jun 2020 22:19:07: 9000000 INFO @ Sun, 21 Jun 2020 22:19:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:08: 5000000 INFO @ Sun, 21 Jun 2020 22:19:15: 10000000 INFO @ Sun, 21 Jun 2020 22:19:16: 6000000 INFO @ Sun, 21 Jun 2020 22:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.05_summits.bed INFO @ Sun, 21 Jun 2020 22:19:20: Done! pass1 - making usageList (684 chroms): 1 millis pass2 - checking and writing primary data (3257 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:19:22: 11000000 INFO @ Sun, 21 Jun 2020 22:19:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:19:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:19:23: #1 total tags in treatment: 11036054 INFO @ Sun, 21 Jun 2020 22:19:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:23: #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 22:19:23: #1 tags after filtering in treatment: 11036050 INFO @ Sun, 21 Jun 2020 22:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:23: 7000000 INFO @ Sun, 21 Jun 2020 22:19:24: #2 number of paired peaks: 646 WARNING @ Sun, 21 Jun 2020 22:19:24: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Sun, 21 Jun 2020 22:19:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:24: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 22:19:24: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 22:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.10_model.r INFO @ Sun, 21 Jun 2020 22:19:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:31: 8000000 INFO @ Sun, 21 Jun 2020 22:19:38: 9000000 INFO @ Sun, 21 Jun 2020 22:19:45: 10000000 INFO @ Sun, 21 Jun 2020 22:19:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:52: 11000000 INFO @ Sun, 21 Jun 2020 22:19:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:19:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:19:53: #1 total tags in treatment: 11036054 INFO @ Sun, 21 Jun 2020 22:19:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:53: #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 22:19:53: #1 tags after filtering in treatment: 11036050 INFO @ Sun, 21 Jun 2020 22:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:53: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:54: #2 number of paired peaks: 646 WARNING @ Sun, 21 Jun 2020 22:19:54: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Sun, 21 Jun 2020 22:19:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:54: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 22:19:54: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 22:19:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.20_model.r INFO @ Sun, 21 Jun 2020 22:19:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.10_summits.bed INFO @ Sun, 21 Jun 2020 22:20:02: Done! pass1 - making usageList (544 chroms): 2 millis pass2 - checking and writing primary data (2017 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661064/SRX661064.20_summits.bed INFO @ Sun, 21 Jun 2020 22:20:31: Done! pass1 - making usageList (305 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 10 millis CompletedMACS2peakCalling