Job ID = 6459235 SRX = SRX6468481 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:09:49 prefetch.2.10.7: 1) Downloading 'SRR9710567'... 2020-06-21T13:09:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:14:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:14:57 prefetch.2.10.7: 1) 'SRR9710567' was downloaded successfully Read 36468445 spots for SRR9710567/SRR9710567.sra Written 36468445 spots for SRR9710567/SRR9710567.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: 00:05:42 36468445 reads; of these: 36468445 (100.00%) were unpaired; of these: 23437423 (64.27%) aligned 0 times 10727365 (29.42%) aligned exactly 1 time 2303657 (6.32%) aligned >1 times 35.73% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 9771427 / 13031022 = 0.7499 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 22:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.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 22:25:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:15: 1000000 INFO @ Sun, 21 Jun 2020 22:25:20: 2000000 INFO @ Sun, 21 Jun 2020 22:25:26: 3000000 INFO @ Sun, 21 Jun 2020 22:25:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:25:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:25:28: #1 total tags in treatment: 3259595 INFO @ Sun, 21 Jun 2020 22:25:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:25:28: #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 22:25:28: #1 tags after filtering in treatment: 3259543 INFO @ Sun, 21 Jun 2020 22:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:25:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:25:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:25:28: #2 number of paired peaks: 918 WARNING @ Sun, 21 Jun 2020 22:25:28: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Sun, 21 Jun 2020 22:25:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:25:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:25:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:25:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:25:28: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 22:25:28: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 22:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.05_model.r INFO @ Sun, 21 Jun 2020 22:25:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:25:36: #3 Call peaks for each chromosome... 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 22:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.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 22:25:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.05_summits.bed INFO @ Sun, 21 Jun 2020 22:25:40: Done! pass1 - making usageList (550 chroms): 1 millis pass2 - checking and writing primary data (3143 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:25:46: 1000000 INFO @ Sun, 21 Jun 2020 22:25:53: 2000000 INFO @ Sun, 21 Jun 2020 22:26:00: 3000000 INFO @ Sun, 21 Jun 2020 22:26:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:26:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:26:02: #1 total tags in treatment: 3259595 INFO @ Sun, 21 Jun 2020 22:26:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:02: #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 22:26:02: #1 tags after filtering in treatment: 3259543 INFO @ Sun, 21 Jun 2020 22:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:02: #2 number of paired peaks: 918 WARNING @ Sun, 21 Jun 2020 22:26:02: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Sun, 21 Jun 2020 22:26:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:03: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 22:26:03: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 22:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.10_model.r INFO @ Sun, 21 Jun 2020 22:26:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:03: #3 Pre-compute pvalue-qvalue table... 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 22:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.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 22:26:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:26:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:26:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.10_summits.bed INFO @ Sun, 21 Jun 2020 22:26:14: Done! pass1 - making usageList (324 chroms): 0 millis pass2 - checking and writing primary data (699 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:26:16: 1000000 INFO @ Sun, 21 Jun 2020 22:26:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:26:30: 3000000 INFO @ Sun, 21 Jun 2020 22:26:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:26:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:26:32: #1 total tags in treatment: 3259595 INFO @ Sun, 21 Jun 2020 22:26:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:26:32: #1 tags after filtering in treatment: 3259543 INFO @ Sun, 21 Jun 2020 22:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:33: #2 number of paired peaks: 918 WARNING @ Sun, 21 Jun 2020 22:26:33: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Sun, 21 Jun 2020 22:26:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:33: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 22:26:33: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 22:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.20_model.r INFO @ Sun, 21 Jun 2020 22:26:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:26:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468481/SRX6468481.20_summits.bed INFO @ Sun, 21 Jun 2020 22:26:45: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 4 millis CompletedMACS2peakCalling