Job ID = 6455611 SRX = SRX287927 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:09:06 prefetch.2.10.7: 1) Downloading 'SRR870116'... 2020-06-21T10:09:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:12:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:12:14 prefetch.2.10.7: 1) 'SRR870116' was downloaded successfully Read 20798631 spots for SRR870116/SRR870116.sra Written 20798631 spots for SRR870116/SRR870116.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: 00:06:11 20798631 reads; of these: 20798631 (100.00%) were unpaired; of these: 1271118 (6.11%) aligned 0 times 13707418 (65.91%) aligned exactly 1 time 5820095 (27.98%) aligned >1 times 93.89% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 3915942 / 19527513 = 0.2005 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 19:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.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 19:24:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:26: 1000000 INFO @ Sun, 21 Jun 2020 19:24:32: 2000000 INFO @ Sun, 21 Jun 2020 19:24:39: 3000000 INFO @ Sun, 21 Jun 2020 19:24:45: 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 19:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.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 19:24:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:51: 5000000 INFO @ Sun, 21 Jun 2020 19:24:56: 1000000 INFO @ Sun, 21 Jun 2020 19:24:58: 6000000 INFO @ Sun, 21 Jun 2020 19:25:03: 2000000 INFO @ Sun, 21 Jun 2020 19:25:05: 7000000 INFO @ Sun, 21 Jun 2020 19:25:09: 3000000 INFO @ Sun, 21 Jun 2020 19:25:12: 8000000 INFO @ Sun, 21 Jun 2020 19:25:16: 4000000 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 19:25:18: 9000000 INFO @ Sun, 21 Jun 2020 19:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.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 19:25:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:22: 5000000 INFO @ Sun, 21 Jun 2020 19:25:25: 10000000 INFO @ Sun, 21 Jun 2020 19:25:26: 1000000 INFO @ Sun, 21 Jun 2020 19:25:29: 6000000 INFO @ Sun, 21 Jun 2020 19:25:31: 11000000 INFO @ Sun, 21 Jun 2020 19:25:33: 2000000 INFO @ Sun, 21 Jun 2020 19:25:35: 7000000 INFO @ Sun, 21 Jun 2020 19:25:38: 12000000 INFO @ Sun, 21 Jun 2020 19:25:40: 3000000 INFO @ Sun, 21 Jun 2020 19:25:42: 8000000 INFO @ Sun, 21 Jun 2020 19:25:45: 13000000 INFO @ Sun, 21 Jun 2020 19:25:47: 4000000 INFO @ Sun, 21 Jun 2020 19:25:49: 9000000 INFO @ Sun, 21 Jun 2020 19:25:51: 14000000 INFO @ Sun, 21 Jun 2020 19:25:53: 5000000 INFO @ Sun, 21 Jun 2020 19:25:55: 10000000 INFO @ Sun, 21 Jun 2020 19:25:58: 15000000 INFO @ Sun, 21 Jun 2020 19:26:00: 6000000 INFO @ Sun, 21 Jun 2020 19:26:01: 11000000 INFO @ Sun, 21 Jun 2020 19:26:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:02: #1 total tags in treatment: 15611571 INFO @ Sun, 21 Jun 2020 19:26:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:02: #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 19:26:03: #1 tags after filtering in treatment: 15611571 INFO @ Sun, 21 Jun 2020 19:26:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:04: #2 number of paired peaks: 844 WARNING @ Sun, 21 Jun 2020 19:26:04: Fewer paired peaks (844) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 844 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:04: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 19:26:04: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 19:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.05_model.r INFO @ Sun, 21 Jun 2020 19:26:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:07: 7000000 INFO @ Sun, 21 Jun 2020 19:26:08: 12000000 INFO @ Sun, 21 Jun 2020 19:26:13: 8000000 INFO @ Sun, 21 Jun 2020 19:26:15: 13000000 INFO @ Sun, 21 Jun 2020 19:26:20: 9000000 INFO @ Sun, 21 Jun 2020 19:26:21: 14000000 INFO @ Sun, 21 Jun 2020 19:26:26: 10000000 INFO @ Sun, 21 Jun 2020 19:26:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:32: #1 total tags in treatment: 15611571 INFO @ Sun, 21 Jun 2020 19:26:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:32: #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 19:26:32: #1 tags after filtering in treatment: 15611571 INFO @ Sun, 21 Jun 2020 19:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:33: 11000000 INFO @ Sun, 21 Jun 2020 19:26:33: #2 number of paired peaks: 844 WARNING @ Sun, 21 Jun 2020 19:26:33: Fewer paired peaks (844) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 844 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:33: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 19:26:33: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 19:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.10_model.r INFO @ Sun, 21 Jun 2020 19:26:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:39: 12000000 INFO @ Sun, 21 Jun 2020 19:26:46: 13000000 INFO @ Sun, 21 Jun 2020 19:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:49: Done! pass1 - making usageList (673 chroms): 1 millis pass2 - checking and writing primary data (1579 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:52: 14000000 INFO @ Sun, 21 Jun 2020 19:26:58: 15000000 INFO @ Sun, 21 Jun 2020 19:27:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:02: #1 total tags in treatment: 15611571 INFO @ Sun, 21 Jun 2020 19:27:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:02: #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 19:27:02: #1 tags after filtering in treatment: 15611571 INFO @ Sun, 21 Jun 2020 19:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:03: #2 number of paired peaks: 844 WARNING @ Sun, 21 Jun 2020 19:27:03: Fewer paired peaks (844) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 844 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:04: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 19:27:04: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 19:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.20_model.r INFO @ Sun, 21 Jun 2020 19:27:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.10_summits.bed INFO @ Sun, 21 Jun 2020 19:27:19: Done! pass1 - making usageList (598 chroms): 1 millis pass2 - checking and writing primary data (1213 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287927/SRX287927.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:49: Done! pass1 - making usageList (479 chroms): 1 millis pass2 - checking and writing primary data (969 records, 4 fields): 13 millis CompletedMACS2peakCalling