Job ID = 6458249 SRX = SRX5011016 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:52 prefetch.2.10.7: 1) Downloading 'SRR8191465'... 2020-06-21T12:20:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:22:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:22:26 prefetch.2.10.7: 'SRR8191465' is valid 2020-06-21T12:22:26 prefetch.2.10.7: 1) 'SRR8191465' was downloaded successfully 2020-06-21T12:22:26 prefetch.2.10.7: 'SRR8191465' has 0 unresolved dependencies Read 20584442 spots for SRR8191465/SRR8191465.sra Written 20584442 spots for SRR8191465/SRR8191465.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: 00:05:05 20584442 reads; of these: 20584442 (100.00%) were unpaired; of these: 2708463 (13.16%) aligned 0 times 13675512 (66.44%) aligned exactly 1 time 4200467 (20.41%) aligned >1 times 86.84% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 9086763 / 17875979 = 0.5083 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 21:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.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 21:31:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:41: 1000000 INFO @ Sun, 21 Jun 2020 21:31:46: 2000000 INFO @ Sun, 21 Jun 2020 21:31:52: 3000000 INFO @ Sun, 21 Jun 2020 21:31:57: 4000000 INFO @ Sun, 21 Jun 2020 21:32:02: 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 21:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.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 21:32:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:08: 6000000 INFO @ Sun, 21 Jun 2020 21:32:11: 1000000 INFO @ Sun, 21 Jun 2020 21:32:13: 7000000 INFO @ Sun, 21 Jun 2020 21:32:17: 2000000 INFO @ Sun, 21 Jun 2020 21:32:19: 8000000 INFO @ Sun, 21 Jun 2020 21:32:22: 3000000 INFO @ Sun, 21 Jun 2020 21:32:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:23: #1 total tags in treatment: 8789216 INFO @ Sun, 21 Jun 2020 21:32:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:23: #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 21:32:24: #1 tags after filtering in treatment: 8789127 INFO @ Sun, 21 Jun 2020 21:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:24: #2 number of paired peaks: 2390 INFO @ Sun, 21 Jun 2020 21:32:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:24: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 21:32:24: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 21:32:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.05_model.r INFO @ Sun, 21 Jun 2020 21:32:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:27: 4000000 INFO @ Sun, 21 Jun 2020 21:32:33: 5000000 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 21:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.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 21:32:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:38: 6000000 INFO @ Sun, 21 Jun 2020 21:32:42: 1000000 INFO @ Sun, 21 Jun 2020 21:32:44: 7000000 INFO @ Sun, 21 Jun 2020 21:32:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:47: 2000000 INFO @ Sun, 21 Jun 2020 21:32:49: 8000000 INFO @ Sun, 21 Jun 2020 21:32:53: 3000000 INFO @ Sun, 21 Jun 2020 21:32:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:54: #1 total tags in treatment: 8789216 INFO @ Sun, 21 Jun 2020 21:32:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:54: #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 21:32:54: #1 tags after filtering in treatment: 8789127 INFO @ Sun, 21 Jun 2020 21:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:55: #2 number of paired peaks: 2390 INFO @ Sun, 21 Jun 2020 21:32:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:55: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 21:32:55: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 21:32:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.10_model.r INFO @ Sun, 21 Jun 2020 21:32:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.05_summits.bed INFO @ Sun, 21 Jun 2020 21:32:56: Done! pass1 - making usageList (725 chroms): 2 millis pass2 - checking and writing primary data (7968 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:32:58: 4000000 INFO @ Sun, 21 Jun 2020 21:33:04: 5000000 INFO @ Sun, 21 Jun 2020 21:33:09: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:15: 7000000 INFO @ Sun, 21 Jun 2020 21:33:21: 8000000 INFO @ Sun, 21 Jun 2020 21:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:24: Done! pass1 - making usageList (601 chroms): 1 millis pass2 - checking and writing primary data (4824 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:33:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:25: #1 total tags in treatment: 8789216 INFO @ Sun, 21 Jun 2020 21:33:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:25: #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 21:33:25: #1 tags after filtering in treatment: 8789127 INFO @ Sun, 21 Jun 2020 21:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:26: #2 number of paired peaks: 2390 INFO @ Sun, 21 Jun 2020 21:33:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:26: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 21:33:26: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 21:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.20_model.r INFO @ Sun, 21 Jun 2020 21:33:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:33:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011016/SRX5011016.20_summits.bed INFO @ Sun, 21 Jun 2020 21:33:57: Done! pass1 - making usageList (382 chroms): 1 millis pass2 - checking and writing primary data (2274 records, 4 fields): 12 millis CompletedMACS2peakCalling