Job ID = 6458316 SRX = SRX5011066 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:17:07 prefetch.2.10.7: 1) Downloading 'SRR8191515'... 2020-06-21T12:17:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:18:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:18:59 prefetch.2.10.7: 'SRR8191515' is valid 2020-06-21T12:18:59 prefetch.2.10.7: 1) 'SRR8191515' was downloaded successfully 2020-06-21T12:18:59 prefetch.2.10.7: 'SRR8191515' has 0 unresolved dependencies Read 20753220 spots for SRR8191515/SRR8191515.sra Written 20753220 spots for SRR8191515/SRR8191515.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: 00:04:47 20753220 reads; of these: 20753220 (100.00%) were unpaired; of these: 2797745 (13.48%) aligned 0 times 14353713 (69.16%) aligned exactly 1 time 3601762 (17.36%) aligned >1 times 86.52% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 8940062 / 17955475 = 0.4979 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 21:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.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 21:28:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:02: 1000000 INFO @ Sun, 21 Jun 2020 21:29:08: 2000000 INFO @ Sun, 21 Jun 2020 21:29:13: 3000000 INFO @ Sun, 21 Jun 2020 21:29:19: 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 21:29:24: 5000000 INFO @ Sun, 21 Jun 2020 21:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.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 21:29:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:30: 6000000 INFO @ Sun, 21 Jun 2020 21:29:32: 1000000 INFO @ Sun, 21 Jun 2020 21:29:36: 7000000 INFO @ Sun, 21 Jun 2020 21:29:39: 2000000 INFO @ Sun, 21 Jun 2020 21:29:43: 8000000 INFO @ Sun, 21 Jun 2020 21:29:45: 3000000 INFO @ Sun, 21 Jun 2020 21:29:49: 9000000 INFO @ Sun, 21 Jun 2020 21:29:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:49: #1 total tags in treatment: 9015413 INFO @ Sun, 21 Jun 2020 21:29:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:49: #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 21:29:50: #1 tags after filtering in treatment: 9015271 INFO @ Sun, 21 Jun 2020 21:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:51: #2 number of paired peaks: 3046 INFO @ Sun, 21 Jun 2020 21:29:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:51: #2 predicted fragment length is 223 bps INFO @ Sun, 21 Jun 2020 21:29:51: #2 alternative fragment length(s) may be 223 bps INFO @ Sun, 21 Jun 2020 21:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.05_model.r INFO @ Sun, 21 Jun 2020 21:29:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:51: 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 21:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.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 21:29:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:57: 5000000 INFO @ Sun, 21 Jun 2020 21:30:02: 1000000 INFO @ Sun, 21 Jun 2020 21:30:04: 6000000 INFO @ Sun, 21 Jun 2020 21:30:08: 2000000 INFO @ Sun, 21 Jun 2020 21:30:10: 7000000 INFO @ Sun, 21 Jun 2020 21:30:14: 3000000 INFO @ Sun, 21 Jun 2020 21:30:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:17: 8000000 INFO @ Sun, 21 Jun 2020 21:30:20: 4000000 INFO @ Sun, 21 Jun 2020 21:30:24: 9000000 INFO @ Sun, 21 Jun 2020 21:30:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:24: #1 total tags in treatment: 9015413 INFO @ Sun, 21 Jun 2020 21:30:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:24: #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 21:30:25: #1 tags after filtering in treatment: 9015271 INFO @ Sun, 21 Jun 2020 21:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:26: #2 number of paired peaks: 3046 INFO @ Sun, 21 Jun 2020 21:30:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:26: #2 predicted fragment length is 223 bps INFO @ Sun, 21 Jun 2020 21:30:26: #2 alternative fragment length(s) may be 223 bps INFO @ Sun, 21 Jun 2020 21:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.10_model.r INFO @ Sun, 21 Jun 2020 21:30:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:26: 5000000 INFO @ Sun, 21 Jun 2020 21:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:28: Done! pass1 - making usageList (397 chroms): 2 millis pass2 - checking and writing primary data (7411 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:31: 6000000 INFO @ Sun, 21 Jun 2020 21:30:37: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:44: 8000000 INFO @ Sun, 21 Jun 2020 21:30:50: 9000000 INFO @ Sun, 21 Jun 2020 21:30:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:50: #1 total tags in treatment: 9015413 INFO @ Sun, 21 Jun 2020 21:30:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:50: #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 21:30:51: #1 tags after filtering in treatment: 9015271 INFO @ Sun, 21 Jun 2020 21:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:52: #2 number of paired peaks: 3046 INFO @ Sun, 21 Jun 2020 21:30:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:52: #2 predicted fragment length is 223 bps INFO @ Sun, 21 Jun 2020 21:30:52: #2 alternative fragment length(s) may be 223 bps INFO @ Sun, 21 Jun 2020 21:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.20_model.r INFO @ Sun, 21 Jun 2020 21:30:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.10_summits.bed INFO @ Sun, 21 Jun 2020 21:31:02: Done! pass1 - making usageList (341 chroms): 1 millis pass2 - checking and writing primary data (5105 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:31:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011066/SRX5011066.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:29: Done! pass1 - making usageList (249 chroms): 2 millis pass2 - checking and writing primary data (2873 records, 4 fields): 17 millis CompletedMACS2peakCalling