Job ID = 6458295 SRX = SRX5011052 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:37 prefetch.2.10.7: 1) Downloading 'SRR8191501'... 2020-06-21T12:30:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:34 prefetch.2.10.7: 'SRR8191501' is valid 2020-06-21T12:32:34 prefetch.2.10.7: 1) 'SRR8191501' was downloaded successfully 2020-06-21T12:32:34 prefetch.2.10.7: 'SRR8191501' has 0 unresolved dependencies Read 24425098 spots for SRR8191501/SRR8191501.sra Written 24425098 spots for SRR8191501/SRR8191501.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: 00:05:12 24425098 reads; of these: 24425098 (100.00%) were unpaired; of these: 7196614 (29.46%) aligned 0 times 13402309 (54.87%) aligned exactly 1 time 3826175 (15.66%) aligned >1 times 70.54% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 11203101 / 17228484 = 0.6503 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 21:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.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 21:41:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:00: 1000000 INFO @ Sun, 21 Jun 2020 21:42:05: 2000000 INFO @ Sun, 21 Jun 2020 21:42:10: 3000000 INFO @ Sun, 21 Jun 2020 21:42:15: 4000000 INFO @ Sun, 21 Jun 2020 21:42:21: 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 21:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.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 21:42:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:27: 6000000 INFO @ Sun, 21 Jun 2020 21:42:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:27: #1 total tags in treatment: 6025383 INFO @ Sun, 21 Jun 2020 21:42:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:27: #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 21:42:27: #1 tags after filtering in treatment: 6025276 INFO @ Sun, 21 Jun 2020 21:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:28: #2 number of paired peaks: 4071 INFO @ Sun, 21 Jun 2020 21:42:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:28: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:42:28: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 21:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.05_model.r INFO @ Sun, 21 Jun 2020 21:42:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:31: 1000000 INFO @ Sun, 21 Jun 2020 21:42:36: 2000000 INFO @ Sun, 21 Jun 2020 21:42:41: 3000000 INFO @ Sun, 21 Jun 2020 21:42:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:46: 4000000 INFO @ Sun, 21 Jun 2020 21:42:52: 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 21:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.05_summits.bed INFO @ Sun, 21 Jun 2020 21:42:54: Done! pass1 - making usageList (730 chroms): 2 millis pass2 - checking and writing primary data (5862 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.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 21:42:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:58: 6000000 INFO @ Sun, 21 Jun 2020 21:42:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:58: #1 total tags in treatment: 6025383 INFO @ Sun, 21 Jun 2020 21:42:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:58: #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 21:42:58: #1 tags after filtering in treatment: 6025276 INFO @ Sun, 21 Jun 2020 21:42:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:59: #2 number of paired peaks: 4071 INFO @ Sun, 21 Jun 2020 21:42:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:59: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:42:59: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 21:42:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.10_model.r INFO @ Sun, 21 Jun 2020 21:42:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:00: 1000000 INFO @ Sun, 21 Jun 2020 21:43:06: 2000000 INFO @ Sun, 21 Jun 2020 21:43:11: 3000000 INFO @ Sun, 21 Jun 2020 21:43:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:17: 4000000 INFO @ Sun, 21 Jun 2020 21:43:23: 5000000 INFO @ Sun, 21 Jun 2020 21:43:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.10_summits.bed INFO @ Sun, 21 Jun 2020 21:43:25: Done! pass1 - making usageList (615 chroms): 1 millis pass2 - checking and writing primary data (3820 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:43:29: 6000000 INFO @ Sun, 21 Jun 2020 21:43:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:29: #1 total tags in treatment: 6025383 INFO @ Sun, 21 Jun 2020 21:43:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:29: #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 21:43:30: #1 tags after filtering in treatment: 6025276 INFO @ Sun, 21 Jun 2020 21:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:30: #2 number of paired peaks: 4071 INFO @ Sun, 21 Jun 2020 21:43:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:31: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:43:31: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 21:43:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.20_model.r INFO @ Sun, 21 Jun 2020 21:43:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:43:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011052/SRX5011052.20_summits.bed INFO @ Sun, 21 Jun 2020 21:43:56: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (2054 records, 4 fields): 15 millis CompletedMACS2peakCalling