Job ID = 6457870 SRX = SRX4823785 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:56:03 prefetch.2.10.7: 1) Downloading 'SRR7992743'... 2020-06-21T11:56:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:00:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:00:17 prefetch.2.10.7: 1) 'SRR7992743' was downloaded successfully 2020-06-21T12:00:17 prefetch.2.10.7: 'SRR7992743' has 0 unresolved dependencies Read 39528548 spots for SRR7992743/SRR7992743.sra Written 39528548 spots for SRR7992743/SRR7992743.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: 00:10:32 39528548 reads; of these: 39528548 (100.00%) were unpaired; of these: 2877240 (7.28%) aligned 0 times 28023139 (70.89%) aligned exactly 1 time 8628169 (21.83%) aligned >1 times 92.72% overall alignment rate Time searching: 00:10:32 Overall time: 00:10:32 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 16 files... [bam_rmdupse_core] 21678422 / 36651308 = 0.5915 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 21:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.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 21:18:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:32: 1000000 INFO @ Sun, 21 Jun 2020 21:18:37: 2000000 INFO @ Sun, 21 Jun 2020 21:18:43: 3000000 INFO @ Sun, 21 Jun 2020 21:18:48: 4000000 INFO @ Sun, 21 Jun 2020 21:18:54: 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 21:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.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 21:18:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:59: 6000000 INFO @ Sun, 21 Jun 2020 21:19:03: 1000000 INFO @ Sun, 21 Jun 2020 21:19:05: 7000000 INFO @ Sun, 21 Jun 2020 21:19:09: 2000000 INFO @ Sun, 21 Jun 2020 21:19:11: 8000000 INFO @ Sun, 21 Jun 2020 21:19:15: 3000000 INFO @ Sun, 21 Jun 2020 21:19:17: 9000000 INFO @ Sun, 21 Jun 2020 21:19:21: 4000000 INFO @ Sun, 21 Jun 2020 21:19:23: 10000000 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 21:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.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 21:19:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:27: 5000000 INFO @ Sun, 21 Jun 2020 21:19:29: 11000000 INFO @ Sun, 21 Jun 2020 21:19:33: 1000000 INFO @ Sun, 21 Jun 2020 21:19:33: 6000000 INFO @ Sun, 21 Jun 2020 21:19:35: 12000000 INFO @ Sun, 21 Jun 2020 21:19:39: 7000000 INFO @ Sun, 21 Jun 2020 21:19:39: 2000000 INFO @ Sun, 21 Jun 2020 21:19:41: 13000000 INFO @ Sun, 21 Jun 2020 21:19:45: 8000000 INFO @ Sun, 21 Jun 2020 21:19:45: 3000000 INFO @ Sun, 21 Jun 2020 21:19:47: 14000000 INFO @ Sun, 21 Jun 2020 21:19:51: 9000000 INFO @ Sun, 21 Jun 2020 21:19:51: 4000000 INFO @ Sun, 21 Jun 2020 21:19:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:19:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:19:53: #1 total tags in treatment: 14972886 INFO @ Sun, 21 Jun 2020 21:19:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:19:53: #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 21:19:54: #1 tags after filtering in treatment: 14972801 INFO @ Sun, 21 Jun 2020 21:19:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:19:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:19:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:19:55: #2 number of paired peaks: 2124 INFO @ Sun, 21 Jun 2020 21:19:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:19:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:19:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:19:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:19:55: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 21:19:55: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 21:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.05_model.r INFO @ Sun, 21 Jun 2020 21:19:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:19:57: 10000000 INFO @ Sun, 21 Jun 2020 21:19:57: 5000000 INFO @ Sun, 21 Jun 2020 21:20:03: 11000000 INFO @ Sun, 21 Jun 2020 21:20:03: 6000000 INFO @ Sun, 21 Jun 2020 21:20:09: 12000000 INFO @ Sun, 21 Jun 2020 21:20:09: 7000000 INFO @ Sun, 21 Jun 2020 21:20:15: 13000000 INFO @ Sun, 21 Jun 2020 21:20:15: 8000000 INFO @ Sun, 21 Jun 2020 21:20:21: 14000000 INFO @ Sun, 21 Jun 2020 21:20:21: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:20:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:27: #1 total tags in treatment: 14972886 INFO @ Sun, 21 Jun 2020 21:20:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:27: #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 21:20:27: 10000000 INFO @ Sun, 21 Jun 2020 21:20:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:20:27: #1 tags after filtering in treatment: 14972801 INFO @ Sun, 21 Jun 2020 21:20:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:29: #2 number of paired peaks: 2124 INFO @ Sun, 21 Jun 2020 21:20:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:29: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 21:20:29: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 21:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.10_model.r INFO @ Sun, 21 Jun 2020 21:20:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:33: 11000000 INFO @ Sun, 21 Jun 2020 21:20:39: 12000000 INFO @ Sun, 21 Jun 2020 21:20:44: 13000000 INFO @ Sun, 21 Jun 2020 21:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.05_summits.bed INFO @ Sun, 21 Jun 2020 21:20:45: Done! pass1 - making usageList (781 chroms): 4 millis pass2 - checking and writing primary data (22304 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:20:50: 14000000 INFO @ Sun, 21 Jun 2020 21:20:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:55: #1 total tags in treatment: 14972886 INFO @ Sun, 21 Jun 2020 21:20:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:55: #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 21:20:56: #1 tags after filtering in treatment: 14972801 INFO @ Sun, 21 Jun 2020 21:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:56: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:20:57: #2 number of paired peaks: 2124 INFO @ Sun, 21 Jun 2020 21:20:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:57: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 21:20:57: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 21:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.20_model.r INFO @ Sun, 21 Jun 2020 21:20:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.10_summits.bed INFO @ Sun, 21 Jun 2020 21:21:18: Done! pass1 - making usageList (702 chroms): 3 millis pass2 - checking and writing primary data (14497 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823785/SRX4823785.20_summits.bed INFO @ Sun, 21 Jun 2020 21:21:47: Done! pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (7255 records, 4 fields): 22 millis CompletedMACS2peakCalling