Job ID = 6456246 SRX = SRX331399 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:34:22 prefetch.2.10.7: 1) Downloading 'SRR947636'... 2020-06-21T10:34:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:29 prefetch.2.10.7: 1) 'SRR947636' was downloaded successfully Read 18988235 spots for SRR947636/SRR947636.sra Written 18988235 spots for SRR947636/SRR947636.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: 00:04:26 18988235 reads; of these: 18988235 (100.00%) were unpaired; of these: 3016961 (15.89%) aligned 0 times 13097266 (68.98%) aligned exactly 1 time 2874008 (15.14%) aligned >1 times 84.11% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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] 6890174 / 15971274 = 0.4314 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 19:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.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 19:46:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:37: 1000000 INFO @ Sun, 21 Jun 2020 19:46:42: 2000000 INFO @ Sun, 21 Jun 2020 19:46:46: 3000000 INFO @ Sun, 21 Jun 2020 19:46:51: 4000000 INFO @ Sun, 21 Jun 2020 19:46:56: 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 19:47:01: 6000000 INFO @ Sun, 21 Jun 2020 19:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.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 19:47:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:05: 7000000 INFO @ Sun, 21 Jun 2020 19:47:07: 1000000 INFO @ Sun, 21 Jun 2020 19:47:10: 8000000 INFO @ Sun, 21 Jun 2020 19:47:12: 2000000 INFO @ Sun, 21 Jun 2020 19:47:15: 9000000 INFO @ Sun, 21 Jun 2020 19:47:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:16: #1 total tags in treatment: 9081100 INFO @ Sun, 21 Jun 2020 19:47:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:16: #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 19:47:16: #1 tags after filtering in treatment: 9081091 INFO @ Sun, 21 Jun 2020 19:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:16: 3000000 INFO @ Sun, 21 Jun 2020 19:47:17: #2 number of paired peaks: 3054 INFO @ Sun, 21 Jun 2020 19:47:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:17: #2 predicted fragment length is 243 bps INFO @ Sun, 21 Jun 2020 19:47:17: #2 alternative fragment length(s) may be 243 bps INFO @ Sun, 21 Jun 2020 19:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.05_model.r INFO @ Sun, 21 Jun 2020 19:47:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:21: 4000000 INFO @ Sun, 21 Jun 2020 19:47:26: 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 19:47:30: 6000000 INFO @ Sun, 21 Jun 2020 19:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.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 19:47:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:35: 7000000 INFO @ Sun, 21 Jun 2020 19:47:38: 1000000 INFO @ Sun, 21 Jun 2020 19:47:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:40: 8000000 INFO @ Sun, 21 Jun 2020 19:47:43: 2000000 INFO @ Sun, 21 Jun 2020 19:47:45: 9000000 INFO @ Sun, 21 Jun 2020 19:47:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:46: #1 total tags in treatment: 9081100 INFO @ Sun, 21 Jun 2020 19:47:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:46: #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 19:47:46: #1 tags after filtering in treatment: 9081091 INFO @ Sun, 21 Jun 2020 19:47:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:47: #2 number of paired peaks: 3054 INFO @ Sun, 21 Jun 2020 19:47:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:47: #2 predicted fragment length is 243 bps INFO @ Sun, 21 Jun 2020 19:47:47: #2 alternative fragment length(s) may be 243 bps INFO @ Sun, 21 Jun 2020 19:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.10_model.r INFO @ Sun, 21 Jun 2020 19:47:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:48: 3000000 INFO @ Sun, 21 Jun 2020 19:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:51: Done! pass1 - making usageList (554 chroms): 2 millis pass2 - checking and writing primary data (5732 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:53: 4000000 INFO @ Sun, 21 Jun 2020 19:47:58: 5000000 INFO @ Sun, 21 Jun 2020 19:48:03: 6000000 INFO @ Sun, 21 Jun 2020 19:48:08: 7000000 INFO @ Sun, 21 Jun 2020 19:48:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:48:13: 8000000 INFO @ Sun, 21 Jun 2020 19:48:18: 9000000 INFO @ Sun, 21 Jun 2020 19:48:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:48:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:48:19: #1 total tags in treatment: 9081100 INFO @ Sun, 21 Jun 2020 19:48:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:19: #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 19:48:19: #1 tags after filtering in treatment: 9081091 INFO @ Sun, 21 Jun 2020 19:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:20: #2 number of paired peaks: 3054 INFO @ Sun, 21 Jun 2020 19:48:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:20: #2 predicted fragment length is 243 bps INFO @ Sun, 21 Jun 2020 19:48:20: #2 alternative fragment length(s) may be 243 bps INFO @ Sun, 21 Jun 2020 19:48:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.20_model.r INFO @ Sun, 21 Jun 2020 19:48:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:21: Done! pass1 - making usageList (463 chroms): 2 millis pass2 - checking and writing primary data (4567 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:48:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331399/SRX331399.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:54: Done! pass1 - making usageList (382 chroms): 1 millis pass2 - checking and writing primary data (3452 records, 4 fields): 13 millis CompletedMACS2peakCalling