Job ID = 6458321 SRX = SRX5011071 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:26:52 prefetch.2.10.7: 1) Downloading 'SRR8191520'... 2020-06-21T12:26:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:29:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:29:47 prefetch.2.10.7: 1) 'SRR8191520' was downloaded successfully 2020-06-21T12:29:47 prefetch.2.10.7: 'SRR8191520' has 0 unresolved dependencies Read 39031841 spots for SRR8191520/SRR8191520.sra Written 39031841 spots for SRR8191520/SRR8191520.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: 00:08:41 39031841 reads; of these: 39031841 (100.00%) were unpaired; of these: 7224436 (18.51%) aligned 0 times 24949789 (63.92%) aligned exactly 1 time 6857616 (17.57%) aligned >1 times 81.49% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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] 19397335 / 31807405 = 0.6098 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 21:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.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 21:45:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:16: 1000000 INFO @ Sun, 21 Jun 2020 21:45:22: 2000000 INFO @ Sun, 21 Jun 2020 21:45:28: 3000000 INFO @ Sun, 21 Jun 2020 21:45:34: 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 21:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.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 21:45:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:41: 5000000 INFO @ Sun, 21 Jun 2020 21:45:46: 1000000 INFO @ Sun, 21 Jun 2020 21:45:47: 6000000 INFO @ Sun, 21 Jun 2020 21:45:53: 2000000 INFO @ Sun, 21 Jun 2020 21:45:54: 7000000 INFO @ Sun, 21 Jun 2020 21:45:59: 3000000 INFO @ Sun, 21 Jun 2020 21:46:01: 8000000 INFO @ Sun, 21 Jun 2020 21:46:06: 4000000 INFO @ Sun, 21 Jun 2020 21:46:07: 9000000 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 21:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.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 21:46:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:13: 5000000 INFO @ Sun, 21 Jun 2020 21:46:14: 10000000 INFO @ Sun, 21 Jun 2020 21:46:17: 1000000 INFO @ Sun, 21 Jun 2020 21:46:20: 6000000 INFO @ Sun, 21 Jun 2020 21:46:21: 11000000 INFO @ Sun, 21 Jun 2020 21:46:23: 2000000 INFO @ Sun, 21 Jun 2020 21:46:27: 7000000 INFO @ Sun, 21 Jun 2020 21:46:28: 12000000 INFO @ Sun, 21 Jun 2020 21:46:30: 3000000 INFO @ Sun, 21 Jun 2020 21:46:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:30: #1 total tags in treatment: 12410070 INFO @ Sun, 21 Jun 2020 21:46:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:30: #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 21:46:31: #1 tags after filtering in treatment: 12409981 INFO @ Sun, 21 Jun 2020 21:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:32: #2 number of paired peaks: 1835 INFO @ Sun, 21 Jun 2020 21:46:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:32: #2 predicted fragment length is 118 bps INFO @ Sun, 21 Jun 2020 21:46:32: #2 alternative fragment length(s) may be 4,118 bps INFO @ Sun, 21 Jun 2020 21:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.05_model.r INFO @ Sun, 21 Jun 2020 21:46:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:33: 8000000 INFO @ Sun, 21 Jun 2020 21:46:36: 4000000 INFO @ Sun, 21 Jun 2020 21:46:40: 9000000 INFO @ Sun, 21 Jun 2020 21:46:43: 5000000 INFO @ Sun, 21 Jun 2020 21:46:47: 10000000 INFO @ Sun, 21 Jun 2020 21:46:50: 6000000 INFO @ Sun, 21 Jun 2020 21:46:54: 11000000 INFO @ Sun, 21 Jun 2020 21:46:56: 7000000 INFO @ Sun, 21 Jun 2020 21:46:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:00: 12000000 INFO @ Sun, 21 Jun 2020 21:47:03: 8000000 INFO @ Sun, 21 Jun 2020 21:47:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:03: #1 total tags in treatment: 12410070 INFO @ Sun, 21 Jun 2020 21:47:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:03: #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 21:47:04: #1 tags after filtering in treatment: 12409981 INFO @ Sun, 21 Jun 2020 21:47:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:05: #2 number of paired peaks: 1835 INFO @ Sun, 21 Jun 2020 21:47:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:05: #2 predicted fragment length is 118 bps INFO @ Sun, 21 Jun 2020 21:47:05: #2 alternative fragment length(s) may be 4,118 bps INFO @ Sun, 21 Jun 2020 21:47:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.10_model.r INFO @ Sun, 21 Jun 2020 21:47:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:09: 9000000 INFO @ Sun, 21 Jun 2020 21:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:11: Done! pass1 - making usageList (758 chroms): 2 millis pass2 - checking and writing primary data (4396 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:16: 10000000 INFO @ Sun, 21 Jun 2020 21:47:22: 11000000 INFO @ Sun, 21 Jun 2020 21:47:28: 12000000 INFO @ Sun, 21 Jun 2020 21:47:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:30: #1 total tags in treatment: 12410070 INFO @ Sun, 21 Jun 2020 21:47:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:30: #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 21:47:31: #1 tags after filtering in treatment: 12409981 INFO @ Sun, 21 Jun 2020 21:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:32: #2 number of paired peaks: 1835 INFO @ Sun, 21 Jun 2020 21:47:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:32: #2 predicted fragment length is 118 bps INFO @ Sun, 21 Jun 2020 21:47:32: #2 alternative fragment length(s) may be 4,118 bps INFO @ Sun, 21 Jun 2020 21:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.20_model.r INFO @ Sun, 21 Jun 2020 21:47:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:45: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2556 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011071/SRX5011071.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:13: Done! pass1 - making usageList (361 chroms): 1 millis pass2 - checking and writing primary data (1288 records, 4 fields): 13 millis CompletedMACS2peakCalling