Job ID = 6457879 SRX = SRX4823794 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:15:50 prefetch.2.10.7: 1) Downloading 'SRR7992752'... 2020-06-21T12:15:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:18:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:18:21 prefetch.2.10.7: 1) 'SRR7992752' was downloaded successfully 2020-06-21T12:18:21 prefetch.2.10.7: 'SRR7992752' has 0 unresolved dependencies Read 26259900 spots for SRR7992752/SRR7992752.sra Written 26259900 spots for SRR7992752/SRR7992752.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: 00:05:03 26259900 reads; of these: 26259900 (100.00%) were unpaired; of these: 10159060 (38.69%) aligned 0 times 11838490 (45.08%) aligned exactly 1 time 4262350 (16.23%) aligned >1 times 61.31% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 6862958 / 16100840 = 0.4262 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 21:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.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 21:28:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:45: 1000000 INFO @ Sun, 21 Jun 2020 21:28:52: 2000000 INFO @ Sun, 21 Jun 2020 21:29:00: 3000000 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 21:29:07: 4000000 INFO @ Sun, 21 Jun 2020 21:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.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 21:29:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:15: 5000000 INFO @ Sun, 21 Jun 2020 21:29:16: 1000000 INFO @ Sun, 21 Jun 2020 21:29:23: 6000000 INFO @ Sun, 21 Jun 2020 21:29:25: 2000000 INFO @ Sun, 21 Jun 2020 21:29:31: 7000000 INFO @ Sun, 21 Jun 2020 21:29:34: 3000000 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 21:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.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 21:29:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:39: 8000000 INFO @ Sun, 21 Jun 2020 21:29:43: 4000000 INFO @ Sun, 21 Jun 2020 21:29:45: 1000000 INFO @ Sun, 21 Jun 2020 21:29:48: 9000000 INFO @ Sun, 21 Jun 2020 21:29:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:50: #1 total tags in treatment: 9237882 INFO @ Sun, 21 Jun 2020 21:29:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:50: #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 21:29:50: #1 tags after filtering in treatment: 9237797 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: 3284 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 208 bps INFO @ Sun, 21 Jun 2020 21:29:51: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 21:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.05_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 21:29:52: 5000000 INFO @ Sun, 21 Jun 2020 21:29:53: 2000000 INFO @ Sun, 21 Jun 2020 21:30:01: 3000000 INFO @ Sun, 21 Jun 2020 21:30:01: 6000000 INFO @ Sun, 21 Jun 2020 21:30:08: 4000000 INFO @ Sun, 21 Jun 2020 21:30:09: 7000000 INFO @ Sun, 21 Jun 2020 21:30:16: 5000000 INFO @ Sun, 21 Jun 2020 21:30:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:18: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:23: 6000000 INFO @ Sun, 21 Jun 2020 21:30:26: 9000000 INFO @ Sun, 21 Jun 2020 21:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:27: Done! INFO @ Sun, 21 Jun 2020 21:30:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:28: #1 total tags in treatment: 9237882 INFO @ Sun, 21 Jun 2020 21:30:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (711 chroms): 2 millis pass2 - checking and writing primary data (7001 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:28: #1 tags after filtering in treatment: 9237797 INFO @ Sun, 21 Jun 2020 21:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:29: #2 number of paired peaks: 3284 INFO @ Sun, 21 Jun 2020 21:30:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:29: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 21:30:29: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 21:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.10_model.r INFO @ Sun, 21 Jun 2020 21:30:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:31: 7000000 INFO @ Sun, 21 Jun 2020 21:30:37: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:30:43: 9000000 INFO @ Sun, 21 Jun 2020 21:30:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:45: #1 total tags in treatment: 9237882 INFO @ Sun, 21 Jun 2020 21:30:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:45: #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 21:30:45: #1 tags after filtering in treatment: 9237797 INFO @ Sun, 21 Jun 2020 21:30:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:46: #2 number of paired peaks: 3284 INFO @ Sun, 21 Jun 2020 21:30:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:46: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 21:30:46: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 21:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.20_model.r INFO @ Sun, 21 Jun 2020 21:30:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.10_summits.bed INFO @ Sun, 21 Jun 2020 21:31:07: Done! pass1 - making usageList (644 chroms): 2 millis pass2 - checking and writing primary data (5730 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:31:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823794/SRX4823794.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:24: Done! pass1 - making usageList (579 chroms): 1 millis pass2 - checking and writing primary data (4397 records, 4 fields): 21 millis CompletedMACS2peakCalling