Job ID = 6454365 SRX = SRX201900 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:08:39 prefetch.2.10.7: 1) Downloading 'SRR609690'... 2020-06-21T09:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:13:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:13:14 prefetch.2.10.7: 1) 'SRR609690' was downloaded successfully Read 28507533 spots for SRR609690/SRR609690.sra Written 28507533 spots for SRR609690/SRR609690.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: 00:05:33 28507533 reads; of these: 28507533 (100.00%) were unpaired; of these: 1521010 (5.34%) aligned 0 times 24697309 (86.63%) aligned exactly 1 time 2289214 (8.03%) aligned >1 times 94.66% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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 12 files... [bam_rmdupse_core] 16068911 / 26986523 = 0.5954 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 18:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.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 18:25:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:21: 1000000 INFO @ Sun, 21 Jun 2020 18:25:27: 2000000 INFO @ Sun, 21 Jun 2020 18:25:33: 3000000 INFO @ Sun, 21 Jun 2020 18:25:39: 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 18:25:44: 5000000 INFO @ Sun, 21 Jun 2020 18:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.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 18:25:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:51: 6000000 INFO @ Sun, 21 Jun 2020 18:25:52: 1000000 INFO @ Sun, 21 Jun 2020 18:25:57: 7000000 INFO @ Sun, 21 Jun 2020 18:25:59: 2000000 INFO @ Sun, 21 Jun 2020 18:26:04: 8000000 INFO @ Sun, 21 Jun 2020 18:26:05: 3000000 INFO @ Sun, 21 Jun 2020 18:26:10: 9000000 INFO @ Sun, 21 Jun 2020 18:26:12: 4000000 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 18:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.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 18:26:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:17: 10000000 INFO @ Sun, 21 Jun 2020 18:26:18: 5000000 INFO @ Sun, 21 Jun 2020 18:26:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:26:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:26:24: #1 total tags in treatment: 10917612 INFO @ Sun, 21 Jun 2020 18:26:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:24: #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 18:26:24: 1000000 INFO @ Sun, 21 Jun 2020 18:26:24: #1 tags after filtering in treatment: 10917375 INFO @ Sun, 21 Jun 2020 18:26:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:25: #2 number of paired peaks: 8513 INFO @ Sun, 21 Jun 2020 18:26:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:26: 6000000 INFO @ Sun, 21 Jun 2020 18:26:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:26: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 18:26:26: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 18:26:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.05_model.r INFO @ Sun, 21 Jun 2020 18:26:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:32: 2000000 INFO @ Sun, 21 Jun 2020 18:26:33: 7000000 INFO @ Sun, 21 Jun 2020 18:26:40: 8000000 INFO @ Sun, 21 Jun 2020 18:26:40: 3000000 INFO @ Sun, 21 Jun 2020 18:26:48: 9000000 INFO @ Sun, 21 Jun 2020 18:26:48: 4000000 INFO @ Sun, 21 Jun 2020 18:26:55: 10000000 INFO @ Sun, 21 Jun 2020 18:26:57: 5000000 INFO @ Sun, 21 Jun 2020 18:27:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:02: #1 total tags in treatment: 10917612 INFO @ Sun, 21 Jun 2020 18:27:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:02: #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 18:27:02: #1 tags after filtering in treatment: 10917375 INFO @ Sun, 21 Jun 2020 18:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:03: #2 number of paired peaks: 8513 INFO @ Sun, 21 Jun 2020 18:27:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:04: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 18:27:04: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 18:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.10_model.r INFO @ Sun, 21 Jun 2020 18:27:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:04: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:27:12: 7000000 INFO @ Sun, 21 Jun 2020 18:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.05_summits.bed INFO @ Sun, 21 Jun 2020 18:27:16: Done! pass1 - making usageList (93 chroms): 2 millis pass2 - checking and writing primary data (10504 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:19: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:27:27: 9000000 INFO @ Sun, 21 Jun 2020 18:27:34: 10000000 INFO @ Sun, 21 Jun 2020 18:27:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:40: #1 total tags in treatment: 10917612 INFO @ Sun, 21 Jun 2020 18:27:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:40: #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 18:27:40: #1 tags after filtering in treatment: 10917375 INFO @ Sun, 21 Jun 2020 18:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:42: #2 number of paired peaks: 8513 INFO @ Sun, 21 Jun 2020 18:27:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:42: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 18:27:42: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 18:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.20_model.r INFO @ Sun, 21 Jun 2020 18:27:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.10_summits.bed INFO @ Sun, 21 Jun 2020 18:27:52: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (8233 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201900/SRX201900.20_summits.bed INFO @ Sun, 21 Jun 2020 18:28:34: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (6196 records, 4 fields): 9 millis CompletedMACS2peakCalling