Job ID = 6455306 SRX = SRX287680 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:43:10 prefetch.2.10.7: 1) Downloading 'SRR869868'... 2020-06-21T09:43:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:18 prefetch.2.10.7: 1) 'SRR869868' was downloaded successfully Read 19146986 spots for SRR869868/SRR869868.sra Written 19146986 spots for SRR869868/SRR869868.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: 00:03:53 19146986 reads; of these: 19146986 (100.00%) were unpaired; of these: 1278658 (6.68%) aligned 0 times 16665669 (87.04%) aligned exactly 1 time 1202659 (6.28%) aligned >1 times 93.32% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 3158363 / 17868328 = 0.1768 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 18:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.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 18:55:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:05: 1000000 INFO @ Sun, 21 Jun 2020 18:56:11: 2000000 INFO @ Sun, 21 Jun 2020 18:56:17: 3000000 INFO @ Sun, 21 Jun 2020 18:56:23: 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 18:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.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 18:56:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:30: 5000000 INFO @ Sun, 21 Jun 2020 18:56:36: 1000000 INFO @ Sun, 21 Jun 2020 18:56:37: 6000000 INFO @ Sun, 21 Jun 2020 18:56:42: 2000000 INFO @ Sun, 21 Jun 2020 18:56:44: 7000000 INFO @ Sun, 21 Jun 2020 18:56:49: 3000000 INFO @ Sun, 21 Jun 2020 18:56:51: 8000000 INFO @ Sun, 21 Jun 2020 18:56:56: 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 18:56:58: 9000000 INFO @ Sun, 21 Jun 2020 18:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.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 18:56:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:03: 5000000 INFO @ Sun, 21 Jun 2020 18:57:06: 10000000 INFO @ Sun, 21 Jun 2020 18:57:07: 1000000 INFO @ Sun, 21 Jun 2020 18:57:11: 6000000 INFO @ Sun, 21 Jun 2020 18:57:13: 11000000 INFO @ Sun, 21 Jun 2020 18:57:15: 2000000 INFO @ Sun, 21 Jun 2020 18:57:19: 7000000 INFO @ Sun, 21 Jun 2020 18:57:21: 12000000 INFO @ Sun, 21 Jun 2020 18:57:23: 3000000 INFO @ Sun, 21 Jun 2020 18:57:27: 8000000 INFO @ Sun, 21 Jun 2020 18:57:30: 13000000 INFO @ Sun, 21 Jun 2020 18:57:32: 4000000 INFO @ Sun, 21 Jun 2020 18:57:35: 9000000 INFO @ Sun, 21 Jun 2020 18:57:37: 14000000 INFO @ Sun, 21 Jun 2020 18:57:40: 5000000 INFO @ Sun, 21 Jun 2020 18:57:42: 10000000 INFO @ Sun, 21 Jun 2020 18:57:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:43: #1 total tags in treatment: 14709965 INFO @ Sun, 21 Jun 2020 18:57:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:43: #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 18:57:44: #1 tags after filtering in treatment: 14709891 INFO @ Sun, 21 Jun 2020 18:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:46: #2 number of paired peaks: 8846 INFO @ Sun, 21 Jun 2020 18:57:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:46: #2 predicted fragment length is 221 bps INFO @ Sun, 21 Jun 2020 18:57:46: #2 alternative fragment length(s) may be 3,221 bps INFO @ Sun, 21 Jun 2020 18:57:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.05_model.r INFO @ Sun, 21 Jun 2020 18:57:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:48: 6000000 INFO @ Sun, 21 Jun 2020 18:57:50: 11000000 INFO @ Sun, 21 Jun 2020 18:57:57: 7000000 INFO @ Sun, 21 Jun 2020 18:57:58: 12000000 INFO @ Sun, 21 Jun 2020 18:58:05: 8000000 INFO @ Sun, 21 Jun 2020 18:58:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:58:13: 9000000 INFO @ Sun, 21 Jun 2020 18:58:14: 14000000 INFO @ Sun, 21 Jun 2020 18:58:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:20: #1 total tags in treatment: 14709965 INFO @ Sun, 21 Jun 2020 18:58:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:20: #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 18:58:20: #1 tags after filtering in treatment: 14709891 INFO @ Sun, 21 Jun 2020 18:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:22: 10000000 INFO @ Sun, 21 Jun 2020 18:58:22: #2 number of paired peaks: 8846 INFO @ Sun, 21 Jun 2020 18:58:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:22: #2 predicted fragment length is 221 bps INFO @ Sun, 21 Jun 2020 18:58:22: #2 alternative fragment length(s) may be 3,221 bps INFO @ Sun, 21 Jun 2020 18:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.10_model.r INFO @ Sun, 21 Jun 2020 18:58:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:29: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:36: 12000000 INFO @ Sun, 21 Jun 2020 18:58:44: 13000000 INFO @ Sun, 21 Jun 2020 18:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.05_summits.bed INFO @ Sun, 21 Jun 2020 18:58:47: Done! pass1 - making usageList (100 chroms): 2 millis pass2 - checking and writing primary data (8937 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:51: 14000000 INFO @ Sun, 21 Jun 2020 18:58:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:57: #1 total tags in treatment: 14709965 INFO @ Sun, 21 Jun 2020 18:58:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:57: #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 18:58:57: #1 tags after filtering in treatment: 14709891 INFO @ Sun, 21 Jun 2020 18:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:59: #2 number of paired peaks: 8846 INFO @ Sun, 21 Jun 2020 18:58:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:59: #2 predicted fragment length is 221 bps INFO @ Sun, 21 Jun 2020 18:58:59: #2 alternative fragment length(s) may be 3,221 bps INFO @ Sun, 21 Jun 2020 18:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.20_model.r INFO @ Sun, 21 Jun 2020 18:58:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:22: Done! pass1 - making usageList (80 chroms): 2 millis pass2 - checking and writing primary data (6837 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287680/SRX287680.20_summits.bed INFO @ Sun, 21 Jun 2020 18:59:57: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (3516 records, 4 fields): 8 millis CompletedMACS2peakCalling