Job ID = 6454498 SRX = SRX2165282 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:07:24 prefetch.2.10.7: 1) Downloading 'SRR4244793'... 2020-06-21T09:07:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:09:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:09:41 prefetch.2.10.7: 'SRR4244793' is valid 2020-06-21T09:09:41 prefetch.2.10.7: 1) 'SRR4244793' was downloaded successfully Read 9704730 spots for SRR4244793/SRR4244793.sra Written 9704730 spots for SRR4244793/SRR4244793.sra 2020-06-21T09:10:20 prefetch.2.10.7: 1) Downloading 'SRR4244794'... 2020-06-21T09:10:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:14:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:14:23 prefetch.2.10.7: 1) 'SRR4244794' was downloaded successfully Read 17760126 spots for SRR4244794/SRR4244794.sra Written 17760126 spots for SRR4244794/SRR4244794.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: 00:08:36 27464856 reads; of these: 27464856 (100.00%) were unpaired; of these: 1556220 (5.67%) aligned 0 times 19374834 (70.54%) aligned exactly 1 time 6533802 (23.79%) aligned >1 times 94.33% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 10734949 / 25908636 = 0.4143 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 18:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.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 18:31:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:09: 1000000 INFO @ Sun, 21 Jun 2020 18:31:15: 2000000 INFO @ Sun, 21 Jun 2020 18:31:20: 3000000 INFO @ Sun, 21 Jun 2020 18:31:26: 4000000 INFO @ Sun, 21 Jun 2020 18:31:31: 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 18:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.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 18:31:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:37: 6000000 INFO @ Sun, 21 Jun 2020 18:31:41: 1000000 INFO @ Sun, 21 Jun 2020 18:31:43: 7000000 INFO @ Sun, 21 Jun 2020 18:31:48: 2000000 INFO @ Sun, 21 Jun 2020 18:31:49: 8000000 INFO @ Sun, 21 Jun 2020 18:31:55: 3000000 INFO @ Sun, 21 Jun 2020 18:31:55: 9000000 INFO @ Sun, 21 Jun 2020 18:32:01: 10000000 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 18:32:02: 4000000 INFO @ Sun, 21 Jun 2020 18:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.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 18:32:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:07: 11000000 INFO @ Sun, 21 Jun 2020 18:32:09: 5000000 INFO @ Sun, 21 Jun 2020 18:32:10: 1000000 INFO @ Sun, 21 Jun 2020 18:32:14: 12000000 INFO @ Sun, 21 Jun 2020 18:32:16: 6000000 INFO @ Sun, 21 Jun 2020 18:32:16: 2000000 INFO @ Sun, 21 Jun 2020 18:32:20: 13000000 INFO @ Sun, 21 Jun 2020 18:32:22: 3000000 INFO @ Sun, 21 Jun 2020 18:32:23: 7000000 INFO @ Sun, 21 Jun 2020 18:32:26: 14000000 INFO @ Sun, 21 Jun 2020 18:32:29: 4000000 INFO @ Sun, 21 Jun 2020 18:32:30: 8000000 INFO @ Sun, 21 Jun 2020 18:32:33: 15000000 INFO @ Sun, 21 Jun 2020 18:32:34: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:32:34: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:32:34: #1 total tags in treatment: 15173687 INFO @ Sun, 21 Jun 2020 18:32:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:34: #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 18:32:35: 5000000 INFO @ Sun, 21 Jun 2020 18:32:35: #1 tags after filtering in treatment: 15173687 INFO @ Sun, 21 Jun 2020 18:32:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:36: #2 number of paired peaks: 1296 INFO @ Sun, 21 Jun 2020 18:32:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:36: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 18:32:36: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 18:32:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.05_model.r INFO @ Sun, 21 Jun 2020 18:32:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:37: 9000000 INFO @ Sun, 21 Jun 2020 18:32:41: 6000000 INFO @ Sun, 21 Jun 2020 18:32:43: 10000000 INFO @ Sun, 21 Jun 2020 18:32:47: 7000000 INFO @ Sun, 21 Jun 2020 18:32:50: 11000000 INFO @ Sun, 21 Jun 2020 18:32:53: 8000000 INFO @ Sun, 21 Jun 2020 18:32:57: 12000000 INFO @ Sun, 21 Jun 2020 18:32:59: 9000000 INFO @ Sun, 21 Jun 2020 18:33:04: 13000000 INFO @ Sun, 21 Jun 2020 18:33:05: 10000000 INFO @ Sun, 21 Jun 2020 18:33:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:11: 11000000 INFO @ Sun, 21 Jun 2020 18:33:11: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:17: 12000000 INFO @ Sun, 21 Jun 2020 18:33:19: 15000000 INFO @ Sun, 21 Jun 2020 18:33:20: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:33:20: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:33:20: #1 total tags in treatment: 15173687 INFO @ Sun, 21 Jun 2020 18:33:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:20: #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 18:33:20: #1 tags after filtering in treatment: 15173687 INFO @ Sun, 21 Jun 2020 18:33:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:22: #2 number of paired peaks: 1296 INFO @ Sun, 21 Jun 2020 18:33:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:22: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 18:33:22: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 18:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.10_model.r INFO @ Sun, 21 Jun 2020 18:33:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:23: 13000000 INFO @ Sun, 21 Jun 2020 18:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:27: Done! pass1 - making usageList (753 chroms): 2 millis pass2 - checking and writing primary data (7101 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:29: 14000000 INFO @ Sun, 21 Jun 2020 18:33:35: 15000000 INFO @ Sun, 21 Jun 2020 18:33:36: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:33:36: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:33:36: #1 total tags in treatment: 15173687 INFO @ Sun, 21 Jun 2020 18:33:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:36: #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 18:33:37: #1 tags after filtering in treatment: 15173687 INFO @ Sun, 21 Jun 2020 18:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:38: #2 number of paired peaks: 1296 INFO @ Sun, 21 Jun 2020 18:33:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:38: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 18:33:38: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 18:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.20_model.r INFO @ Sun, 21 Jun 2020 18:33:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:33:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:13: Done! pass1 - making usageList (659 chroms): 2 millis pass2 - checking and writing primary data (4593 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165282/SRX2165282.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:28: Done! pass1 - making usageList (528 chroms): 1 millis pass2 - checking and writing primary data (2590 records, 4 fields): 15 millis CompletedMACS2peakCalling