Job ID = 6454531 SRX = SRX220300 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:08:24 prefetch.2.10.7: 1) Downloading 'SRR653345'... 2020-06-21T09:08:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:14:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:14:32 prefetch.2.10.7: 1) 'SRR653345' was downloaded successfully Read 21817500 spots for SRR653345/SRR653345.sra Written 21817500 spots for SRR653345/SRR653345.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:27 21817500 reads; of these: 21817500 (100.00%) were unpaired; of these: 1707667 (7.83%) aligned 0 times 18084117 (82.89%) aligned exactly 1 time 2025716 (9.28%) aligned >1 times 92.17% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 8033316 / 20109833 = 0.3995 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 18:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.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 18:22:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:48: 1000000 INFO @ Sun, 21 Jun 2020 18:22:53: 2000000 INFO @ Sun, 21 Jun 2020 18:22:57: 3000000 INFO @ Sun, 21 Jun 2020 18:23:01: 4000000 INFO @ Sun, 21 Jun 2020 18:23:05: 5000000 INFO @ Sun, 21 Jun 2020 18:23:10: 6000000 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 18:23:14: 7000000 INFO @ Sun, 21 Jun 2020 18:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.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 18:23:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:18: 8000000 INFO @ Sun, 21 Jun 2020 18:23:19: 1000000 INFO @ Sun, 21 Jun 2020 18:23:22: 9000000 INFO @ Sun, 21 Jun 2020 18:23:24: 2000000 INFO @ Sun, 21 Jun 2020 18:23:27: 10000000 INFO @ Sun, 21 Jun 2020 18:23:29: 3000000 INFO @ Sun, 21 Jun 2020 18:23:31: 11000000 INFO @ Sun, 21 Jun 2020 18:23:34: 4000000 INFO @ Sun, 21 Jun 2020 18:23:36: 12000000 INFO @ Sun, 21 Jun 2020 18:23:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:23:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:23:36: #1 total tags in treatment: 12076517 INFO @ Sun, 21 Jun 2020 18:23:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:36: #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 18:23:37: #1 tags after filtering in treatment: 12076289 INFO @ Sun, 21 Jun 2020 18:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:38: #2 number of paired peaks: 5710 INFO @ Sun, 21 Jun 2020 18:23:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:38: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 18:23:38: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 18:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.05_model.r INFO @ Sun, 21 Jun 2020 18:23:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:39: 5000000 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 18:23:44: 6000000 INFO @ Sun, 21 Jun 2020 18:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.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 18:23:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:48: 1000000 INFO @ Sun, 21 Jun 2020 18:23:49: 7000000 INFO @ Sun, 21 Jun 2020 18:23:53: 2000000 INFO @ Sun, 21 Jun 2020 18:23:53: 8000000 INFO @ Sun, 21 Jun 2020 18:23:57: 3000000 INFO @ Sun, 21 Jun 2020 18:23:58: 9000000 INFO @ Sun, 21 Jun 2020 18:24:02: 4000000 INFO @ Sun, 21 Jun 2020 18:24:04: 10000000 INFO @ Sun, 21 Jun 2020 18:24:06: 5000000 INFO @ Sun, 21 Jun 2020 18:24:09: 11000000 INFO @ Sun, 21 Jun 2020 18:24:10: 6000000 INFO @ Sun, 21 Jun 2020 18:24:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:14: 12000000 INFO @ Sun, 21 Jun 2020 18:24:15: 7000000 INFO @ Sun, 21 Jun 2020 18:24:15: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:24:15: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:24:15: #1 total tags in treatment: 12076517 INFO @ Sun, 21 Jun 2020 18:24:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:15: #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 18:24:16: #1 tags after filtering in treatment: 12076289 INFO @ Sun, 21 Jun 2020 18:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:17: #2 number of paired peaks: 5710 INFO @ Sun, 21 Jun 2020 18:24:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:17: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 18:24:17: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 18:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.10_model.r INFO @ Sun, 21 Jun 2020 18:24:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:19: 8000000 INFO @ Sun, 21 Jun 2020 18:24:23: 9000000 INFO @ Sun, 21 Jun 2020 18:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.05_summits.bed INFO @ Sun, 21 Jun 2020 18:24:26: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (8757 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:28: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:24:32: 11000000 INFO @ Sun, 21 Jun 2020 18:24:36: 12000000 INFO @ Sun, 21 Jun 2020 18:24:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:24:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:24:37: #1 total tags in treatment: 12076517 INFO @ Sun, 21 Jun 2020 18:24:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:37: #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 18:24:37: #1 tags after filtering in treatment: 12076289 INFO @ Sun, 21 Jun 2020 18:24:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:39: #2 number of paired peaks: 5710 INFO @ Sun, 21 Jun 2020 18:24:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:39: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 18:24:39: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 18:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.20_model.r INFO @ Sun, 21 Jun 2020 18:24:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:25:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.10_summits.bed INFO @ Sun, 21 Jun 2020 18:25:06: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (6022 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:25:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220300/SRX220300.20_summits.bed INFO @ Sun, 21 Jun 2020 18:25:26: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (3967 records, 4 fields): 5 millis CompletedMACS2peakCalling