Job ID = 6456940 SRX = SRX4158167 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:18:28 prefetch.2.10.7: 1) Downloading 'SRR7253447'... 2020-06-21T11:18:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:51 prefetch.2.10.7: 'SRR7253447' is valid 2020-06-21T11:20:51 prefetch.2.10.7: 1) 'SRR7253447' was downloaded successfully Read 13652212 spots for SRR7253447/SRR7253447.sra Written 13652212 spots for SRR7253447/SRR7253447.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: 00:02:59 13652212 reads; of these: 13652212 (100.00%) were unpaired; of these: 274180 (2.01%) aligned 0 times 12459722 (91.27%) aligned exactly 1 time 918310 (6.73%) aligned >1 times 97.99% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 1932328 / 13378032 = 0.1444 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 20:28:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.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 20:28:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:26: 1000000 INFO @ Sun, 21 Jun 2020 20:28:33: 2000000 INFO @ Sun, 21 Jun 2020 20:28:40: 3000000 INFO @ Sun, 21 Jun 2020 20:28:47: 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 20:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.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 20:28:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:54: 5000000 INFO @ Sun, 21 Jun 2020 20:28:56: 1000000 INFO @ Sun, 21 Jun 2020 20:29:01: 6000000 INFO @ Sun, 21 Jun 2020 20:29:03: 2000000 INFO @ Sun, 21 Jun 2020 20:29:08: 7000000 INFO @ Sun, 21 Jun 2020 20:29:10: 3000000 INFO @ Sun, 21 Jun 2020 20:29:16: 8000000 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 20:29:18: 4000000 INFO @ Sun, 21 Jun 2020 20:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.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 20:29:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:23: 9000000 INFO @ Sun, 21 Jun 2020 20:29:26: 1000000 INFO @ Sun, 21 Jun 2020 20:29:27: 5000000 INFO @ Sun, 21 Jun 2020 20:29:31: 10000000 INFO @ Sun, 21 Jun 2020 20:29:33: 2000000 INFO @ Sun, 21 Jun 2020 20:29:34: 6000000 INFO @ Sun, 21 Jun 2020 20:29:38: 11000000 INFO @ Sun, 21 Jun 2020 20:29:41: 3000000 INFO @ Sun, 21 Jun 2020 20:29:41: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:29:41: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:29:41: #1 total tags in treatment: 11445704 INFO @ Sun, 21 Jun 2020 20:29:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:41: #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 20:29:41: 7000000 INFO @ Sun, 21 Jun 2020 20:29:42: #1 tags after filtering in treatment: 11445493 INFO @ Sun, 21 Jun 2020 20:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:43: #2 number of paired peaks: 10599 INFO @ Sun, 21 Jun 2020 20:29:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:43: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:29:43: #2 alternative fragment length(s) may be 3,150 bps INFO @ Sun, 21 Jun 2020 20:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.05_model.r INFO @ Sun, 21 Jun 2020 20:29:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:48: 4000000 INFO @ Sun, 21 Jun 2020 20:29:49: 8000000 INFO @ Sun, 21 Jun 2020 20:29:55: 5000000 INFO @ Sun, 21 Jun 2020 20:29:56: 9000000 INFO @ Sun, 21 Jun 2020 20:30:02: 6000000 INFO @ Sun, 21 Jun 2020 20:30:03: 10000000 INFO @ Sun, 21 Jun 2020 20:30:08: 7000000 INFO @ Sun, 21 Jun 2020 20:30:10: 11000000 INFO @ Sun, 21 Jun 2020 20:30:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:14: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:30:14: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:30:14: #1 total tags in treatment: 11445704 INFO @ Sun, 21 Jun 2020 20:30:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:14: #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 20:30:14: #1 tags after filtering in treatment: 11445493 INFO @ Sun, 21 Jun 2020 20:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:15: 8000000 INFO @ Sun, 21 Jun 2020 20:30:16: #2 number of paired peaks: 10599 INFO @ Sun, 21 Jun 2020 20:30:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:16: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:30:16: #2 alternative fragment length(s) may be 3,150 bps INFO @ Sun, 21 Jun 2020 20:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.10_model.r INFO @ Sun, 21 Jun 2020 20:30:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:30:22: 9000000 INFO @ Sun, 21 Jun 2020 20:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.05_summits.bed INFO @ Sun, 21 Jun 2020 20:30:25: Done! pass1 - making usageList (75 chroms): 2 millis pass2 - checking and writing primary data (9308 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:29: 10000000 INFO @ Sun, 21 Jun 2020 20:30:36: 11000000 INFO @ Sun, 21 Jun 2020 20:30:39: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:30:39: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:30:39: #1 total tags in treatment: 11445704 INFO @ Sun, 21 Jun 2020 20:30:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:39: #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 20:30:39: #1 tags after filtering in treatment: 11445493 INFO @ Sun, 21 Jun 2020 20:30:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:41: #2 number of paired peaks: 10599 INFO @ Sun, 21 Jun 2020 20:30:41: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:30:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:41: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:30:41: #2 alternative fragment length(s) may be 3,150 bps INFO @ Sun, 21 Jun 2020 20:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.20_model.r INFO @ Sun, 21 Jun 2020 20:30:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:58: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (5606 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:31:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158167/SRX4158167.20_summits.bed INFO @ Sun, 21 Jun 2020 20:31:25: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1795 records, 4 fields): 4 millis CompletedMACS2peakCalling