Job ID = 6457951 SRX = SRX4923194 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:10:52 prefetch.2.10.7: 1) Downloading 'SRR8096344'... 2020-06-21T12:10:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:38 prefetch.2.10.7: 'SRR8096344' is valid 2020-06-21T12:13:38 prefetch.2.10.7: 1) 'SRR8096344' was downloaded successfully 2020-06-21T12:13:38 prefetch.2.10.7: 'SRR8096344' has 0 unresolved dependencies Read 32581526 spots for SRR8096344/SRR8096344.sra Written 32581526 spots for SRR8096344/SRR8096344.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: 00:06:56 32581526 reads; of these: 32581526 (100.00%) were unpaired; of these: 888197 (2.73%) aligned 0 times 25751522 (79.04%) aligned exactly 1 time 5941807 (18.24%) aligned >1 times 97.27% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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 16 files... [bam_rmdupse_core] 18003442 / 31693329 = 0.5681 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 21:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.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 21:26:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:47: 1000000 INFO @ Sun, 21 Jun 2020 21:26:54: 2000000 INFO @ Sun, 21 Jun 2020 21:27:00: 3000000 INFO @ Sun, 21 Jun 2020 21:27:07: 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 21:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.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 21:27:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:13: 5000000 INFO @ Sun, 21 Jun 2020 21:27:17: 1000000 INFO @ Sun, 21 Jun 2020 21:27:20: 6000000 INFO @ Sun, 21 Jun 2020 21:27:24: 2000000 INFO @ Sun, 21 Jun 2020 21:27:28: 7000000 INFO @ Sun, 21 Jun 2020 21:27:31: 3000000 INFO @ Sun, 21 Jun 2020 21:27:35: 8000000 INFO @ Sun, 21 Jun 2020 21:27:37: 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 21:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.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 21:27:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:42: 9000000 INFO @ Sun, 21 Jun 2020 21:27:44: 5000000 INFO @ Sun, 21 Jun 2020 21:27:47: 1000000 INFO @ Sun, 21 Jun 2020 21:27:49: 10000000 INFO @ Sun, 21 Jun 2020 21:27:50: 6000000 INFO @ Sun, 21 Jun 2020 21:27:54: 2000000 INFO @ Sun, 21 Jun 2020 21:27:57: 11000000 INFO @ Sun, 21 Jun 2020 21:27:57: 7000000 INFO @ Sun, 21 Jun 2020 21:28:01: 3000000 INFO @ Sun, 21 Jun 2020 21:28:04: 8000000 INFO @ Sun, 21 Jun 2020 21:28:04: 12000000 INFO @ Sun, 21 Jun 2020 21:28:07: 4000000 INFO @ Sun, 21 Jun 2020 21:28:11: 9000000 INFO @ Sun, 21 Jun 2020 21:28:11: 13000000 INFO @ Sun, 21 Jun 2020 21:28:14: 5000000 INFO @ Sun, 21 Jun 2020 21:28:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:16: #1 total tags in treatment: 13689887 INFO @ Sun, 21 Jun 2020 21:28:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:16: #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 21:28:17: #1 tags after filtering in treatment: 13689738 INFO @ Sun, 21 Jun 2020 21:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:17: 10000000 INFO @ Sun, 21 Jun 2020 21:28:18: #2 number of paired peaks: 13648 INFO @ Sun, 21 Jun 2020 21:28:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:19: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 21:28:19: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 21:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.05_model.r INFO @ Sun, 21 Jun 2020 21:28:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:21: 6000000 INFO @ Sun, 21 Jun 2020 21:28:24: 11000000 INFO @ Sun, 21 Jun 2020 21:28:27: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:28:30: 12000000 INFO @ Sun, 21 Jun 2020 21:28:34: 8000000 INFO @ Sun, 21 Jun 2020 21:28:36: 13000000 INFO @ Sun, 21 Jun 2020 21:28:40: 9000000 INFO @ Sun, 21 Jun 2020 21:28:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:41: #1 total tags in treatment: 13689887 INFO @ Sun, 21 Jun 2020 21:28:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:41: #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 21:28:41: #1 tags after filtering in treatment: 13689738 INFO @ Sun, 21 Jun 2020 21:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:43: #2 number of paired peaks: 13648 INFO @ Sun, 21 Jun 2020 21:28:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:43: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 21:28:43: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 21:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.10_model.r INFO @ Sun, 21 Jun 2020 21:28:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:46: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:28:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:52: 11000000 INFO @ Sun, 21 Jun 2020 21:28:57: 12000000 INFO @ Sun, 21 Jun 2020 21:29:03: 13000000 INFO @ Sun, 21 Jun 2020 21:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:05: Done! pass1 - making usageList (219 chroms): 2 millis pass2 - checking and writing primary data (10904 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:07: #1 total tags in treatment: 13689887 INFO @ Sun, 21 Jun 2020 21:29:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:07: #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 21:29:07: #1 tags after filtering in treatment: 13689738 INFO @ Sun, 21 Jun 2020 21:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:09: #2 number of paired peaks: 13648 INFO @ Sun, 21 Jun 2020 21:29:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:09: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 21:29:09: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 21:29:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.20_model.r INFO @ Sun, 21 Jun 2020 21:29:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:30: Done! pass1 - making usageList (142 chroms): 2 millis pass2 - checking and writing primary data (9375 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923194/SRX4923194.20_summits.bed INFO @ Sun, 21 Jun 2020 21:29:56: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (7610 records, 4 fields): 11 millis CompletedMACS2peakCalling