Job ID = 8184566 SRX = SRX8047614 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:38:04 prefetch.2.10.7: 1) Downloading 'SRR11471338'... 2020-08-10T04:38:04 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:39:04 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:39:04 prefetch.2.10.7: 1) 'SRR11471338' was downloaded successfully Read 17783748 spots for SRR11471338/SRR11471338.sra Written 17783748 spots for SRR11471338/SRR11471338.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:29 17783748 reads; of these: 17783748 (100.00%) were unpaired; of these: 1552590 (8.73%) aligned 0 times 13522290 (76.04%) aligned exactly 1 time 2708868 (15.23%) aligned >1 times 91.27% overall alignment rate Time searching: 00:13:33 Overall time: 00:13:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7326151 / 16231158 = 0.4514 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 @ Mon, 10 Aug 2020 13:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 13:57:19: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:57:19: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:57:26: 1000000 INFO @ Mon, 10 Aug 2020 13:57:32: 2000000 INFO @ Mon, 10 Aug 2020 13:57:38: 3000000 INFO @ Mon, 10 Aug 2020 13:57:44: 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 @ Mon, 10 Aug 2020 13:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 13:57:49: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:57:49: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:57:51: 5000000 INFO @ Mon, 10 Aug 2020 13:57:56: 1000000 INFO @ Mon, 10 Aug 2020 13:57:57: 6000000 INFO @ Mon, 10 Aug 2020 13:58:03: 2000000 INFO @ Mon, 10 Aug 2020 13:58:04: 7000000 INFO @ Mon, 10 Aug 2020 13:58:09: 3000000 INFO @ Mon, 10 Aug 2020 13:58:10: 8000000 INFO @ Mon, 10 Aug 2020 13:58:16: 4000000 INFO @ Mon, 10 Aug 2020 13:58:16: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:58:16: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:58:16: #1 total tags in treatment: 8905007 INFO @ Mon, 10 Aug 2020 13:58:16: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:58:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:58:17: #1 tags after filtering in treatment: 8904773 INFO @ Mon, 10 Aug 2020 13:58:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:58:17: #1 finished! INFO @ Mon, 10 Aug 2020 13:58:17: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:58:17: #2 looking for paired plus/minus strand peaks... 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 @ Mon, 10 Aug 2020 13:58:18: #2 number of paired peaks: 41075 INFO @ Mon, 10 Aug 2020 13:58:18: start model_add_line... INFO @ Mon, 10 Aug 2020 13:58:19: start X-correlation... INFO @ Mon, 10 Aug 2020 13:58:19: end of X-cor INFO @ Mon, 10 Aug 2020 13:58:19: #2 finished! INFO @ Mon, 10 Aug 2020 13:58:19: #2 predicted fragment length is 105 bps INFO @ Mon, 10 Aug 2020 13:58:19: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 10 Aug 2020 13:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.05_model.r INFO @ Mon, 10 Aug 2020 13:58:19: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 13:58:19: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:58:19: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:58:22: 5000000 INFO @ Mon, 10 Aug 2020 13:58:26: 1000000 INFO @ Mon, 10 Aug 2020 13:58:29: 6000000 INFO @ Mon, 10 Aug 2020 13:58:32: 2000000 INFO @ Mon, 10 Aug 2020 13:58:35: 7000000 INFO @ Mon, 10 Aug 2020 13:58:38: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:58:39: 3000000 INFO @ Mon, 10 Aug 2020 13:58:42: 8000000 INFO @ Mon, 10 Aug 2020 13:58:45: 4000000 INFO @ Mon, 10 Aug 2020 13:58:48: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:58:48: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:58:48: #1 total tags in treatment: 8905007 INFO @ Mon, 10 Aug 2020 13:58:48: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:58:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:58:48: #1 tags after filtering in treatment: 8904773 INFO @ Mon, 10 Aug 2020 13:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:58:48: #1 finished! INFO @ Mon, 10 Aug 2020 13:58:48: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.05_summits.bed INFO @ Mon, 10 Aug 2020 13:58:50: Done! pass1 - making usageList (144 chroms): 5 millis INFO @ Mon, 10 Aug 2020 13:58:50: #2 number of paired peaks: 41075 INFO @ Mon, 10 Aug 2020 13:58:50: start model_add_line... pass2 - checking and writing primary data (32683 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:58:50: start X-correlation... INFO @ Mon, 10 Aug 2020 13:58:50: end of X-cor INFO @ Mon, 10 Aug 2020 13:58:50: #2 finished! INFO @ Mon, 10 Aug 2020 13:58:50: #2 predicted fragment length is 105 bps INFO @ Mon, 10 Aug 2020 13:58:50: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 10 Aug 2020 13:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.10_model.r INFO @ Mon, 10 Aug 2020 13:58:50: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:58:52: 5000000 INFO @ Mon, 10 Aug 2020 13:58:58: 6000000 INFO @ Mon, 10 Aug 2020 13:59:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:59:10: 8000000 INFO @ Mon, 10 Aug 2020 13:59:10: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:59:15: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:59:15: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:59:15: #1 total tags in treatment: 8905007 INFO @ Mon, 10 Aug 2020 13:59:15: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:59:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:59:16: #1 tags after filtering in treatment: 8904773 INFO @ Mon, 10 Aug 2020 13:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:59:16: #1 finished! INFO @ Mon, 10 Aug 2020 13:59:16: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:59:17: #2 number of paired peaks: 41075 INFO @ Mon, 10 Aug 2020 13:59:17: start model_add_line... INFO @ Mon, 10 Aug 2020 13:59:18: start X-correlation... INFO @ Mon, 10 Aug 2020 13:59:18: end of X-cor INFO @ Mon, 10 Aug 2020 13:59:18: #2 finished! INFO @ Mon, 10 Aug 2020 13:59:18: #2 predicted fragment length is 105 bps INFO @ Mon, 10 Aug 2020 13:59:18: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 10 Aug 2020 13:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.20_model.r INFO @ Mon, 10 Aug 2020 13:59:18: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:59:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:59:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:59:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.10_summits.bed INFO @ Mon, 10 Aug 2020 13:59:21: Done! pass1 - making usageList (111 chroms): 4 millis pass2 - checking and writing primary data (22993 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:59:38: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047614/SRX8047614.20_summits.bed INFO @ Mon, 10 Aug 2020 13:59:48: Done! pass1 - making usageList (86 chroms): 2 millis pass2 - checking and writing primary data (13605 records, 4 fields): 14 millis CompletedMACS2peakCalling