Job ID = 6368105 SRX = SRX466568 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:59:05 prefetch.2.10.7: 1) Downloading 'SRR1163634'... 2020-06-15T23:59:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:09 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:09 prefetch.2.10.7: 1) 'SRR1163634' was downloaded successfully Read 20261247 spots for SRR1163634/SRR1163634.sra Written 20261247 spots for SRR1163634/SRR1163634.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: 00:04:43 20261247 reads; of these: 20261247 (100.00%) were unpaired; of these: 3121078 (15.40%) aligned 0 times 13592806 (67.09%) aligned exactly 1 time 3547363 (17.51%) aligned >1 times 84.60% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10037450 / 17140169 = 0.5856 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 @ Tue, 16 Jun 2020 09:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:10:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:39: 1000000 INFO @ Tue, 16 Jun 2020 09:10:45: 2000000 INFO @ Tue, 16 Jun 2020 09:10:51: 3000000 INFO @ Tue, 16 Jun 2020 09:10:57: 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 @ Tue, 16 Jun 2020 09:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:11:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:04: 5000000 INFO @ Tue, 16 Jun 2020 09:11:09: 1000000 INFO @ Tue, 16 Jun 2020 09:11:10: 6000000 INFO @ Tue, 16 Jun 2020 09:11:14: 2000000 INFO @ Tue, 16 Jun 2020 09:11:16: 7000000 INFO @ Tue, 16 Jun 2020 09:11:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:17: #1 total tags in treatment: 7102719 INFO @ Tue, 16 Jun 2020 09:11:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:17: #1 tags after filtering in treatment: 7102719 INFO @ Tue, 16 Jun 2020 09:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:18: #2 number of paired peaks: 3092 INFO @ Tue, 16 Jun 2020 09:11:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:18: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:11:18: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 09:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.05_model.r INFO @ Tue, 16 Jun 2020 09:11:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:20: 3000000 INFO @ Tue, 16 Jun 2020 09:11:25: 4000000 INFO @ Tue, 16 Jun 2020 09:11:30: 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 @ Tue, 16 Jun 2020 09:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:11:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:36: 6000000 INFO @ Tue, 16 Jun 2020 09:11:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:38: 1000000 INFO @ Tue, 16 Jun 2020 09:11:41: 7000000 INFO @ Tue, 16 Jun 2020 09:11:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:42: #1 total tags in treatment: 7102719 INFO @ Tue, 16 Jun 2020 09:11:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:42: #1 tags after filtering in treatment: 7102719 INFO @ Tue, 16 Jun 2020 09:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:43: #2 number of paired peaks: 3092 INFO @ Tue, 16 Jun 2020 09:11:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:43: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:11:43: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 09:11:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.10_model.r INFO @ Tue, 16 Jun 2020 09:11:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:43: 2000000 INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6397 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:48: 3000000 INFO @ Tue, 16 Jun 2020 09:11:54: 4000000 INFO @ Tue, 16 Jun 2020 09:11:59: 5000000 INFO @ Tue, 16 Jun 2020 09:12:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:04: 6000000 INFO @ Tue, 16 Jun 2020 09:12:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:10: #1 total tags in treatment: 7102719 INFO @ Tue, 16 Jun 2020 09:12:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:10: #1 tags after filtering in treatment: 7102719 INFO @ Tue, 16 Jun 2020 09:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:11: #2 number of paired peaks: 3092 INFO @ Tue, 16 Jun 2020 09:12:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:11: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:12:11: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 09:12:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.20_model.r INFO @ Tue, 16 Jun 2020 09:12:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4504 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466568/SRX466568.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2922 records, 4 fields): 4 millis CompletedMACS2peakCalling