Job ID = 6367023 SRX = SRX2710284 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:01 prefetch.2.10.7: 1) Downloading 'SRR5418738'... 2020-06-15T23:10:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:17 prefetch.2.10.7: 1) 'SRR5418738' was downloaded successfully Read 37102286 spots for SRR5418738/SRR5418738.sra Written 37102286 spots for SRR5418738/SRR5418738.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: 00:09:01 37102286 reads; of these: 37102286 (100.00%) were unpaired; of these: 7904647 (21.31%) aligned 0 times 15628849 (42.12%) aligned exactly 1 time 13568790 (36.57%) aligned >1 times 78.69% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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 12 files... [bam_rmdupse_core] 15849326 / 29197639 = 0.5428 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 08:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.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 08:31:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:25: 1000000 INFO @ Tue, 16 Jun 2020 08:31:31: 2000000 INFO @ Tue, 16 Jun 2020 08:31:36: 3000000 INFO @ Tue, 16 Jun 2020 08:31:42: 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 08:31:48: 5000000 INFO @ Tue, 16 Jun 2020 08:31:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.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 08:31:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:53: 6000000 INFO @ Tue, 16 Jun 2020 08:31:55: 1000000 INFO @ Tue, 16 Jun 2020 08:32:00: 7000000 INFO @ Tue, 16 Jun 2020 08:32:02: 2000000 INFO @ Tue, 16 Jun 2020 08:32:06: 8000000 INFO @ Tue, 16 Jun 2020 08:32:08: 3000000 INFO @ Tue, 16 Jun 2020 08:32:12: 9000000 INFO @ Tue, 16 Jun 2020 08:32:14: 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 @ Tue, 16 Jun 2020 08:32:18: 10000000 INFO @ Tue, 16 Jun 2020 08:32:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.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 08:32:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:20: 5000000 INFO @ Tue, 16 Jun 2020 08:32:24: 11000000 INFO @ Tue, 16 Jun 2020 08:32:27: 6000000 INFO @ Tue, 16 Jun 2020 08:32:27: 1000000 INFO @ Tue, 16 Jun 2020 08:32:31: 12000000 INFO @ Tue, 16 Jun 2020 08:32:33: 7000000 INFO @ Tue, 16 Jun 2020 08:32:34: 2000000 INFO @ Tue, 16 Jun 2020 08:32:37: 13000000 INFO @ Tue, 16 Jun 2020 08:32:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:32:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:32:40: #1 total tags in treatment: 13348313 INFO @ Tue, 16 Jun 2020 08:32:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:40: #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 08:32:40: 8000000 INFO @ Tue, 16 Jun 2020 08:32:40: #1 tags after filtering in treatment: 13348313 INFO @ Tue, 16 Jun 2020 08:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:41: #2 number of paired peaks: 1283 INFO @ Tue, 16 Jun 2020 08:32:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:41: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:32:41: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.05_model.r INFO @ Tue, 16 Jun 2020 08:32:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:42: 3000000 INFO @ Tue, 16 Jun 2020 08:32:46: 9000000 INFO @ Tue, 16 Jun 2020 08:32:49: 4000000 INFO @ Tue, 16 Jun 2020 08:32:53: 10000000 INFO @ Tue, 16 Jun 2020 08:32:56: 5000000 INFO @ Tue, 16 Jun 2020 08:32:59: 11000000 INFO @ Tue, 16 Jun 2020 08:33:04: 6000000 INFO @ Tue, 16 Jun 2020 08:33:06: 12000000 INFO @ Tue, 16 Jun 2020 08:33:11: 7000000 INFO @ Tue, 16 Jun 2020 08:33:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:12: 13000000 INFO @ Tue, 16 Jun 2020 08:33:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:14: #1 total tags in treatment: 13348313 INFO @ Tue, 16 Jun 2020 08:33:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:14: #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 08:33:15: #1 tags after filtering in treatment: 13348313 INFO @ Tue, 16 Jun 2020 08:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #2 number of paired peaks: 1283 INFO @ Tue, 16 Jun 2020 08:33:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:16: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.10_model.r INFO @ Tue, 16 Jun 2020 08:33:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:18: 8000000 INFO @ Tue, 16 Jun 2020 08:33:25: 9000000 INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14198 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:32: 10000000 INFO @ Tue, 16 Jun 2020 08:33:39: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:46: 12000000 INFO @ Tue, 16 Jun 2020 08:33:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:53: 13000000 INFO @ Tue, 16 Jun 2020 08:33:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:55: #1 total tags in treatment: 13348313 INFO @ Tue, 16 Jun 2020 08:33:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:55: #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 08:33:55: #1 tags after filtering in treatment: 13348313 INFO @ Tue, 16 Jun 2020 08:33:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:56: #2 number of paired peaks: 1283 INFO @ Tue, 16 Jun 2020 08:33:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:57: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:33:57: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.20_model.r INFO @ Tue, 16 Jun 2020 08:33:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9450 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710284/SRX2710284.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5300 records, 4 fields): 6 millis CompletedMACS2peakCalling