Job ID = 6366936 SRX = SRX2576638 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:47 prefetch.2.10.7: 1) Downloading 'SRR5272595'... 2020-06-15T23:13:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:08 prefetch.2.10.7: 'SRR5272595' is valid 2020-06-15T23:15:08 prefetch.2.10.7: 1) 'SRR5272595' was downloaded successfully 2020-06-15T23:15:08 prefetch.2.10.7: 'SRR5272595' has 0 unresolved dependencies Read 23329304 spots for SRR5272595/SRR5272595.sra Written 23329304 spots for SRR5272595/SRR5272595.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: 00:05:20 23329304 reads; of these: 23329304 (100.00%) were unpaired; of these: 1500708 (6.43%) aligned 0 times 17632206 (75.58%) aligned exactly 1 time 4196390 (17.99%) aligned >1 times 93.57% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 10067546 / 21828596 = 0.4612 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 08:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.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 08:25:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:26: 1000000 INFO @ Tue, 16 Jun 2020 08:25:33: 2000000 INFO @ Tue, 16 Jun 2020 08:25:39: 3000000 INFO @ Tue, 16 Jun 2020 08:25:45: 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 08:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.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 08:25:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:52: 5000000 INFO @ Tue, 16 Jun 2020 08:25:57: 1000000 INFO @ Tue, 16 Jun 2020 08:25:59: 6000000 INFO @ Tue, 16 Jun 2020 08:26:04: 2000000 INFO @ Tue, 16 Jun 2020 08:26:06: 7000000 INFO @ Tue, 16 Jun 2020 08:26:11: 3000000 INFO @ Tue, 16 Jun 2020 08:26:14: 8000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:26:18: 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 08:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.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 08:26:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:21: 9000000 INFO @ Tue, 16 Jun 2020 08:26:25: 5000000 INFO @ Tue, 16 Jun 2020 08:26:28: 1000000 INFO @ Tue, 16 Jun 2020 08:26:29: 10000000 INFO @ Tue, 16 Jun 2020 08:26:32: 6000000 INFO @ Tue, 16 Jun 2020 08:26:35: 2000000 INFO @ Tue, 16 Jun 2020 08:26:36: 11000000 INFO @ Tue, 16 Jun 2020 08:26:38: 7000000 INFO @ Tue, 16 Jun 2020 08:26:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:42: #1 total tags in treatment: 11761050 INFO @ Tue, 16 Jun 2020 08:26:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:42: #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 08:26:42: #1 tags after filtering in treatment: 11761050 INFO @ Tue, 16 Jun 2020 08:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:43: 3000000 INFO @ Tue, 16 Jun 2020 08:26:43: #2 number of paired peaks: 1480 INFO @ Tue, 16 Jun 2020 08:26:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:43: #2 predicted fragment length is 211 bps INFO @ Tue, 16 Jun 2020 08:26:43: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 16 Jun 2020 08:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.05_model.r INFO @ Tue, 16 Jun 2020 08:26:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:45: 8000000 INFO @ Tue, 16 Jun 2020 08:26:51: 4000000 INFO @ Tue, 16 Jun 2020 08:26:52: 9000000 INFO @ Tue, 16 Jun 2020 08:26:58: 5000000 INFO @ Tue, 16 Jun 2020 08:26:58: 10000000 INFO @ Tue, 16 Jun 2020 08:27:05: 11000000 INFO @ Tue, 16 Jun 2020 08:27:06: 6000000 INFO @ Tue, 16 Jun 2020 08:27:10: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:10: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:10: #1 total tags in treatment: 11761050 INFO @ Tue, 16 Jun 2020 08:27:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:10: #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 08:27:10: #1 tags after filtering in treatment: 11761050 INFO @ Tue, 16 Jun 2020 08:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:11: #2 number of paired peaks: 1480 INFO @ Tue, 16 Jun 2020 08:27:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:11: #2 predicted fragment length is 211 bps INFO @ Tue, 16 Jun 2020 08:27:11: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 16 Jun 2020 08:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.10_model.r INFO @ Tue, 16 Jun 2020 08:27:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:13: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:27:20: 8000000 INFO @ Tue, 16 Jun 2020 08:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3347 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:27: 9000000 INFO @ Tue, 16 Jun 2020 08:27:34: 10000000 INFO @ Tue, 16 Jun 2020 08:27:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:40: 11000000 INFO @ Tue, 16 Jun 2020 08:27:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:45: #1 total tags in treatment: 11761050 INFO @ Tue, 16 Jun 2020 08:27:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:45: #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 08:27:46: #1 tags after filtering in treatment: 11761050 INFO @ Tue, 16 Jun 2020 08:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:47: #2 number of paired peaks: 1480 INFO @ Tue, 16 Jun 2020 08:27:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:47: #2 predicted fragment length is 211 bps INFO @ Tue, 16 Jun 2020 08:27:47: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 16 Jun 2020 08:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.20_model.r INFO @ Tue, 16 Jun 2020 08:27:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2571 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576638/SRX2576638.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1899 records, 4 fields): 3 millis CompletedMACS2peakCalling