Job ID = 6366067 SRX = SRX059239 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:31:14 prefetch.2.10.7: 1) Downloading 'SRR190679'... 2020-06-15T22:31:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:33 prefetch.2.10.7: 1) 'SRR190679' was downloaded successfully Read 27183911 spots for SRR190679/SRR190679.sra Written 27183911 spots for SRR190679/SRR190679.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: 00:04:32 27183911 reads; of these: 27183911 (100.00%) were unpaired; of these: 1785844 (6.57%) aligned 0 times 21742320 (79.98%) aligned exactly 1 time 3655747 (13.45%) aligned >1 times 93.43% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 3779873 / 25398067 = 0.1488 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 07:45:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.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 07:45:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:11: 1000000 INFO @ Tue, 16 Jun 2020 07:45:17: 2000000 INFO @ Tue, 16 Jun 2020 07:45:22: 3000000 INFO @ Tue, 16 Jun 2020 07:45:27: 4000000 INFO @ Tue, 16 Jun 2020 07:45:32: 5000000 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 07:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.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 07:45:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:37: 6000000 INFO @ Tue, 16 Jun 2020 07:45:42: 1000000 INFO @ Tue, 16 Jun 2020 07:45:43: 7000000 INFO @ Tue, 16 Jun 2020 07:45:47: 2000000 INFO @ Tue, 16 Jun 2020 07:45:49: 8000000 INFO @ Tue, 16 Jun 2020 07:45:53: 3000000 INFO @ Tue, 16 Jun 2020 07:45:54: 9000000 INFO @ Tue, 16 Jun 2020 07:45:58: 4000000 INFO @ Tue, 16 Jun 2020 07:46:00: 10000000 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 07:46:04: 5000000 INFO @ Tue, 16 Jun 2020 07:46:06: 11000000 INFO @ Tue, 16 Jun 2020 07:46:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.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 07:46:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:10: 6000000 INFO @ Tue, 16 Jun 2020 07:46:11: 12000000 INFO @ Tue, 16 Jun 2020 07:46:12: 1000000 INFO @ Tue, 16 Jun 2020 07:46:15: 7000000 INFO @ Tue, 16 Jun 2020 07:46:17: 13000000 INFO @ Tue, 16 Jun 2020 07:46:17: 2000000 INFO @ Tue, 16 Jun 2020 07:46:21: 8000000 INFO @ Tue, 16 Jun 2020 07:46:22: 14000000 INFO @ Tue, 16 Jun 2020 07:46:23: 3000000 INFO @ Tue, 16 Jun 2020 07:46:27: 9000000 INFO @ Tue, 16 Jun 2020 07:46:28: 15000000 INFO @ Tue, 16 Jun 2020 07:46:29: 4000000 INFO @ Tue, 16 Jun 2020 07:46:32: 10000000 INFO @ Tue, 16 Jun 2020 07:46:34: 16000000 INFO @ Tue, 16 Jun 2020 07:46:35: 5000000 INFO @ Tue, 16 Jun 2020 07:46:38: 11000000 INFO @ Tue, 16 Jun 2020 07:46:39: 17000000 INFO @ Tue, 16 Jun 2020 07:46:40: 6000000 INFO @ Tue, 16 Jun 2020 07:46:44: 12000000 INFO @ Tue, 16 Jun 2020 07:46:45: 18000000 INFO @ Tue, 16 Jun 2020 07:46:46: 7000000 INFO @ Tue, 16 Jun 2020 07:46:49: 13000000 INFO @ Tue, 16 Jun 2020 07:46:51: 19000000 INFO @ Tue, 16 Jun 2020 07:46:52: 8000000 INFO @ Tue, 16 Jun 2020 07:46:55: 14000000 INFO @ Tue, 16 Jun 2020 07:46:57: 20000000 INFO @ Tue, 16 Jun 2020 07:46:58: 9000000 INFO @ Tue, 16 Jun 2020 07:47:01: 15000000 INFO @ Tue, 16 Jun 2020 07:47:02: 21000000 INFO @ Tue, 16 Jun 2020 07:47:03: 10000000 INFO @ Tue, 16 Jun 2020 07:47:06: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:06: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:06: #1 total tags in treatment: 21618194 INFO @ Tue, 16 Jun 2020 07:47:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:06: #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 07:47:07: #1 tags after filtering in treatment: 21618194 INFO @ Tue, 16 Jun 2020 07:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:07: 16000000 INFO @ Tue, 16 Jun 2020 07:47:08: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 07:47:08: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:08: #2 predicted fragment length is 82 bps INFO @ Tue, 16 Jun 2020 07:47:08: #2 alternative fragment length(s) may be 2,59,82,570 bps INFO @ Tue, 16 Jun 2020 07:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.05_model.r INFO @ Tue, 16 Jun 2020 07:47:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:09: 11000000 INFO @ Tue, 16 Jun 2020 07:47:13: 17000000 INFO @ Tue, 16 Jun 2020 07:47:15: 12000000 INFO @ Tue, 16 Jun 2020 07:47:18: 18000000 INFO @ Tue, 16 Jun 2020 07:47:21: 13000000 INFO @ Tue, 16 Jun 2020 07:47:24: 19000000 INFO @ Tue, 16 Jun 2020 07:47:26: 14000000 INFO @ Tue, 16 Jun 2020 07:47:30: 20000000 INFO @ Tue, 16 Jun 2020 07:47:32: 15000000 INFO @ Tue, 16 Jun 2020 07:47:36: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:47:38: 16000000 INFO @ Tue, 16 Jun 2020 07:47:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:39: #1 total tags in treatment: 21618194 INFO @ Tue, 16 Jun 2020 07:47:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:39: #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 07:47:40: #1 tags after filtering in treatment: 21618194 INFO @ Tue, 16 Jun 2020 07:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:41: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 07:47:41: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:41: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:41: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:41: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:41: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:41: #2 predicted fragment length is 82 bps INFO @ Tue, 16 Jun 2020 07:47:41: #2 alternative fragment length(s) may be 2,59,82,570 bps INFO @ Tue, 16 Jun 2020 07:47:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.10_model.r INFO @ Tue, 16 Jun 2020 07:47:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:43: 17000000 INFO @ Tue, 16 Jun 2020 07:47:49: 18000000 INFO @ Tue, 16 Jun 2020 07:47:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:54: 19000000 INFO @ Tue, 16 Jun 2020 07:48:00: 20000000 INFO @ Tue, 16 Jun 2020 07:48:06: 21000000 INFO @ Tue, 16 Jun 2020 07:48:09: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:48:09: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:48:09: #1 total tags in treatment: 21618194 INFO @ Tue, 16 Jun 2020 07:48:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:09: #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 07:48:10: #1 tags after filtering in treatment: 21618194 INFO @ Tue, 16 Jun 2020 07:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:10: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:11: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 07:48:11: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 07:48:11: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:11: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:11: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:11: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:11: #2 predicted fragment length is 82 bps INFO @ Tue, 16 Jun 2020 07:48:11: #2 alternative fragment length(s) may be 2,59,82,570 bps INFO @ Tue, 16 Jun 2020 07:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.20_model.r INFO @ Tue, 16 Jun 2020 07:48:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.05_summits.bed INFO @ Tue, 16 Jun 2020 07:48:16: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (14586 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.10_summits.bed INFO @ Tue, 16 Jun 2020 07:48:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6600 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059239/SRX059239.20_summits.bed INFO @ Tue, 16 Jun 2020 07:49:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1783 records, 4 fields): 3 millis CompletedMACS2peakCalling