Job ID = 6368661 SRX = SRX529221 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:16 prefetch.2.10.7: 1) Downloading 'SRR1265825'... 2020-06-16T00:28:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:35 prefetch.2.10.7: 1) 'SRR1265825' was downloaded successfully Read 26022245 spots for SRR1265825/SRR1265825.sra Written 26022245 spots for SRR1265825/SRR1265825.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: 00:04:10 26022245 reads; of these: 26022245 (100.00%) were unpaired; of these: 4977290 (19.13%) aligned 0 times 17210328 (66.14%) aligned exactly 1 time 3834627 (14.74%) aligned >1 times 80.87% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 3725593 / 21044955 = 0.1770 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 09:40:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.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 09:40:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:38: 1000000 INFO @ Tue, 16 Jun 2020 09:40:43: 2000000 INFO @ Tue, 16 Jun 2020 09:40:49: 3000000 INFO @ Tue, 16 Jun 2020 09:40:55: 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 09:41:01: 5000000 INFO @ Tue, 16 Jun 2020 09:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.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 09:41:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:07: 6000000 INFO @ Tue, 16 Jun 2020 09:41:08: 1000000 INFO @ Tue, 16 Jun 2020 09:41:14: 7000000 INFO @ Tue, 16 Jun 2020 09:41:14: 2000000 INFO @ Tue, 16 Jun 2020 09:41:20: 8000000 INFO @ Tue, 16 Jun 2020 09:41:20: 3000000 INFO @ Tue, 16 Jun 2020 09:41:27: 9000000 INFO @ Tue, 16 Jun 2020 09:41:27: 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 09:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.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 09:41:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:33: 10000000 INFO @ Tue, 16 Jun 2020 09:41:33: 5000000 INFO @ Tue, 16 Jun 2020 09:41:38: 1000000 INFO @ Tue, 16 Jun 2020 09:41:40: 11000000 INFO @ Tue, 16 Jun 2020 09:41:40: 6000000 INFO @ Tue, 16 Jun 2020 09:41:45: 2000000 INFO @ Tue, 16 Jun 2020 09:41:46: 12000000 INFO @ Tue, 16 Jun 2020 09:41:47: 7000000 INFO @ Tue, 16 Jun 2020 09:41:51: 3000000 INFO @ Tue, 16 Jun 2020 09:41:53: 13000000 INFO @ Tue, 16 Jun 2020 09:41:53: 8000000 INFO @ Tue, 16 Jun 2020 09:41:58: 4000000 INFO @ Tue, 16 Jun 2020 09:41:59: 14000000 INFO @ Tue, 16 Jun 2020 09:42:00: 9000000 INFO @ Tue, 16 Jun 2020 09:42:05: 5000000 INFO @ Tue, 16 Jun 2020 09:42:06: 15000000 INFO @ Tue, 16 Jun 2020 09:42:07: 10000000 INFO @ Tue, 16 Jun 2020 09:42:12: 6000000 INFO @ Tue, 16 Jun 2020 09:42:13: 16000000 INFO @ Tue, 16 Jun 2020 09:42:14: 11000000 INFO @ Tue, 16 Jun 2020 09:42:19: 7000000 INFO @ Tue, 16 Jun 2020 09:42:20: 17000000 INFO @ Tue, 16 Jun 2020 09:42:21: 12000000 INFO @ Tue, 16 Jun 2020 09:42:22: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:42:22: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:42:22: #1 total tags in treatment: 17319362 INFO @ Tue, 16 Jun 2020 09:42:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:22: #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 09:42:22: #1 tags after filtering in treatment: 17319362 INFO @ Tue, 16 Jun 2020 09:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:23: #2 number of paired peaks: 374 WARNING @ Tue, 16 Jun 2020 09:42:23: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:23: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 09:42:23: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 09:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.05_model.r INFO @ Tue, 16 Jun 2020 09:42:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:26: 8000000 INFO @ Tue, 16 Jun 2020 09:42:28: 13000000 INFO @ Tue, 16 Jun 2020 09:42:33: 9000000 INFO @ Tue, 16 Jun 2020 09:42:35: 14000000 INFO @ Tue, 16 Jun 2020 09:42:39: 10000000 INFO @ Tue, 16 Jun 2020 09:42:42: 15000000 INFO @ Tue, 16 Jun 2020 09:42:46: 11000000 INFO @ Tue, 16 Jun 2020 09:42:49: 16000000 INFO @ Tue, 16 Jun 2020 09:42:53: 12000000 INFO @ Tue, 16 Jun 2020 09:42:56: 17000000 INFO @ Tue, 16 Jun 2020 09:42:57: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:42:59: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:42:59: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:42:59: #1 total tags in treatment: 17319362 INFO @ Tue, 16 Jun 2020 09:42:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:59: #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 09:42:59: #1 tags after filtering in treatment: 17319362 INFO @ Tue, 16 Jun 2020 09:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:00: 13000000 INFO @ Tue, 16 Jun 2020 09:43:00: #2 number of paired peaks: 374 WARNING @ Tue, 16 Jun 2020 09:43:00: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:00: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 09:43:00: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 09:43:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.10_model.r INFO @ Tue, 16 Jun 2020 09:43:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:07: 14000000 INFO @ Tue, 16 Jun 2020 09:43:13: 15000000 INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2963 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:19: 16000000 INFO @ Tue, 16 Jun 2020 09:43:26: 17000000 INFO @ Tue, 16 Jun 2020 09:43:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:43:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:43:28: #1 total tags in treatment: 17319362 INFO @ Tue, 16 Jun 2020 09:43:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:28: #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 09:43:28: #1 tags after filtering in treatment: 17319362 INFO @ Tue, 16 Jun 2020 09:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:29: #2 number of paired peaks: 374 WARNING @ Tue, 16 Jun 2020 09:43:29: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:30: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 09:43:30: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 09:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.20_model.r INFO @ Tue, 16 Jun 2020 09:43:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2033 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529221/SRX529221.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1367 records, 4 fields): 3 millis CompletedMACS2peakCalling