Job ID = 6366072 SRX = SRX059244 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:07 prefetch.2.10.7: 1) Downloading 'SRR190684'... 2020-06-15T22:45:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:33 prefetch.2.10.7: 'SRR190684' is valid 2020-06-15T22:46:33 prefetch.2.10.7: 1) 'SRR190684' was downloaded successfully Read 16597845 spots for SRR190684/SRR190684.sra Written 16597845 spots for SRR190684/SRR190684.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: 00:02:57 16597845 reads; of these: 16597845 (100.00%) were unpaired; of these: 323365 (1.95%) aligned 0 times 13614008 (82.02%) aligned exactly 1 time 2660472 (16.03%) aligned >1 times 98.05% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 1938995 / 16274480 = 0.1191 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 07:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.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 07:53:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:46: 1000000 INFO @ Tue, 16 Jun 2020 07:53:51: 2000000 INFO @ Tue, 16 Jun 2020 07:53:57: 3000000 INFO @ Tue, 16 Jun 2020 07:54:02: 4000000 INFO @ Tue, 16 Jun 2020 07:54:08: 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 07:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.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 07:54:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:13: 6000000 INFO @ Tue, 16 Jun 2020 07:54:16: 1000000 INFO @ Tue, 16 Jun 2020 07:54:19: 7000000 INFO @ Tue, 16 Jun 2020 07:54:21: 2000000 INFO @ Tue, 16 Jun 2020 07:54:25: 8000000 INFO @ Tue, 16 Jun 2020 07:54:27: 3000000 INFO @ Tue, 16 Jun 2020 07:54:30: 9000000 INFO @ Tue, 16 Jun 2020 07:54:33: 4000000 INFO @ Tue, 16 Jun 2020 07:54:36: 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 07:54:39: 5000000 INFO @ Tue, 16 Jun 2020 07:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.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 07:54:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:42: 11000000 INFO @ Tue, 16 Jun 2020 07:54:45: 6000000 INFO @ Tue, 16 Jun 2020 07:54:46: 1000000 INFO @ Tue, 16 Jun 2020 07:54:48: 12000000 INFO @ Tue, 16 Jun 2020 07:54:50: 7000000 INFO @ Tue, 16 Jun 2020 07:54:52: 2000000 INFO @ Tue, 16 Jun 2020 07:54:54: 13000000 INFO @ Tue, 16 Jun 2020 07:54:56: 8000000 INFO @ Tue, 16 Jun 2020 07:54:57: 3000000 INFO @ Tue, 16 Jun 2020 07:55:00: 14000000 INFO @ Tue, 16 Jun 2020 07:55:02: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:55:02: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:55:02: #1 total tags in treatment: 14335485 INFO @ Tue, 16 Jun 2020 07:55:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:02: #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 07:55:02: #1 tags after filtering in treatment: 14335485 INFO @ Tue, 16 Jun 2020 07:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:02: 9000000 INFO @ Tue, 16 Jun 2020 07:55:03: 4000000 INFO @ Tue, 16 Jun 2020 07:55:03: #2 number of paired peaks: 596 WARNING @ Tue, 16 Jun 2020 07:55:03: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:03: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 07:55:03: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 16 Jun 2020 07:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.05_model.r INFO @ Tue, 16 Jun 2020 07:55:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:55:08: 10000000 INFO @ Tue, 16 Jun 2020 07:55:08: 5000000 INFO @ Tue, 16 Jun 2020 07:55:14: 11000000 INFO @ Tue, 16 Jun 2020 07:55:14: 6000000 INFO @ Tue, 16 Jun 2020 07:55:19: 7000000 INFO @ Tue, 16 Jun 2020 07:55:20: 12000000 INFO @ Tue, 16 Jun 2020 07:55:25: 8000000 INFO @ Tue, 16 Jun 2020 07:55:25: 13000000 INFO @ Tue, 16 Jun 2020 07:55:30: 9000000 INFO @ Tue, 16 Jun 2020 07:55:31: 14000000 INFO @ Tue, 16 Jun 2020 07:55:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:55:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:55:33: #1 total tags in treatment: 14335485 INFO @ Tue, 16 Jun 2020 07:55:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:33: #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 07:55:33: #1 tags after filtering in treatment: 14335485 INFO @ Tue, 16 Jun 2020 07:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:34: #2 number of paired peaks: 596 WARNING @ Tue, 16 Jun 2020 07:55:34: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:34: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:34: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:34: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:34: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:34: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 07:55:34: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 16 Jun 2020 07:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.10_model.r INFO @ Tue, 16 Jun 2020 07:55:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:55:36: 10000000 INFO @ Tue, 16 Jun 2020 07:55:41: 11000000 INFO @ Tue, 16 Jun 2020 07:55:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.05_summits.bed INFO @ Tue, 16 Jun 2020 07:55:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9305 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:55:50: 13000000 INFO @ Tue, 16 Jun 2020 07:55:55: 14000000 INFO @ Tue, 16 Jun 2020 07:55:57: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:55:57: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:55:57: #1 total tags in treatment: 14335485 INFO @ Tue, 16 Jun 2020 07:55:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:57: #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 07:55:57: #1 tags after filtering in treatment: 14335485 INFO @ Tue, 16 Jun 2020 07:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:59: #2 number of paired peaks: 596 WARNING @ Tue, 16 Jun 2020 07:55:59: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:59: #2 predicted fragment length is 113 bps INFO @ Tue, 16 Jun 2020 07:55:59: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 16 Jun 2020 07:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.20_model.r INFO @ Tue, 16 Jun 2020 07:55:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.10_summits.bed INFO @ Tue, 16 Jun 2020 07:56:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4364 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:56:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059244/SRX059244.20_summits.bed INFO @ Tue, 16 Jun 2020 07:56:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1698 records, 4 fields): 3 millis CompletedMACS2peakCalling