Job ID = 6366351 SRX = SRX118227 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:22 prefetch.2.10.7: 1) Downloading 'SRR403234'... 2020-06-15T22:42:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:42:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:42:48 prefetch.2.10.7: 'SRR403234' is valid 2020-06-15T22:42:48 prefetch.2.10.7: 1) 'SRR403234' was downloaded successfully Read 4432009 spots for SRR403234/SRR403234.sra Written 4432009 spots for SRR403234/SRR403234.sra 2020-06-15T22:43:10 prefetch.2.10.7: 1) Downloading 'SRR403235'... 2020-06-15T22:43:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:49 prefetch.2.10.7: 'SRR403235' is valid 2020-06-15T22:43:49 prefetch.2.10.7: 1) 'SRR403235' was downloaded successfully Read 6810026 spots for SRR403235/SRR403235.sra Written 6810026 spots for SRR403235/SRR403235.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: 00:00:45 11242035 reads; of these: 11242035 (100.00%) were unpaired; of these: 9724936 (86.51%) aligned 0 times 1254202 (11.16%) aligned exactly 1 time 262897 (2.34%) aligned >1 times 13.49% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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_rmdupse_core] 91113 / 1517099 = 0.0601 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 07:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.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 07:45:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:54: 1000000 INFO @ Tue, 16 Jun 2020 07:45:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:45:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:45:57: #1 total tags in treatment: 1425986 INFO @ Tue, 16 Jun 2020 07:45:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:57: #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 07:45:57: #1 tags after filtering in treatment: 1425986 INFO @ Tue, 16 Jun 2020 07:45:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:57: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:45:57: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:57: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:45:57: #2 alternative fragment length(s) may be 37,563 bps INFO @ Tue, 16 Jun 2020 07:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.05_model.r WARNING @ Tue, 16 Jun 2020 07:45:57: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:45:57: #2 You may need to consider one of the other alternative d(s): 37,563 WARNING @ Tue, 16 Jun 2020 07:45:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:45:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.05_summits.bed INFO @ Tue, 16 Jun 2020 07:46:02: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (263 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.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 07:46:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:24: 1000000 INFO @ Tue, 16 Jun 2020 07:46:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:46:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:46:26: #1 total tags in treatment: 1425986 INFO @ Tue, 16 Jun 2020 07:46:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:26: #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 07:46:26: #1 tags after filtering in treatment: 1425986 INFO @ Tue, 16 Jun 2020 07:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:26: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:46:26: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:46:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:26: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:46:26: #2 alternative fragment length(s) may be 37,563 bps INFO @ Tue, 16 Jun 2020 07:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.10_model.r WARNING @ Tue, 16 Jun 2020 07:46:26: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:46:26: #2 You may need to consider one of the other alternative d(s): 37,563 WARNING @ Tue, 16 Jun 2020 07:46:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:46:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.10_summits.bed INFO @ Tue, 16 Jun 2020 07:46:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.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 07:46:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:49: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:46:56: 1000000 INFO @ Tue, 16 Jun 2020 07:46:59: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:46:59: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:46:59: #1 total tags in treatment: 1425986 INFO @ Tue, 16 Jun 2020 07:46:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:59: #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 07:46:59: #1 tags after filtering in treatment: 1425986 INFO @ Tue, 16 Jun 2020 07:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:59: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:46:59: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:46:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:59: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 07:46:59: #2 alternative fragment length(s) may be 37,563 bps INFO @ Tue, 16 Jun 2020 07:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.20_model.r WARNING @ Tue, 16 Jun 2020 07:46:59: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:46:59: #2 You may need to consider one of the other alternative d(s): 37,563 WARNING @ Tue, 16 Jun 2020 07:46:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:46:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX118227/SRX118227.20_summits.bed INFO @ Tue, 16 Jun 2020 07:47:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (24 records, 4 fields): 1 millis CompletedMACS2peakCalling