Job ID = 6366933 SRX = SRX2576635 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:05 prefetch.2.10.7: 1) Downloading 'SRR5272592'... 2020-06-15T23:31:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:12 prefetch.2.10.7: 1) 'SRR5272592' was downloaded successfully Read 21938757 spots for SRR5272592/SRR5272592.sra Written 21938757 spots for SRR5272592/SRR5272592.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: 00:02:43 21938757 reads; of these: 21938757 (100.00%) were unpaired; of these: 15348864 (69.96%) aligned 0 times 5392666 (24.58%) aligned exactly 1 time 1197227 (5.46%) aligned >1 times 30.04% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 2856906 / 6589893 = 0.4335 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 08:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.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 08:41:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:37: 1000000 INFO @ Tue, 16 Jun 2020 08:41:43: 2000000 INFO @ Tue, 16 Jun 2020 08:41:49: 3000000 INFO @ Tue, 16 Jun 2020 08:41:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:41:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:41:54: #1 total tags in treatment: 3732987 INFO @ Tue, 16 Jun 2020 08:41:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:54: #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 08:41:54: #1 tags after filtering in treatment: 3732987 INFO @ Tue, 16 Jun 2020 08:41:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:54: #2 number of paired peaks: 498 WARNING @ Tue, 16 Jun 2020 08:41:54: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:54: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:41:54: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 08:41:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:55: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 08:41:55: #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 08:41:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:55: #3 Pre-compute pvalue-qvalue table... 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 08:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.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 08:42:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:05: 1000000 INFO @ Tue, 16 Jun 2020 08:42:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (692 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:11: 2000000 INFO @ Tue, 16 Jun 2020 08:42:16: 3000000 INFO @ Tue, 16 Jun 2020 08:42:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:42:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:42:20: #1 total tags in treatment: 3732987 INFO @ Tue, 16 Jun 2020 08:42:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:20: #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 08:42:20: #1 tags after filtering in treatment: 3732987 INFO @ Tue, 16 Jun 2020 08:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:20: #2 number of paired peaks: 498 WARNING @ Tue, 16 Jun 2020 08:42:20: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:20: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:42:20: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 08:42:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.10_model.r WARNING @ Tue, 16 Jun 2020 08:42:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:20: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 08:42:20: #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 08:42:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:27: #3 Call peaks for each chromosome... 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 08:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.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 08:42:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:35: 1000000 INFO @ Tue, 16 Jun 2020 08:42:41: 2000000 INFO @ Tue, 16 Jun 2020 08:42:46: 3000000 INFO @ Tue, 16 Jun 2020 08:42:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:42:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:42:50: #1 total tags in treatment: 3732987 INFO @ Tue, 16 Jun 2020 08:42:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:50: #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 08:42:50: #1 tags after filtering in treatment: 3732987 INFO @ Tue, 16 Jun 2020 08:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:50: #2 number of paired peaks: 498 WARNING @ Tue, 16 Jun 2020 08:42:50: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:50: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:42:50: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 08:42:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:50: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 08:42:50: #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 08:42:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576635/SRX2576635.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (152 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。