Job ID = 6368062 SRX = SRX466525 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:07:54 prefetch.2.10.7: 1) Downloading 'SRR1163591'... 2020-06-16T00:07:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:08 prefetch.2.10.7: 1) 'SRR1163591' was downloaded successfully Read 14151570 spots for SRR1163591/SRR1163591.sra Written 14151570 spots for SRR1163591/SRR1163591.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: 00:02:46 14151570 reads; of these: 14151570 (100.00%) were unpaired; of these: 532541 (3.76%) aligned 0 times 11017376 (77.85%) aligned exactly 1 time 2601653 (18.38%) aligned >1 times 96.24% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 6440976 / 13619029 = 0.4729 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 09:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.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 09:17:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:48: 1000000 INFO @ Tue, 16 Jun 2020 09:17:53: 2000000 INFO @ Tue, 16 Jun 2020 09:17:59: 3000000 INFO @ Tue, 16 Jun 2020 09:18:04: 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 09:18:10: 5000000 INFO @ Tue, 16 Jun 2020 09:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.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 09:18:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:16: 6000000 INFO @ Tue, 16 Jun 2020 09:18:19: 1000000 INFO @ Tue, 16 Jun 2020 09:18:23: 7000000 INFO @ Tue, 16 Jun 2020 09:18:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:18:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:18:24: #1 total tags in treatment: 7178053 INFO @ Tue, 16 Jun 2020 09:18:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:24: #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 09:18:24: #1 tags after filtering in treatment: 7178053 INFO @ Tue, 16 Jun 2020 09:18:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:25: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 09:18:25: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:25: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:18:25: #2 alternative fragment length(s) may be 2,43,594 bps INFO @ Tue, 16 Jun 2020 09:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.05_model.r WARNING @ Tue, 16 Jun 2020 09:18:25: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:18:25: #2 You may need to consider one of the other alternative d(s): 2,43,594 WARNING @ Tue, 16 Jun 2020 09:18:25: #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 09:18:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:25: 2000000 INFO @ Tue, 16 Jun 2020 09:18:32: 3000000 INFO @ Tue, 16 Jun 2020 09:18:38: 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 09:18:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.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 09:18:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:45: 5000000 INFO @ Tue, 16 Jun 2020 09:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.05_summits.bed INFO @ Tue, 16 Jun 2020 09:18:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (880 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:18:49: 1000000 INFO @ Tue, 16 Jun 2020 09:18:52: 6000000 INFO @ Tue, 16 Jun 2020 09:18:56: 2000000 INFO @ Tue, 16 Jun 2020 09:18:59: 7000000 INFO @ Tue, 16 Jun 2020 09:19:01: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:01: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:01: #1 total tags in treatment: 7178053 INFO @ Tue, 16 Jun 2020 09:19:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:01: #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 09:19:01: #1 tags after filtering in treatment: 7178053 INFO @ Tue, 16 Jun 2020 09:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:01: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 09:19:01: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:01: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:19:01: #2 alternative fragment length(s) may be 2,43,594 bps INFO @ Tue, 16 Jun 2020 09:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.10_model.r WARNING @ Tue, 16 Jun 2020 09:19:01: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:01: #2 You may need to consider one of the other alternative d(s): 2,43,594 WARNING @ Tue, 16 Jun 2020 09:19:01: #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 09:19:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:03: 3000000 INFO @ Tue, 16 Jun 2020 09:19:10: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:19:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:17: 5000000 INFO @ Tue, 16 Jun 2020 09:19:23: 6000000 INFO @ Tue, 16 Jun 2020 09:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.10_summits.bed INFO @ Tue, 16 Jun 2020 09:19:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (461 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:30: 7000000 INFO @ Tue, 16 Jun 2020 09:19:31: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:31: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:31: #1 total tags in treatment: 7178053 INFO @ Tue, 16 Jun 2020 09:19:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:31: #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 09:19:32: #1 tags after filtering in treatment: 7178053 INFO @ Tue, 16 Jun 2020 09:19:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:32: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 09:19:32: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:32: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:19:32: #2 alternative fragment length(s) may be 2,43,594 bps INFO @ Tue, 16 Jun 2020 09:19:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.20_model.r WARNING @ Tue, 16 Jun 2020 09:19:32: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:32: #2 You may need to consider one of the other alternative d(s): 2,43,594 WARNING @ Tue, 16 Jun 2020 09:19:32: #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 09:19:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:19:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466525/SRX466525.20_summits.bed INFO @ Tue, 16 Jun 2020 09:19:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling