Job ID = 6507922 SRX = SRX495018 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:22:48 prefetch.2.10.7: 1) Downloading 'SRR1198550'... 2020-06-26T13:22:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:24:38 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:24:38 prefetch.2.10.7: 1) 'SRR1198550' was downloaded successfully Read 13809537 spots for SRR1198550/SRR1198550.sra Written 13809537 spots for SRR1198550/SRR1198550.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: 00:02:22 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268850 (16.43%) aligned 0 times 9710106 (70.31%) aligned exactly 1 time 1830581 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1987826 / 11540687 = 0.1722 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 @ Fri, 26 Jun 2020 22:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.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 @ Fri, 26 Jun 2020 22:30:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:42: 1000000 INFO @ Fri, 26 Jun 2020 22:30:47: 2000000 INFO @ Fri, 26 Jun 2020 22:30:52: 3000000 INFO @ Fri, 26 Jun 2020 22:30:58: 4000000 INFO @ Fri, 26 Jun 2020 22:31:03: 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 @ Fri, 26 Jun 2020 22:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.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 @ Fri, 26 Jun 2020 22:31:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:31:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:31:08: 6000000 INFO @ Fri, 26 Jun 2020 22:31:12: 1000000 INFO @ Fri, 26 Jun 2020 22:31:14: 7000000 INFO @ Fri, 26 Jun 2020 22:31:18: 2000000 INFO @ Fri, 26 Jun 2020 22:31:19: 8000000 INFO @ Fri, 26 Jun 2020 22:31:24: 3000000 INFO @ Fri, 26 Jun 2020 22:31:24: 9000000 INFO @ Fri, 26 Jun 2020 22:31:27: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:31:27: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:31:27: #1 total tags in treatment: 9552861 INFO @ Fri, 26 Jun 2020 22:31:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:31:27: #1 tags after filtering in treatment: 9552861 INFO @ Fri, 26 Jun 2020 22:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:27: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:28: #2 number of paired peaks: 289 WARNING @ Fri, 26 Jun 2020 22:31:28: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:28: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:31:28: #2 alternative fragment length(s) may be 2,44,80,583 bps INFO @ Fri, 26 Jun 2020 22:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.05_model.r WARNING @ Fri, 26 Jun 2020 22:31:28: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:31:28: #2 You may need to consider one of the other alternative d(s): 2,44,80,583 WARNING @ Fri, 26 Jun 2020 22:31:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:31:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:29: 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 @ Fri, 26 Jun 2020 22:31:35: 5000000 INFO @ Fri, 26 Jun 2020 22:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.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 @ Fri, 26 Jun 2020 22:31:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:31:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:31:41: 6000000 INFO @ Fri, 26 Jun 2020 22:31:43: 1000000 INFO @ Fri, 26 Jun 2020 22:31:47: 7000000 INFO @ Fri, 26 Jun 2020 22:31:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:31:48: 2000000 INFO @ Fri, 26 Jun 2020 22:31:52: 8000000 INFO @ Fri, 26 Jun 2020 22:31:54: 3000000 INFO @ Fri, 26 Jun 2020 22:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.05_summits.bed INFO @ Fri, 26 Jun 2020 22:31:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:31:58: 9000000 INFO @ Fri, 26 Jun 2020 22:32:00: 4000000 INFO @ Fri, 26 Jun 2020 22:32:01: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:32:01: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:32:01: #1 total tags in treatment: 9552861 INFO @ Fri, 26 Jun 2020 22:32:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:02: #1 tags after filtering in treatment: 9552861 INFO @ Fri, 26 Jun 2020 22:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:02: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:02: #2 number of paired peaks: 289 WARNING @ Fri, 26 Jun 2020 22:32:02: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:02: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:32:02: #2 alternative fragment length(s) may be 2,44,80,583 bps INFO @ Fri, 26 Jun 2020 22:32:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.10_model.r WARNING @ Fri, 26 Jun 2020 22:32:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:32:02: #2 You may need to consider one of the other alternative d(s): 2,44,80,583 WARNING @ Fri, 26 Jun 2020 22:32:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:32:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:06: 5000000 INFO @ Fri, 26 Jun 2020 22:32:11: 6000000 INFO @ Fri, 26 Jun 2020 22:32:17: 7000000 INFO @ Fri, 26 Jun 2020 22:32:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:23: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:32:29: 9000000 INFO @ Fri, 26 Jun 2020 22:32:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:32:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:32:32: #1 total tags in treatment: 9552861 INFO @ Fri, 26 Jun 2020 22:32:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:32: #1 tags after filtering in treatment: 9552861 INFO @ Fri, 26 Jun 2020 22:32:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:33: #2 number of paired peaks: 289 WARNING @ Fri, 26 Jun 2020 22:32:33: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:33: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:33: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:33: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:33: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:33: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:32:33: #2 alternative fragment length(s) may be 2,44,80,583 bps INFO @ Fri, 26 Jun 2020 22:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.20_model.r WARNING @ Fri, 26 Jun 2020 22:32:33: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:32:33: #2 You may need to consider one of the other alternative d(s): 2,44,80,583 WARNING @ Fri, 26 Jun 2020 22:32:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:32:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.10_summits.bed INFO @ Fri, 26 Jun 2020 22:32:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:32:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495018/SRX495018.20_summits.bed INFO @ Fri, 26 Jun 2020 22:33:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 1 millis CompletedMACS2peakCalling