Job ID = 6367345 SRX = SRX331105 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:01 prefetch.2.10.7: 1) Downloading 'SRR947336'... 2020-06-15T23:22:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:34 prefetch.2.10.7: 'SRR947336' is valid 2020-06-15T23:22:34 prefetch.2.10.7: 1) 'SRR947336' was downloaded successfully Read 8387479 spots for SRR947336/SRR947336.sra Written 8387479 spots for SRR947336/SRR947336.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: 00:01:17 8387479 reads; of these: 8387479 (100.00%) were unpaired; of these: 545037 (6.50%) aligned 0 times 6532136 (77.88%) aligned exactly 1 time 1310306 (15.62%) aligned >1 times 93.50% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 637410 / 7842442 = 0.0813 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 08:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.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 08:26:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:20: 1000000 INFO @ Tue, 16 Jun 2020 08:26:25: 2000000 INFO @ Tue, 16 Jun 2020 08:26:30: 3000000 INFO @ Tue, 16 Jun 2020 08:26:34: 4000000 INFO @ Tue, 16 Jun 2020 08:26:39: 5000000 INFO @ Tue, 16 Jun 2020 08:26:43: 6000000 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 08:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.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 08:26:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:48: 7000000 INFO @ Tue, 16 Jun 2020 08:26:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:49: #1 total tags in treatment: 7205032 INFO @ Tue, 16 Jun 2020 08:26:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:49: #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 08:26:49: #1 tags after filtering in treatment: 7205032 INFO @ Tue, 16 Jun 2020 08:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:50: #2 number of paired peaks: 365 WARNING @ Tue, 16 Jun 2020 08:26:50: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:50: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:26:50: #2 alternative fragment length(s) may be 2,31,552,595 bps INFO @ Tue, 16 Jun 2020 08:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:50: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:50: #2 You may need to consider one of the other alternative d(s): 2,31,552,595 WARNING @ Tue, 16 Jun 2020 08:26:50: #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 08:26:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:51: 1000000 INFO @ Tue, 16 Jun 2020 08:26:55: 2000000 INFO @ Tue, 16 Jun 2020 08:27:00: 3000000 INFO @ Tue, 16 Jun 2020 08:27:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:04: 4000000 INFO @ Tue, 16 Jun 2020 08:27:09: 5000000 INFO @ Tue, 16 Jun 2020 08:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:13: 6000000 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 08:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.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 08:27:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:17: 7000000 INFO @ Tue, 16 Jun 2020 08:27:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:18: #1 total tags in treatment: 7205032 INFO @ Tue, 16 Jun 2020 08:27:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:18: #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 08:27:18: #1 tags after filtering in treatment: 7205032 INFO @ Tue, 16 Jun 2020 08:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:19: #2 number of paired peaks: 365 WARNING @ Tue, 16 Jun 2020 08:27:19: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:19: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:27:19: #2 alternative fragment length(s) may be 2,31,552,595 bps INFO @ Tue, 16 Jun 2020 08:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.10_model.r WARNING @ Tue, 16 Jun 2020 08:27:19: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:19: #2 You may need to consider one of the other alternative d(s): 2,31,552,595 WARNING @ Tue, 16 Jun 2020 08:27:19: #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 08:27:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:20: 1000000 INFO @ Tue, 16 Jun 2020 08:27:25: 2000000 INFO @ Tue, 16 Jun 2020 08:27:29: 3000000 INFO @ Tue, 16 Jun 2020 08:27:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:34: 4000000 INFO @ Tue, 16 Jun 2020 08:27:38: 5000000 INFO @ Tue, 16 Jun 2020 08:27:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:43: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:27:47: 7000000 INFO @ Tue, 16 Jun 2020 08:27:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:48: #1 total tags in treatment: 7205032 INFO @ Tue, 16 Jun 2020 08:27:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:48: #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 08:27:48: #1 tags after filtering in treatment: 7205032 INFO @ Tue, 16 Jun 2020 08:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:49: #2 number of paired peaks: 365 WARNING @ Tue, 16 Jun 2020 08:27:49: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:49: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:27:49: #2 alternative fragment length(s) may be 2,31,552,595 bps INFO @ Tue, 16 Jun 2020 08:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.20_model.r WARNING @ Tue, 16 Jun 2020 08:27:49: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:49: #2 You may need to consider one of the other alternative d(s): 2,31,552,595 WARNING @ Tue, 16 Jun 2020 08:27:49: #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 08:27:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331105/SRX331105.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 1 millis CompletedMACS2peakCalling