Job ID = 6366075 SRX = SRX059247 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:52 prefetch.2.10.7: 1) Downloading 'SRR190687'... 2020-06-15T22:45:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:45 prefetch.2.10.7: 'SRR190687' is valid 2020-06-15T22:46:45 prefetch.2.10.7: 1) 'SRR190687' was downloaded successfully Read 9286228 spots for SRR190687/SRR190687.sra Written 9286228 spots for SRR190687/SRR190687.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: 00:01:25 9286228 reads; of these: 9286228 (100.00%) were unpaired; of these: 27699 (0.30%) aligned 0 times 7662891 (82.52%) aligned exactly 1 time 1595638 (17.18%) aligned >1 times 99.70% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 604681 / 9258529 = 0.0653 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 07:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.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 07:50:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:51: 1000000 INFO @ Tue, 16 Jun 2020 07:50:56: 2000000 INFO @ Tue, 16 Jun 2020 07:51:01: 3000000 INFO @ Tue, 16 Jun 2020 07:51:06: 4000000 INFO @ Tue, 16 Jun 2020 07:51:12: 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 @ Tue, 16 Jun 2020 07:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.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 07:51:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:18: 6000000 INFO @ Tue, 16 Jun 2020 07:51:22: 1000000 INFO @ Tue, 16 Jun 2020 07:51:24: 7000000 INFO @ Tue, 16 Jun 2020 07:51:28: 2000000 INFO @ Tue, 16 Jun 2020 07:51:30: 8000000 INFO @ Tue, 16 Jun 2020 07:51:34: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:51:34: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:51:34: #1 total tags in treatment: 8653848 INFO @ Tue, 16 Jun 2020 07:51:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:34: #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 07:51:34: #1 tags after filtering in treatment: 8653848 INFO @ Tue, 16 Jun 2020 07:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:35: 3000000 INFO @ Tue, 16 Jun 2020 07:51:35: #2 number of paired peaks: 364 WARNING @ Tue, 16 Jun 2020 07:51:35: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:35: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:51:35: #2 alternative fragment length(s) may be 3,28,518,561 bps INFO @ Tue, 16 Jun 2020 07:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.05_model.r WARNING @ Tue, 16 Jun 2020 07:51:35: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:35: #2 You may need to consider one of the other alternative d(s): 3,28,518,561 WARNING @ Tue, 16 Jun 2020 07:51:35: #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 07:51:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:41: 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 07:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.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 07:51:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:48: 5000000 INFO @ Tue, 16 Jun 2020 07:51:51: 1000000 INFO @ Tue, 16 Jun 2020 07:51:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:55: 6000000 INFO @ Tue, 16 Jun 2020 07:51:58: 2000000 INFO @ Tue, 16 Jun 2020 07:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (536 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:01: 7000000 INFO @ Tue, 16 Jun 2020 07:52:04: 3000000 INFO @ Tue, 16 Jun 2020 07:52:08: 8000000 INFO @ Tue, 16 Jun 2020 07:52:10: 4000000 INFO @ Tue, 16 Jun 2020 07:52:12: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:52:12: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:52:12: #1 total tags in treatment: 8653848 INFO @ Tue, 16 Jun 2020 07:52:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:12: #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 07:52:13: #1 tags after filtering in treatment: 8653848 INFO @ Tue, 16 Jun 2020 07:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:13: #2 number of paired peaks: 364 WARNING @ Tue, 16 Jun 2020 07:52:13: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:13: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:52:13: #2 alternative fragment length(s) may be 3,28,518,561 bps INFO @ Tue, 16 Jun 2020 07:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:13: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:13: #2 You may need to consider one of the other alternative d(s): 3,28,518,561 WARNING @ Tue, 16 Jun 2020 07:52:13: #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 07:52:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:16: 5000000 INFO @ Tue, 16 Jun 2020 07:52:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:27: 7000000 INFO @ Tue, 16 Jun 2020 07:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:32: 8000000 INFO @ Tue, 16 Jun 2020 07:52:36: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:52:36: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:52:36: #1 total tags in treatment: 8653848 INFO @ Tue, 16 Jun 2020 07:52:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:36: #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 07:52:36: #1 tags after filtering in treatment: 8653848 INFO @ Tue, 16 Jun 2020 07:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:36: #2 number of paired peaks: 364 WARNING @ Tue, 16 Jun 2020 07:52:36: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:36: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:52:36: #2 alternative fragment length(s) may be 3,28,518,561 bps INFO @ Tue, 16 Jun 2020 07:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.20_model.r WARNING @ Tue, 16 Jun 2020 07:52:36: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:36: #2 You may need to consider one of the other alternative d(s): 3,28,518,561 WARNING @ Tue, 16 Jun 2020 07:52:36: #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 07:52:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (244 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:52:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059247/SRX059247.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 1 millis CompletedMACS2peakCalling