Job ID = 6368805 SRX = SRX5709770 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:36 prefetch.2.10.7: 1) Downloading 'SRR8928720'... 2020-06-16T00:24:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:32 prefetch.2.10.7: 1) 'SRR8928720' was downloaded successfully 2020-06-16T00:27:32 prefetch.2.10.7: 'SRR8928720' has 0 unresolved dependencies Read 28106398 spots for SRR8928720/SRR8928720.sra Written 28106398 spots for SRR8928720/SRR8928720.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: 00:05:27 28106398 reads; of these: 28106398 (100.00%) were unpaired; of these: 4925207 (17.52%) aligned 0 times 19324838 (68.76%) aligned exactly 1 time 3856353 (13.72%) aligned >1 times 82.48% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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_sort_core] merging from 12 files... [bam_rmdupse_core] 9534938 / 23181191 = 0.4113 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 09:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.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 09:39:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:13: 1000000 INFO @ Tue, 16 Jun 2020 09:39:19: 2000000 INFO @ Tue, 16 Jun 2020 09:39:24: 3000000 INFO @ Tue, 16 Jun 2020 09:39:29: 4000000 INFO @ Tue, 16 Jun 2020 09:39:35: 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 09:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.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 09:39:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:40: 6000000 INFO @ Tue, 16 Jun 2020 09:39:44: 1000000 INFO @ Tue, 16 Jun 2020 09:39:46: 7000000 INFO @ Tue, 16 Jun 2020 09:39:50: 2000000 INFO @ Tue, 16 Jun 2020 09:39:52: 8000000 INFO @ Tue, 16 Jun 2020 09:39:56: 3000000 INFO @ Tue, 16 Jun 2020 09:39:58: 9000000 INFO @ Tue, 16 Jun 2020 09:40:02: 4000000 INFO @ Tue, 16 Jun 2020 09:40:04: 10000000 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 09:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.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 09:40:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:08: 5000000 INFO @ Tue, 16 Jun 2020 09:40:10: 11000000 INFO @ Tue, 16 Jun 2020 09:40:14: 1000000 INFO @ Tue, 16 Jun 2020 09:40:14: 6000000 INFO @ Tue, 16 Jun 2020 09:40:17: 12000000 INFO @ Tue, 16 Jun 2020 09:40:20: 2000000 INFO @ Tue, 16 Jun 2020 09:40:20: 7000000 INFO @ Tue, 16 Jun 2020 09:40:23: 13000000 INFO @ Tue, 16 Jun 2020 09:40:26: 3000000 INFO @ Tue, 16 Jun 2020 09:40:26: 8000000 INFO @ Tue, 16 Jun 2020 09:40:27: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:40:27: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:40:27: #1 total tags in treatment: 13646253 INFO @ Tue, 16 Jun 2020 09:40:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:27: #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 09:40:27: #1 tags after filtering in treatment: 13646253 INFO @ Tue, 16 Jun 2020 09:40:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:28: #2 number of paired peaks: 408 WARNING @ Tue, 16 Jun 2020 09:40:28: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:28: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:40:28: #2 alternative fragment length(s) may be 2,45,561 bps INFO @ Tue, 16 Jun 2020 09:40:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:28: #2 You may need to consider one of the other alternative d(s): 2,45,561 WARNING @ Tue, 16 Jun 2020 09:40:28: #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 09:40:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:32: 4000000 INFO @ Tue, 16 Jun 2020 09:40:33: 9000000 INFO @ Tue, 16 Jun 2020 09:40:38: 5000000 INFO @ Tue, 16 Jun 2020 09:40:39: 10000000 INFO @ Tue, 16 Jun 2020 09:40:44: 6000000 INFO @ Tue, 16 Jun 2020 09:40:45: 11000000 INFO @ Tue, 16 Jun 2020 09:40:51: 7000000 INFO @ Tue, 16 Jun 2020 09:40:51: 12000000 INFO @ Tue, 16 Jun 2020 09:40:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:57: 8000000 INFO @ Tue, 16 Jun 2020 09:40:57: 13000000 INFO @ Tue, 16 Jun 2020 09:41:01: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:41:01: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:41:01: #1 total tags in treatment: 13646253 INFO @ Tue, 16 Jun 2020 09:41:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:01: #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 09:41:01: #1 tags after filtering in treatment: 13646253 INFO @ Tue, 16 Jun 2020 09:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:02: #2 number of paired peaks: 408 WARNING @ Tue, 16 Jun 2020 09:41:02: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:02: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:41:02: #2 alternative fragment length(s) may be 2,45,561 bps INFO @ Tue, 16 Jun 2020 09:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:02: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:02: #2 You may need to consider one of the other alternative d(s): 2,45,561 WARNING @ Tue, 16 Jun 2020 09:41:02: #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 09:41:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:03: 9000000 INFO @ Tue, 16 Jun 2020 09:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (801 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:08: 10000000 INFO @ Tue, 16 Jun 2020 09:41:14: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:20: 12000000 INFO @ Tue, 16 Jun 2020 09:41:26: 13000000 INFO @ Tue, 16 Jun 2020 09:41:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:30: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:41:30: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:41:30: #1 total tags in treatment: 13646253 INFO @ Tue, 16 Jun 2020 09:41:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:30: #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 09:41:30: #1 tags after filtering in treatment: 13646253 INFO @ Tue, 16 Jun 2020 09:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:31: #2 number of paired peaks: 408 WARNING @ Tue, 16 Jun 2020 09:41:31: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:31: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:41:31: #2 alternative fragment length(s) may be 2,45,561 bps INFO @ Tue, 16 Jun 2020 09:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:31: #2 You may need to consider one of the other alternative d(s): 2,45,561 WARNING @ Tue, 16 Jun 2020 09:41:31: #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 09:41:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (532 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709770/SRX5709770.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling