Job ID = 6368542 SRX = SRX5020770 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:21 prefetch.2.10.7: 1) Downloading 'SRR8201393'... 2020-06-16T00:18:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:28 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:29 prefetch.2.10.7: 'SRR8201393' is valid 2020-06-16T00:20:29 prefetch.2.10.7: 1) 'SRR8201393' was downloaded successfully 2020-06-16T00:20:29 prefetch.2.10.7: 'SRR8201393' has 0 unresolved dependencies Read 13436168 spots for SRR8201393/SRR8201393.sra Written 13436168 spots for SRR8201393/SRR8201393.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: 00:04:20 13436168 reads; of these: 13436168 (100.00%) were unpaired; of these: 1504355 (11.20%) aligned 0 times 9949613 (74.05%) aligned exactly 1 time 1982200 (14.75%) aligned >1 times 88.80% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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 8 files... [bam_rmdupse_core] 2052062 / 11931813 = 0.1720 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 09:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.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 09:29:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:32: 1000000 INFO @ Tue, 16 Jun 2020 09:29:38: 2000000 INFO @ Tue, 16 Jun 2020 09:29:44: 3000000 INFO @ Tue, 16 Jun 2020 09:29:49: 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 09:29:55: 5000000 INFO @ Tue, 16 Jun 2020 09:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.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 09:29:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:01: 6000000 INFO @ Tue, 16 Jun 2020 09:30:03: 1000000 INFO @ Tue, 16 Jun 2020 09:30:08: 7000000 INFO @ Tue, 16 Jun 2020 09:30:10: 2000000 INFO @ Tue, 16 Jun 2020 09:30:14: 8000000 INFO @ Tue, 16 Jun 2020 09:30:18: 3000000 INFO @ Tue, 16 Jun 2020 09:30:20: 9000000 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 09:30:25: 4000000 INFO @ Tue, 16 Jun 2020 09:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.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 09:30:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:30:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:30:26: #1 total tags in treatment: 9879751 INFO @ Tue, 16 Jun 2020 09:30:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:26: #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 09:30:26: #1 tags after filtering in treatment: 9879751 INFO @ Tue, 16 Jun 2020 09:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:27: #2 number of paired peaks: 398 WARNING @ Tue, 16 Jun 2020 09:30:27: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:27: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:30:27: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 09:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:27: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:27: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 09:30:27: #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 09:30:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:32: 5000000 INFO @ Tue, 16 Jun 2020 09:30:32: 1000000 INFO @ Tue, 16 Jun 2020 09:30:39: 6000000 INFO @ Tue, 16 Jun 2020 09:30:39: 2000000 INFO @ Tue, 16 Jun 2020 09:30:45: 3000000 INFO @ Tue, 16 Jun 2020 09:30:46: 7000000 INFO @ Tue, 16 Jun 2020 09:30:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:52: 4000000 INFO @ Tue, 16 Jun 2020 09:30:53: 8000000 INFO @ Tue, 16 Jun 2020 09:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.05_summits.bed INFO @ Tue, 16 Jun 2020 09:30:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (738 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:58: 5000000 INFO @ Tue, 16 Jun 2020 09:31:00: 9000000 INFO @ Tue, 16 Jun 2020 09:31:04: 6000000 INFO @ Tue, 16 Jun 2020 09:31:06: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:31:06: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:31:06: #1 total tags in treatment: 9879751 INFO @ Tue, 16 Jun 2020 09:31:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:06: #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 09:31:07: #1 tags after filtering in treatment: 9879751 INFO @ Tue, 16 Jun 2020 09:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:07: #2 number of paired peaks: 398 WARNING @ Tue, 16 Jun 2020 09:31:07: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:07: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:31:07: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 09:31:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:07: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:07: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 09:31:07: #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 09:31:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:11: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:17: 8000000 INFO @ Tue, 16 Jun 2020 09:31:23: 9000000 INFO @ Tue, 16 Jun 2020 09:31:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:29: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:31:29: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:31:29: #1 total tags in treatment: 9879751 INFO @ Tue, 16 Jun 2020 09:31:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:29: #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 09:31:29: #1 tags after filtering in treatment: 9879751 INFO @ Tue, 16 Jun 2020 09:31:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:30: #2 number of paired peaks: 398 WARNING @ Tue, 16 Jun 2020 09:31:30: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:30: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:31:30: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 09:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:30: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:30: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 09:31:30: #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 09:31:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:31:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020770/SRX5020770.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 1 millis CompletedMACS2peakCalling