Job ID = 6368598 SRX = SRX5020823 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:06 prefetch.2.10.7: 1) Downloading 'SRR8201446'... 2020-06-16T00:21:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:04 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:05 prefetch.2.10.7: 'SRR8201446' is valid 2020-06-16T00:23:05 prefetch.2.10.7: 1) 'SRR8201446' was downloaded successfully Read 12656369 spots for SRR8201446/SRR8201446.sra Written 12656369 spots for SRR8201446/SRR8201446.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: 00:03:01 12656369 reads; of these: 12656369 (100.00%) were unpaired; of these: 114691 (0.91%) aligned 0 times 10459053 (82.64%) aligned exactly 1 time 2082625 (16.46%) aligned >1 times 99.09% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 884625 / 12541678 = 0.0705 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 09:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.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 09:30:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:30: 1000000 INFO @ Tue, 16 Jun 2020 09:30:36: 2000000 INFO @ Tue, 16 Jun 2020 09:30:42: 3000000 INFO @ Tue, 16 Jun 2020 09:30:49: 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 09:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.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 09:30:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:55: 5000000 INFO @ Tue, 16 Jun 2020 09:31:00: 1000000 INFO @ Tue, 16 Jun 2020 09:31:02: 6000000 INFO @ Tue, 16 Jun 2020 09:31:07: 2000000 INFO @ Tue, 16 Jun 2020 09:31:09: 7000000 INFO @ Tue, 16 Jun 2020 09:31:13: 3000000 INFO @ Tue, 16 Jun 2020 09:31:15: 8000000 INFO @ Tue, 16 Jun 2020 09:31:20: 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 09:31:22: 9000000 INFO @ Tue, 16 Jun 2020 09:31:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.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 09:31:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:27: 5000000 INFO @ Tue, 16 Jun 2020 09:31:29: 10000000 INFO @ Tue, 16 Jun 2020 09:31:30: 1000000 INFO @ Tue, 16 Jun 2020 09:31:33: 6000000 INFO @ Tue, 16 Jun 2020 09:31:36: 11000000 INFO @ Tue, 16 Jun 2020 09:31:37: 2000000 INFO @ Tue, 16 Jun 2020 09:31:40: 7000000 INFO @ Tue, 16 Jun 2020 09:31:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:41: #1 total tags in treatment: 11657053 INFO @ Tue, 16 Jun 2020 09:31:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:41: #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 09:31:41: #1 tags after filtering in treatment: 11657053 INFO @ Tue, 16 Jun 2020 09:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:42: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 09:31:42: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:42: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:31:42: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 16 Jun 2020 09:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:42: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 16 Jun 2020 09:31:42: #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 09:31:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:44: 3000000 INFO @ Tue, 16 Jun 2020 09:31:47: 8000000 INFO @ Tue, 16 Jun 2020 09:31:51: 4000000 INFO @ Tue, 16 Jun 2020 09:31:53: 9000000 INFO @ Tue, 16 Jun 2020 09:31:58: 5000000 INFO @ Tue, 16 Jun 2020 09:32:00: 10000000 INFO @ Tue, 16 Jun 2020 09:32:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:05: 6000000 INFO @ Tue, 16 Jun 2020 09:32:06: 11000000 INFO @ Tue, 16 Jun 2020 09:32:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:11: #1 total tags in treatment: 11657053 INFO @ Tue, 16 Jun 2020 09:32:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:11: #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 09:32:11: #1 tags after filtering in treatment: 11657053 INFO @ Tue, 16 Jun 2020 09:32:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:12: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 09:32:12: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:12: 7000000 INFO @ Tue, 16 Jun 2020 09:32:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:12: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:32:12: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 16 Jun 2020 09:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.10_model.r WARNING @ Tue, 16 Jun 2020 09:32:12: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:12: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 16 Jun 2020 09:32:12: #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 09:32:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:18: 8000000 INFO @ Tue, 16 Jun 2020 09:32:25: 9000000 INFO @ Tue, 16 Jun 2020 09:32:31: 10000000 INFO @ Tue, 16 Jun 2020 09:32:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:38: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:42: #1 total tags in treatment: 11657053 INFO @ Tue, 16 Jun 2020 09:32:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:42: #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 09:32:42: #1 tags after filtering in treatment: 11657053 INFO @ Tue, 16 Jun 2020 09:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:43: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 09:32:43: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:43: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:32:43: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 16 Jun 2020 09:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:43: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:43: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 16 Jun 2020 09:32:43: #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 09:32:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020823/SRX5020823.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 4 millis CompletedMACS2peakCalling