Job ID = 6368621 SRX = SRX5020845 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:01 prefetch.2.10.7: 1) Downloading 'SRR8201468'... 2020-06-16T00:29:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:18 prefetch.2.10.7: 1) 'SRR8201468' was downloaded successfully Read 18812743 spots for SRR8201468/SRR8201468.sra Written 18812743 spots for SRR8201468/SRR8201468.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: 00:04:27 18812743 reads; of these: 18812743 (100.00%) were unpaired; of these: 149752 (0.80%) aligned 0 times 15591082 (82.88%) aligned exactly 1 time 3071909 (16.33%) aligned >1 times 99.20% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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 8 files... [bam_rmdupse_core] 8433331 / 18662991 = 0.4519 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 09:41:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.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 09:41:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:19: 1000000 INFO @ Tue, 16 Jun 2020 09:41:26: 2000000 INFO @ Tue, 16 Jun 2020 09:41:32: 3000000 INFO @ Tue, 16 Jun 2020 09:41:39: 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 09:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.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 09:41:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:46: 5000000 INFO @ Tue, 16 Jun 2020 09:41:49: 1000000 INFO @ Tue, 16 Jun 2020 09:41:53: 6000000 INFO @ Tue, 16 Jun 2020 09:41:55: 2000000 INFO @ Tue, 16 Jun 2020 09:42:00: 7000000 INFO @ Tue, 16 Jun 2020 09:42:01: 3000000 INFO @ Tue, 16 Jun 2020 09:42:07: 8000000 INFO @ Tue, 16 Jun 2020 09:42:08: 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 09:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.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 09:42:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:14: 5000000 INFO @ Tue, 16 Jun 2020 09:42:14: 9000000 INFO @ Tue, 16 Jun 2020 09:42:19: 1000000 INFO @ Tue, 16 Jun 2020 09:42:21: 6000000 INFO @ Tue, 16 Jun 2020 09:42:21: 10000000 INFO @ Tue, 16 Jun 2020 09:42:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:23: #1 total tags in treatment: 10229660 INFO @ Tue, 16 Jun 2020 09:42:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:23: #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 09:42:23: #1 tags after filtering in treatment: 10229660 INFO @ Tue, 16 Jun 2020 09:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:24: #2 number of paired peaks: 434 WARNING @ Tue, 16 Jun 2020 09:42:24: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:24: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:42:24: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:24: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:42:24: #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 09:42:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:25: 2000000 INFO @ Tue, 16 Jun 2020 09:42:27: 7000000 INFO @ Tue, 16 Jun 2020 09:42:31: 3000000 INFO @ Tue, 16 Jun 2020 09:42:33: 8000000 INFO @ Tue, 16 Jun 2020 09:42:38: 4000000 INFO @ Tue, 16 Jun 2020 09:42:39: 9000000 INFO @ Tue, 16 Jun 2020 09:42:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:44: 5000000 INFO @ Tue, 16 Jun 2020 09:42:45: 10000000 INFO @ Tue, 16 Jun 2020 09:42:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:47: #1 total tags in treatment: 10229660 INFO @ Tue, 16 Jun 2020 09:42:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:47: #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 09:42:47: #1 tags after filtering in treatment: 10229660 INFO @ Tue, 16 Jun 2020 09:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:47: #2 number of paired peaks: 434 WARNING @ Tue, 16 Jun 2020 09:42:47: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:48: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:42:48: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:42:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.10_model.r WARNING @ Tue, 16 Jun 2020 09:42:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:48: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:42:48: #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 09:42:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:50: 6000000 INFO @ Tue, 16 Jun 2020 09:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (752 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:55: 7000000 INFO @ Tue, 16 Jun 2020 09:43:01: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:07: 9000000 INFO @ Tue, 16 Jun 2020 09:43:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:13: 10000000 INFO @ Tue, 16 Jun 2020 09:43:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:14: #1 total tags in treatment: 10229660 INFO @ Tue, 16 Jun 2020 09:43:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:14: #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 09:43:15: #1 tags after filtering in treatment: 10229660 INFO @ Tue, 16 Jun 2020 09:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:15: #2 number of paired peaks: 434 WARNING @ Tue, 16 Jun 2020 09:43:15: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:15: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:43:15: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.20_model.r WARNING @ Tue, 16 Jun 2020 09:43:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:16: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:43:16: #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 09:43:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (567 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:43:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020845/SRX5020845.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 1 millis CompletedMACS2peakCalling