Job ID = 6368537 SRX = SRX5020765 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:12:20 prefetch.2.10.7: 1) Downloading 'SRR8201388'... 2020-06-16T00:12:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:22 prefetch.2.10.7: 'SRR8201388' is valid 2020-06-16T00:14:22 prefetch.2.10.7: 1) 'SRR8201388' was downloaded successfully Read 15513693 spots for SRR8201388/SRR8201388.sra Written 15513693 spots for SRR8201388/SRR8201388.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: 00:03:28 15513693 reads; of these: 15513693 (100.00%) were unpaired; of these: 1929362 (12.44%) aligned 0 times 11353839 (73.19%) aligned exactly 1 time 2230492 (14.38%) aligned >1 times 87.56% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 7477579 / 13584331 = 0.5505 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 09:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.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 09:22:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:39: 1000000 INFO @ Tue, 16 Jun 2020 09:22:45: 2000000 INFO @ Tue, 16 Jun 2020 09:22:51: 3000000 INFO @ Tue, 16 Jun 2020 09:22:56: 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 09:23:02: 5000000 INFO @ Tue, 16 Jun 2020 09:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.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 09:23:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:08: 6000000 INFO @ Tue, 16 Jun 2020 09:23:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:23:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:23:09: #1 total tags in treatment: 6106752 INFO @ Tue, 16 Jun 2020 09:23:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:09: #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 09:23:09: #1 tags after filtering in treatment: 6106752 INFO @ Tue, 16 Jun 2020 09:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:09: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 09:23:09: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:09: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:23:09: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 16 Jun 2020 09:23:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.05_model.r WARNING @ Tue, 16 Jun 2020 09:23:09: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:09: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 16 Jun 2020 09:23:09: #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 09:23:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:11: 1000000 INFO @ Tue, 16 Jun 2020 09:23:18: 2000000 INFO @ Tue, 16 Jun 2020 09:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:25: 3000000 INFO @ Tue, 16 Jun 2020 09:23:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.05_summits.bed INFO @ Tue, 16 Jun 2020 09:23:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (779 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 09:23:32: 4000000 INFO @ Tue, 16 Jun 2020 09:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.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 09:23:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:39: 5000000 INFO @ Tue, 16 Jun 2020 09:23:40: 1000000 INFO @ Tue, 16 Jun 2020 09:23:46: 6000000 INFO @ Tue, 16 Jun 2020 09:23:47: 2000000 INFO @ Tue, 16 Jun 2020 09:23:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:23:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:23:47: #1 total tags in treatment: 6106752 INFO @ Tue, 16 Jun 2020 09:23:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:47: #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 09:23:47: #1 tags after filtering in treatment: 6106752 INFO @ Tue, 16 Jun 2020 09:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:48: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 09:23:48: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:48: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:23:48: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 16 Jun 2020 09:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.10_model.r WARNING @ Tue, 16 Jun 2020 09:23:48: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:48: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 16 Jun 2020 09:23:48: #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 09:23:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:53: 3000000 INFO @ Tue, 16 Jun 2020 09:24:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:00: 4000000 INFO @ Tue, 16 Jun 2020 09:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.10_summits.bed INFO @ Tue, 16 Jun 2020 09:24:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:24:07: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:24:14: 6000000 INFO @ Tue, 16 Jun 2020 09:24:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:24:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:24:15: #1 total tags in treatment: 6106752 INFO @ Tue, 16 Jun 2020 09:24:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:15: #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 09:24:15: #1 tags after filtering in treatment: 6106752 INFO @ Tue, 16 Jun 2020 09:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:15: #2 number of paired peaks: 629 WARNING @ Tue, 16 Jun 2020 09:24:15: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:15: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:24:15: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 16 Jun 2020 09:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.20_model.r WARNING @ Tue, 16 Jun 2020 09:24:15: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:15: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 16 Jun 2020 09:24:15: #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 09:24:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:24:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020765/SRX5020765.20_summits.bed INFO @ Tue, 16 Jun 2020 09:24:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 1 millis CompletedMACS2peakCalling