Job ID = 6368603 SRX = SRX5020828 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:48 prefetch.2.10.7: 1) Downloading 'SRR8201451'... 2020-06-16T00:24:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:18 prefetch.2.10.7: 'SRR8201451' is valid 2020-06-16T00:26:18 prefetch.2.10.7: 1) 'SRR8201451' was downloaded successfully Read 12901860 spots for SRR8201451/SRR8201451.sra Written 12901860 spots for SRR8201451/SRR8201451.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: 00:03:02 12901860 reads; of these: 12901860 (100.00%) were unpaired; of these: 117960 (0.91%) aligned 0 times 10601619 (82.17%) aligned exactly 1 time 2182281 (16.91%) aligned >1 times 99.09% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 1011676 / 12783900 = 0.0791 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 09:33:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.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 09:33:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:58: 1000000 INFO @ Tue, 16 Jun 2020 09:34:03: 2000000 INFO @ Tue, 16 Jun 2020 09:34:09: 3000000 INFO @ Tue, 16 Jun 2020 09:34:14: 4000000 INFO @ Tue, 16 Jun 2020 09:34:19: 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 09:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.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 09:34:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:25: 6000000 INFO @ Tue, 16 Jun 2020 09:34:27: 1000000 INFO @ Tue, 16 Jun 2020 09:34:30: 7000000 INFO @ Tue, 16 Jun 2020 09:34:33: 2000000 INFO @ Tue, 16 Jun 2020 09:34:36: 8000000 INFO @ Tue, 16 Jun 2020 09:34:39: 3000000 INFO @ Tue, 16 Jun 2020 09:34:42: 9000000 INFO @ Tue, 16 Jun 2020 09:34:45: 4000000 INFO @ Tue, 16 Jun 2020 09:34:48: 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 09:34:50: 5000000 INFO @ Tue, 16 Jun 2020 09:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.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 09:34:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:54: 11000000 INFO @ Tue, 16 Jun 2020 09:34:56: 6000000 INFO @ Tue, 16 Jun 2020 09:34:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:58: #1 total tags in treatment: 11772224 INFO @ Tue, 16 Jun 2020 09:34:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:58: #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 09:34:58: 1000000 INFO @ Tue, 16 Jun 2020 09:34:58: #1 tags after filtering in treatment: 11772224 INFO @ Tue, 16 Jun 2020 09:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:59: #2 number of paired peaks: 307 WARNING @ Tue, 16 Jun 2020 09:34:59: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:59: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:34:59: #2 alternative fragment length(s) may be 3,48,578 bps INFO @ Tue, 16 Jun 2020 09:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:59: #2 You may need to consider one of the other alternative d(s): 3,48,578 WARNING @ Tue, 16 Jun 2020 09:34:59: #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 09:34:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:02: 7000000 INFO @ Tue, 16 Jun 2020 09:35:05: 2000000 INFO @ Tue, 16 Jun 2020 09:35:08: 8000000 INFO @ Tue, 16 Jun 2020 09:35:11: 3000000 INFO @ Tue, 16 Jun 2020 09:35:14: 9000000 INFO @ Tue, 16 Jun 2020 09:35:18: 4000000 INFO @ Tue, 16 Jun 2020 09:35:20: 10000000 INFO @ Tue, 16 Jun 2020 09:35:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:25: 5000000 INFO @ Tue, 16 Jun 2020 09:35:26: 11000000 INFO @ Tue, 16 Jun 2020 09:35:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:31: #1 total tags in treatment: 11772224 INFO @ Tue, 16 Jun 2020 09:35:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:31: #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 09:35:31: #1 tags after filtering in treatment: 11772224 INFO @ Tue, 16 Jun 2020 09:35:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:32: 6000000 INFO @ Tue, 16 Jun 2020 09:35:32: #2 number of paired peaks: 307 WARNING @ Tue, 16 Jun 2020 09:35:32: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:32: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:35:32: #2 alternative fragment length(s) may be 3,48,578 bps INFO @ Tue, 16 Jun 2020 09:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:32: #2 You may need to consider one of the other alternative d(s): 3,48,578 WARNING @ Tue, 16 Jun 2020 09:35:32: #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 09:35:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:38: 7000000 INFO @ Tue, 16 Jun 2020 09:35:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:51: 9000000 INFO @ Tue, 16 Jun 2020 09:35:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:58: 10000000 INFO @ Tue, 16 Jun 2020 09:36:04: 11000000 INFO @ Tue, 16 Jun 2020 09:36:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:07: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:09: #1 total tags in treatment: 11772224 INFO @ Tue, 16 Jun 2020 09:36:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:09: #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 09:36:10: #1 tags after filtering in treatment: 11772224 INFO @ Tue, 16 Jun 2020 09:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:10: #2 number of paired peaks: 307 WARNING @ Tue, 16 Jun 2020 09:36:10: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:11: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:36:11: #2 alternative fragment length(s) may be 3,48,578 bps INFO @ Tue, 16 Jun 2020 09:36:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:11: #2 You may need to consider one of the other alternative d(s): 3,48,578 WARNING @ Tue, 16 Jun 2020 09:36:11: #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 09:36:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020828/SRX5020828.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (171 records, 4 fields): 3 millis CompletedMACS2peakCalling