Job ID = 6368562 SRX = SRX5020788 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:12:50 prefetch.2.10.7: 1) Downloading 'SRR8201411'... 2020-06-16T00:12:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:53 prefetch.2.10.7: 'SRR8201411' is valid 2020-06-16T00:14:53 prefetch.2.10.7: 1) 'SRR8201411' was downloaded successfully 2020-06-16T00:14:53 prefetch.2.10.7: 'SRR8201411' has 0 unresolved dependencies Read 13151464 spots for SRR8201411/SRR8201411.sra Written 13151464 spots for SRR8201411/SRR8201411.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: 00:03:47 13151464 reads; of these: 13151464 (100.00%) were unpaired; of these: 4291879 (32.63%) aligned 0 times 7400135 (56.27%) aligned exactly 1 time 1459450 (11.10%) aligned >1 times 67.37% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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_rmdupse_core] 2299929 / 8859585 = 0.2596 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 09:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.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 09:22:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:17: 1000000 INFO @ Tue, 16 Jun 2020 09:22:23: 2000000 INFO @ Tue, 16 Jun 2020 09:22:29: 3000000 INFO @ Tue, 16 Jun 2020 09:22:35: 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 09:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.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 09:22:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:41: 5000000 INFO @ Tue, 16 Jun 2020 09:22:47: 1000000 INFO @ Tue, 16 Jun 2020 09:22:47: 6000000 INFO @ Tue, 16 Jun 2020 09:22:51: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:22:51: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:22:51: #1 total tags in treatment: 6559656 INFO @ Tue, 16 Jun 2020 09:22:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:51: #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 09:22:51: #1 tags after filtering in treatment: 6559656 INFO @ Tue, 16 Jun 2020 09:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:52: #2 number of paired peaks: 475 WARNING @ Tue, 16 Jun 2020 09:22:52: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:52: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 09:22:52: #2 alternative fragment length(s) may be 77,561 bps INFO @ Tue, 16 Jun 2020 09:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.05_model.r WARNING @ Tue, 16 Jun 2020 09:22:52: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:52: #2 You may need to consider one of the other alternative d(s): 77,561 WARNING @ Tue, 16 Jun 2020 09:22:52: #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 09:22:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:53: 2000000 INFO @ Tue, 16 Jun 2020 09:22:59: 3000000 INFO @ Tue, 16 Jun 2020 09:23:05: 4000000 INFO @ Tue, 16 Jun 2020 09:23:06: #3 Call peaks for each chromosome... 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 09:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.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 09:23:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:11: 5000000 INFO @ Tue, 16 Jun 2020 09:23:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.05_summits.bed INFO @ Tue, 16 Jun 2020 09:23:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:18: 6000000 INFO @ Tue, 16 Jun 2020 09:23:18: 1000000 INFO @ Tue, 16 Jun 2020 09:23:21: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:23:21: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:23:21: #1 total tags in treatment: 6559656 INFO @ Tue, 16 Jun 2020 09:23:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:21: #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 09:23:21: #1 tags after filtering in treatment: 6559656 INFO @ Tue, 16 Jun 2020 09:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:22: #2 number of paired peaks: 475 WARNING @ Tue, 16 Jun 2020 09:23:22: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:22: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 09:23:22: #2 alternative fragment length(s) may be 77,561 bps INFO @ Tue, 16 Jun 2020 09:23:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.10_model.r WARNING @ Tue, 16 Jun 2020 09:23:22: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:22: #2 You may need to consider one of the other alternative d(s): 77,561 WARNING @ Tue, 16 Jun 2020 09:23:22: #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 09:23:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:25: 2000000 INFO @ Tue, 16 Jun 2020 09:23:33: 3000000 INFO @ Tue, 16 Jun 2020 09:23:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.10_summits.bed INFO @ Tue, 16 Jun 2020 09:23:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (659 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:46: 5000000 INFO @ Tue, 16 Jun 2020 09:23:53: 6000000 INFO @ Tue, 16 Jun 2020 09:23:57: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:23:57: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:23:57: #1 total tags in treatment: 6559656 INFO @ Tue, 16 Jun 2020 09:23:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:57: #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 09:23:57: #1 tags after filtering in treatment: 6559656 INFO @ Tue, 16 Jun 2020 09:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:58: #2 number of paired peaks: 475 WARNING @ Tue, 16 Jun 2020 09:23:58: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:58: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 09:23:58: #2 alternative fragment length(s) may be 77,561 bps INFO @ Tue, 16 Jun 2020 09:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.20_model.r WARNING @ Tue, 16 Jun 2020 09:23:58: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:58: #2 You may need to consider one of the other alternative d(s): 77,561 WARNING @ Tue, 16 Jun 2020 09:23:58: #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 09:23:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:24:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020788/SRX5020788.20_summits.bed INFO @ Tue, 16 Jun 2020 09:24:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling