Job ID = 6368691 SRX = SRX5402717 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:49 prefetch.2.10.7: 1) Downloading 'SRR8602951'... 2020-06-16T00:27:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:39 prefetch.2.10.7: 1) 'SRR8602951' was downloaded successfully Read 24869622 spots for SRR8602951/SRR8602951.sra Written 24869622 spots for SRR8602951/SRR8602951.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: 00:05:10 24869622 reads; of these: 24869622 (100.00%) were unpaired; of these: 3248028 (13.06%) aligned 0 times 18836117 (75.74%) aligned exactly 1 time 2785477 (11.20%) aligned >1 times 86.94% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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 12 files... [bam_rmdupse_core] 3688881 / 21621594 = 0.1706 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 09:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.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 09:42:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:46: 1000000 INFO @ Tue, 16 Jun 2020 09:42:52: 2000000 INFO @ Tue, 16 Jun 2020 09:42:59: 3000000 INFO @ Tue, 16 Jun 2020 09:43:05: 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 09:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.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 09:43:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:12: 5000000 INFO @ Tue, 16 Jun 2020 09:43:17: 1000000 INFO @ Tue, 16 Jun 2020 09:43:18: 6000000 INFO @ Tue, 16 Jun 2020 09:43:24: 2000000 INFO @ Tue, 16 Jun 2020 09:43:25: 7000000 INFO @ Tue, 16 Jun 2020 09:43:31: 3000000 INFO @ Tue, 16 Jun 2020 09:43:32: 8000000 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 09:43:38: 4000000 INFO @ Tue, 16 Jun 2020 09:43:39: 9000000 INFO @ Tue, 16 Jun 2020 09:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.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 09:43:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:45: 5000000 INFO @ Tue, 16 Jun 2020 09:43:46: 10000000 INFO @ Tue, 16 Jun 2020 09:43:47: 1000000 INFO @ Tue, 16 Jun 2020 09:43:52: 6000000 INFO @ Tue, 16 Jun 2020 09:43:53: 11000000 INFO @ Tue, 16 Jun 2020 09:43:54: 2000000 INFO @ Tue, 16 Jun 2020 09:43:59: 7000000 INFO @ Tue, 16 Jun 2020 09:44:00: 12000000 INFO @ Tue, 16 Jun 2020 09:44:01: 3000000 INFO @ Tue, 16 Jun 2020 09:44:06: 8000000 INFO @ Tue, 16 Jun 2020 09:44:07: 13000000 INFO @ Tue, 16 Jun 2020 09:44:08: 4000000 INFO @ Tue, 16 Jun 2020 09:44:13: 9000000 INFO @ Tue, 16 Jun 2020 09:44:14: 14000000 INFO @ Tue, 16 Jun 2020 09:44:15: 5000000 INFO @ Tue, 16 Jun 2020 09:44:19: 10000000 INFO @ Tue, 16 Jun 2020 09:44:21: 15000000 INFO @ Tue, 16 Jun 2020 09:44:21: 6000000 INFO @ Tue, 16 Jun 2020 09:44:26: 11000000 INFO @ Tue, 16 Jun 2020 09:44:28: 16000000 INFO @ Tue, 16 Jun 2020 09:44:28: 7000000 INFO @ Tue, 16 Jun 2020 09:44:33: 12000000 INFO @ Tue, 16 Jun 2020 09:44:35: 17000000 INFO @ Tue, 16 Jun 2020 09:44:35: 8000000 INFO @ Tue, 16 Jun 2020 09:44:40: 13000000 INFO @ Tue, 16 Jun 2020 09:44:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:41: #1 total tags in treatment: 17932713 INFO @ Tue, 16 Jun 2020 09:44:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:41: #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 09:44:42: #1 tags after filtering in treatment: 17932713 INFO @ Tue, 16 Jun 2020 09:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:42: 9000000 INFO @ Tue, 16 Jun 2020 09:44:43: #2 number of paired peaks: 713 WARNING @ Tue, 16 Jun 2020 09:44:43: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:43: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 09:44:43: #2 alternative fragment length(s) may be 3,61,80 bps INFO @ Tue, 16 Jun 2020 09:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.05_model.r WARNING @ Tue, 16 Jun 2020 09:44:43: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:43: #2 You may need to consider one of the other alternative d(s): 3,61,80 WARNING @ Tue, 16 Jun 2020 09:44:43: #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 09:44:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:47: 14000000 INFO @ Tue, 16 Jun 2020 09:44:49: 10000000 INFO @ Tue, 16 Jun 2020 09:44:54: 15000000 INFO @ Tue, 16 Jun 2020 09:44:56: 11000000 INFO @ Tue, 16 Jun 2020 09:45:01: 16000000 INFO @ Tue, 16 Jun 2020 09:45:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:07: 17000000 INFO @ Tue, 16 Jun 2020 09:45:10: 13000000 INFO @ Tue, 16 Jun 2020 09:45:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:14: #1 total tags in treatment: 17932713 INFO @ Tue, 16 Jun 2020 09:45:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:14: #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 09:45:14: #1 tags after filtering in treatment: 17932713 INFO @ Tue, 16 Jun 2020 09:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:16: #2 number of paired peaks: 713 WARNING @ Tue, 16 Jun 2020 09:45:16: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:16: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 09:45:16: #2 alternative fragment length(s) may be 3,61,80 bps INFO @ Tue, 16 Jun 2020 09:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.10_model.r WARNING @ Tue, 16 Jun 2020 09:45:16: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:16: #2 You may need to consider one of the other alternative d(s): 3,61,80 WARNING @ Tue, 16 Jun 2020 09:45:16: #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 09:45:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:16: 14000000 INFO @ Tue, 16 Jun 2020 09:45:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:23: 15000000 INFO @ Tue, 16 Jun 2020 09:45:29: 16000000 INFO @ Tue, 16 Jun 2020 09:45:35: 17000000 INFO @ Tue, 16 Jun 2020 09:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14185 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:40: #1 total tags in treatment: 17932713 INFO @ Tue, 16 Jun 2020 09:45:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:40: #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 09:45:41: #1 tags after filtering in treatment: 17932713 INFO @ Tue, 16 Jun 2020 09:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:41: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:45:42: #2 number of paired peaks: 713 WARNING @ Tue, 16 Jun 2020 09:45:42: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:42: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 09:45:42: #2 alternative fragment length(s) may be 3,61,80 bps INFO @ Tue, 16 Jun 2020 09:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.20_model.r WARNING @ Tue, 16 Jun 2020 09:45:42: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:42: #2 You may need to consider one of the other alternative d(s): 3,61,80 WARNING @ Tue, 16 Jun 2020 09:45:42: #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 09:45:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7062 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402717/SRX5402717.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 3 millis CompletedMACS2peakCalling