Job ID = 6368686 SRX = SRX5402712 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:24 prefetch.2.10.7: 1) Downloading 'SRR8602946'... 2020-06-16T00:22:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:35 prefetch.2.10.7: 1) 'SRR8602946' was downloaded successfully Read 20399108 spots for SRR8602946/SRR8602946.sra Written 20399108 spots for SRR8602946/SRR8602946.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: 00:04:07 20399108 reads; of these: 20399108 (100.00%) were unpaired; of these: 2342738 (11.48%) aligned 0 times 15755181 (77.23%) aligned exactly 1 time 2301189 (11.28%) aligned >1 times 88.52% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 7220159 / 18056370 = 0.3999 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 09:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.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 09:33:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:48: 1000000 INFO @ Tue, 16 Jun 2020 09:33:54: 2000000 INFO @ Tue, 16 Jun 2020 09:34:00: 3000000 INFO @ Tue, 16 Jun 2020 09:34:06: 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 09:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.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 09:34:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:12: 5000000 INFO @ Tue, 16 Jun 2020 09:34:17: 1000000 INFO @ Tue, 16 Jun 2020 09:34:18: 6000000 INFO @ Tue, 16 Jun 2020 09:34:23: 2000000 INFO @ Tue, 16 Jun 2020 09:34:24: 7000000 INFO @ Tue, 16 Jun 2020 09:34:29: 3000000 INFO @ Tue, 16 Jun 2020 09:34:30: 8000000 INFO @ Tue, 16 Jun 2020 09:34:35: 4000000 INFO @ Tue, 16 Jun 2020 09:34:36: 9000000 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 09:34:40: 5000000 INFO @ Tue, 16 Jun 2020 09:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.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 09:34:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:42: 10000000 INFO @ Tue, 16 Jun 2020 09:34:46: 6000000 INFO @ Tue, 16 Jun 2020 09:34:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:34:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:34:48: #1 total tags in treatment: 10836211 INFO @ Tue, 16 Jun 2020 09:34:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:48: #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 09:34:48: #1 tags after filtering in treatment: 10836211 INFO @ Tue, 16 Jun 2020 09:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:48: 1000000 INFO @ Tue, 16 Jun 2020 09:34:48: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:34:48: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:49: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:34:49: #2 alternative fragment length(s) may be 3,43,558 bps INFO @ Tue, 16 Jun 2020 09:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:49: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:49: #2 You may need to consider one of the other alternative d(s): 3,43,558 WARNING @ Tue, 16 Jun 2020 09:34:49: #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 09:34:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:52: 7000000 INFO @ Tue, 16 Jun 2020 09:34:54: 2000000 INFO @ Tue, 16 Jun 2020 09:34:57: 8000000 INFO @ Tue, 16 Jun 2020 09:35:01: 3000000 INFO @ Tue, 16 Jun 2020 09:35:03: 9000000 INFO @ Tue, 16 Jun 2020 09:35:07: 4000000 INFO @ Tue, 16 Jun 2020 09:35:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:09: 10000000 INFO @ Tue, 16 Jun 2020 09:35:13: 5000000 INFO @ Tue, 16 Jun 2020 09:35:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:13: #1 total tags in treatment: 10836211 INFO @ Tue, 16 Jun 2020 09:35:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:13: #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 09:35:14: #1 tags after filtering in treatment: 10836211 INFO @ Tue, 16 Jun 2020 09:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:14: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:35:14: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:14: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:35:14: #2 alternative fragment length(s) may be 3,43,558 bps INFO @ Tue, 16 Jun 2020 09:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:14: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:14: #2 You may need to consider one of the other alternative d(s): 3,43,558 WARNING @ Tue, 16 Jun 2020 09:35:14: #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 09:35:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1972 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:19: 6000000 INFO @ Tue, 16 Jun 2020 09:35:25: 7000000 INFO @ Tue, 16 Jun 2020 09:35:31: 8000000 INFO @ Tue, 16 Jun 2020 09:35:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:37: 9000000 INFO @ Tue, 16 Jun 2020 09:35:43: 10000000 INFO @ Tue, 16 Jun 2020 09:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (360 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:47: #1 total tags in treatment: 10836211 INFO @ Tue, 16 Jun 2020 09:35:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:47: #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 09:35:48: #1 tags after filtering in treatment: 10836211 INFO @ Tue, 16 Jun 2020 09:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:48: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:35:48: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:48: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:35:48: #2 alternative fragment length(s) may be 3,43,558 bps INFO @ Tue, 16 Jun 2020 09:35:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:48: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:48: #2 You may need to consider one of the other alternative d(s): 3,43,558 WARNING @ Tue, 16 Jun 2020 09:35:48: #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 09:35:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402712/SRX5402712.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 1 millis CompletedMACS2peakCalling