Job ID = 6368809 SRX = SRX5729151 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:36:05 prefetch.2.10.7: 1) Downloading 'SRR8949163'... 2020-06-16T00:36:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:06 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:07 prefetch.2.10.7: 'SRR8949163' is valid 2020-06-16T00:37:07 prefetch.2.10.7: 1) 'SRR8949163' was downloaded successfully 2020-06-16T00:37:07 prefetch.2.10.7: 'SRR8949163' has 0 unresolved dependencies Read 11001637 spots for SRR8949163/SRR8949163.sra Written 11001637 spots for SRR8949163/SRR8949163.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: 00:03:37 11001637 reads; of these: 11001637 (100.00%) were unpaired; of these: 1066034 (9.69%) aligned 0 times 8289743 (75.35%) aligned exactly 1 time 1645860 (14.96%) aligned >1 times 90.31% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 789939 / 9935603 = 0.0795 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 09:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.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 09:44:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:37: 1000000 INFO @ Tue, 16 Jun 2020 09:44:44: 2000000 INFO @ Tue, 16 Jun 2020 09:44:51: 3000000 INFO @ Tue, 16 Jun 2020 09:44:58: 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 09:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.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 09:45:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:05: 5000000 INFO @ Tue, 16 Jun 2020 09:45:07: 1000000 INFO @ Tue, 16 Jun 2020 09:45:13: 6000000 INFO @ Tue, 16 Jun 2020 09:45:14: 2000000 INFO @ Tue, 16 Jun 2020 09:45:20: 7000000 INFO @ Tue, 16 Jun 2020 09:45:21: 3000000 INFO @ Tue, 16 Jun 2020 09:45:28: 4000000 INFO @ Tue, 16 Jun 2020 09:45:28: 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 09:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.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 09:45:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:35: 5000000 INFO @ Tue, 16 Jun 2020 09:45:35: 9000000 INFO @ Tue, 16 Jun 2020 09:45:36: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:45:36: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:45:36: #1 total tags in treatment: 9145664 INFO @ Tue, 16 Jun 2020 09:45:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:36: #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 09:45:37: #1 tags after filtering in treatment: 9145664 INFO @ Tue, 16 Jun 2020 09:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:37: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 09:45:37: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:37: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:45:37: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 16 Jun 2020 09:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:37: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:37: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 16 Jun 2020 09:45:37: #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 09:45:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:38: 1000000 INFO @ Tue, 16 Jun 2020 09:45:42: 6000000 INFO @ Tue, 16 Jun 2020 09:45:45: 2000000 INFO @ Tue, 16 Jun 2020 09:45:50: 7000000 INFO @ Tue, 16 Jun 2020 09:45:53: 3000000 INFO @ Tue, 16 Jun 2020 09:45:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:57: 8000000 INFO @ Tue, 16 Jun 2020 09:46:01: 4000000 INFO @ Tue, 16 Jun 2020 09:46:05: 9000000 INFO @ Tue, 16 Jun 2020 09:46:06: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:46:06: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:46:06: #1 total tags in treatment: 9145664 INFO @ Tue, 16 Jun 2020 09:46:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:06: #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 09:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.05_summits.bed INFO @ Tue, 16 Jun 2020 09:46:06: Done! INFO @ Tue, 16 Jun 2020 09:46:06: #1 tags after filtering in treatment: 9145664 INFO @ Tue, 16 Jun 2020 09:46:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:06: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:07: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 09:46:07: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:07: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:46:07: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 16 Jun 2020 09:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:07: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:07: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 16 Jun 2020 09:46:07: #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 09:46:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:08: 5000000 INFO @ Tue, 16 Jun 2020 09:46:14: 6000000 INFO @ Tue, 16 Jun 2020 09:46:20: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:46:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:27: 8000000 INFO @ Tue, 16 Jun 2020 09:46:33: 9000000 INFO @ Tue, 16 Jun 2020 09:46:34: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:46:34: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:46:34: #1 total tags in treatment: 9145664 INFO @ Tue, 16 Jun 2020 09:46:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:34: #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 09:46:34: #1 tags after filtering in treatment: 9145664 INFO @ Tue, 16 Jun 2020 09:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:34: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 09:46:34: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:35: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:46:35: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 16 Jun 2020 09:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.20_model.r WARNING @ Tue, 16 Jun 2020 09:46:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:35: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 16 Jun 2020 09:46:35: #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 09:46:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729151/SRX5729151.20_summits.bed INFO @ Tue, 16 Jun 2020 09:47:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling