Job ID = 6368633 SRX = SRX5073500 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:01 prefetch.2.10.7: 1) Downloading 'SRR8255720'... 2020-06-16T00:28:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:12 prefetch.2.10.7: 'SRR8255720' is valid 2020-06-16T00:30:12 prefetch.2.10.7: 1) 'SRR8255720' was downloaded successfully 2020-06-16T00:30:12 prefetch.2.10.7: 'SRR8255720' has 0 unresolved dependencies Read 25496409 spots for SRR8255720/SRR8255720.sra Written 25496409 spots for SRR8255720/SRR8255720.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: 00:05:37 25496409 reads; of these: 25496409 (100.00%) were unpaired; of these: 1158622 (4.54%) aligned 0 times 20217855 (79.30%) aligned exactly 1 time 4119932 (16.16%) aligned >1 times 95.46% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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 12 files... [bam_rmdupse_core] 6117481 / 24337787 = 0.2514 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 09:41:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.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 09:41:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:12: 1000000 INFO @ Tue, 16 Jun 2020 09:41:19: 2000000 INFO @ Tue, 16 Jun 2020 09:41:25: 3000000 INFO @ Tue, 16 Jun 2020 09:41:31: 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 09:41:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.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 09:41:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:38: 5000000 INFO @ Tue, 16 Jun 2020 09:41:42: 1000000 INFO @ Tue, 16 Jun 2020 09:41:45: 6000000 INFO @ Tue, 16 Jun 2020 09:41:50: 2000000 INFO @ Tue, 16 Jun 2020 09:41:53: 7000000 INFO @ Tue, 16 Jun 2020 09:41:57: 3000000 INFO @ Tue, 16 Jun 2020 09:42:00: 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 09:42:04: 4000000 INFO @ Tue, 16 Jun 2020 09:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.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 09:42:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:08: 9000000 INFO @ Tue, 16 Jun 2020 09:42:11: 5000000 INFO @ Tue, 16 Jun 2020 09:42:12: 1000000 INFO @ Tue, 16 Jun 2020 09:42:15: 10000000 INFO @ Tue, 16 Jun 2020 09:42:18: 6000000 INFO @ Tue, 16 Jun 2020 09:42:18: 2000000 INFO @ Tue, 16 Jun 2020 09:42:23: 11000000 INFO @ Tue, 16 Jun 2020 09:42:25: 3000000 INFO @ Tue, 16 Jun 2020 09:42:26: 7000000 INFO @ Tue, 16 Jun 2020 09:42:31: 12000000 INFO @ Tue, 16 Jun 2020 09:42:32: 4000000 INFO @ Tue, 16 Jun 2020 09:42:33: 8000000 INFO @ Tue, 16 Jun 2020 09:42:38: 5000000 INFO @ Tue, 16 Jun 2020 09:42:38: 13000000 INFO @ Tue, 16 Jun 2020 09:42:41: 9000000 INFO @ Tue, 16 Jun 2020 09:42:45: 6000000 INFO @ Tue, 16 Jun 2020 09:42:46: 14000000 INFO @ Tue, 16 Jun 2020 09:42:49: 10000000 INFO @ Tue, 16 Jun 2020 09:42:52: 7000000 INFO @ Tue, 16 Jun 2020 09:42:55: 15000000 INFO @ Tue, 16 Jun 2020 09:42:57: 11000000 INFO @ Tue, 16 Jun 2020 09:42:59: 8000000 INFO @ Tue, 16 Jun 2020 09:43:03: 16000000 INFO @ Tue, 16 Jun 2020 09:43:05: 12000000 INFO @ Tue, 16 Jun 2020 09:43:06: 9000000 INFO @ Tue, 16 Jun 2020 09:43:10: 17000000 INFO @ Tue, 16 Jun 2020 09:43:12: 13000000 INFO @ Tue, 16 Jun 2020 09:43:12: 10000000 INFO @ Tue, 16 Jun 2020 09:43:18: 18000000 INFO @ Tue, 16 Jun 2020 09:43:19: 11000000 INFO @ Tue, 16 Jun 2020 09:43:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:20: #1 total tags in treatment: 18220306 INFO @ Tue, 16 Jun 2020 09:43:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:20: #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 09:43:20: #1 tags after filtering in treatment: 18220306 INFO @ Tue, 16 Jun 2020 09:43:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:20: 14000000 INFO @ Tue, 16 Jun 2020 09:43:21: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:43:21: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:21: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:43:21: #2 alternative fragment length(s) may be 1,50,568 bps INFO @ Tue, 16 Jun 2020 09:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.05_model.r WARNING @ Tue, 16 Jun 2020 09:43:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:21: #2 You may need to consider one of the other alternative d(s): 1,50,568 WARNING @ Tue, 16 Jun 2020 09:43:21: #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 09:43:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:26: 12000000 INFO @ Tue, 16 Jun 2020 09:43:28: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:33: 13000000 INFO @ Tue, 16 Jun 2020 09:43:35: 16000000 INFO @ Tue, 16 Jun 2020 09:43:39: 14000000 INFO @ Tue, 16 Jun 2020 09:43:42: 17000000 INFO @ Tue, 16 Jun 2020 09:43:46: 15000000 INFO @ Tue, 16 Jun 2020 09:43:50: 18000000 INFO @ Tue, 16 Jun 2020 09:43:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:51: #1 total tags in treatment: 18220306 INFO @ Tue, 16 Jun 2020 09:43:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:51: #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 09:43:52: #1 tags after filtering in treatment: 18220306 INFO @ Tue, 16 Jun 2020 09:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:52: 16000000 INFO @ Tue, 16 Jun 2020 09:43:53: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:43:53: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:53: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:43:53: #2 alternative fragment length(s) may be 1,50,568 bps INFO @ Tue, 16 Jun 2020 09:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:53: #2 You may need to consider one of the other alternative d(s): 1,50,568 WARNING @ Tue, 16 Jun 2020 09:43:53: #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 09:43:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:58: 17000000 INFO @ Tue, 16 Jun 2020 09:44:04: 18000000 INFO @ Tue, 16 Jun 2020 09:44:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:05: #1 total tags in treatment: 18220306 INFO @ Tue, 16 Jun 2020 09:44:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:05: #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 09:44:05: #1 tags after filtering in treatment: 18220306 INFO @ Tue, 16 Jun 2020 09:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:06: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:44:06: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:06: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:44:06: #2 alternative fragment length(s) may be 1,50,568 bps INFO @ Tue, 16 Jun 2020 09:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:06: #2 You may need to consider one of the other alternative d(s): 1,50,568 WARNING @ Tue, 16 Jun 2020 09:44:06: #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 09:44:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (773 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073500/SRX5073500.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling