Job ID = 6368510 SRX = SRX5020740 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:18 prefetch.2.10.7: 1) Downloading 'SRR8201363'... 2020-06-16T00:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:09 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:10 prefetch.2.10.7: 'SRR8201363' is valid 2020-06-16T00:24:10 prefetch.2.10.7: 1) 'SRR8201363' was downloaded successfully Read 4768014 spots for SRR8201363/SRR8201363.sra Written 4768014 spots for SRR8201363/SRR8201363.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: 00:01:01 4768014 reads; of these: 4768014 (100.00%) were unpaired; of these: 953578 (20.00%) aligned 0 times 3118540 (65.41%) aligned exactly 1 time 695896 (14.60%) aligned >1 times 80.00% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 324616 / 3814436 = 0.0851 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 09:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.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 09:26:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:04: 1000000 INFO @ Tue, 16 Jun 2020 09:27:10: 2000000 INFO @ Tue, 16 Jun 2020 09:27:16: 3000000 INFO @ Tue, 16 Jun 2020 09:27:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:19: #1 total tags in treatment: 3489820 INFO @ Tue, 16 Jun 2020 09:27:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:19: #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 09:27:19: #1 tags after filtering in treatment: 3489820 INFO @ Tue, 16 Jun 2020 09:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:19: #2 number of paired peaks: 395 WARNING @ Tue, 16 Jun 2020 09:27:19: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:19: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:27:19: #2 alternative fragment length(s) may be 52,568 bps INFO @ Tue, 16 Jun 2020 09:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.05_model.r WARNING @ Tue, 16 Jun 2020 09:27:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:19: #2 You may need to consider one of the other alternative d(s): 52,568 WARNING @ Tue, 16 Jun 2020 09:27:19: #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 09:27:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:19: #3 Pre-compute pvalue-qvalue table... 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 09:27:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.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 09:27:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.05_summits.bed INFO @ Tue, 16 Jun 2020 09:27:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (390 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:35: 1000000 INFO @ Tue, 16 Jun 2020 09:27:42: 2000000 INFO @ Tue, 16 Jun 2020 09:27:49: 3000000 INFO @ Tue, 16 Jun 2020 09:27:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:53: #1 total tags in treatment: 3489820 INFO @ Tue, 16 Jun 2020 09:27:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:53: #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 09:27:53: #1 tags after filtering in treatment: 3489820 INFO @ Tue, 16 Jun 2020 09:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:53: #2 number of paired peaks: 395 WARNING @ Tue, 16 Jun 2020 09:27:53: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:53: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:27:53: #2 alternative fragment length(s) may be 52,568 bps INFO @ Tue, 16 Jun 2020 09:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.10_model.r WARNING @ Tue, 16 Jun 2020 09:27:53: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:53: #2 You may need to consider one of the other alternative d(s): 52,568 WARNING @ Tue, 16 Jun 2020 09:27:53: #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 09:27:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:53: #3 Pre-compute pvalue-qvalue table... 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 09:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.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 09:27:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:04: 1000000 INFO @ Tue, 16 Jun 2020 09:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.10_summits.bed INFO @ Tue, 16 Jun 2020 09:28:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (232 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:10: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:16: 3000000 INFO @ Tue, 16 Jun 2020 09:28:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:19: #1 total tags in treatment: 3489820 INFO @ Tue, 16 Jun 2020 09:28:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:19: #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 09:28:19: #1 tags after filtering in treatment: 3489820 INFO @ Tue, 16 Jun 2020 09:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:20: #2 number of paired peaks: 395 WARNING @ Tue, 16 Jun 2020 09:28:20: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:20: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:28:20: #2 alternative fragment length(s) may be 52,568 bps INFO @ Tue, 16 Jun 2020 09:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.20_model.r WARNING @ Tue, 16 Jun 2020 09:28:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:20: #2 You may need to consider one of the other alternative d(s): 52,568 WARNING @ Tue, 16 Jun 2020 09:28:20: #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 09:28:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:28:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020740/SRX5020740.20_summits.bed INFO @ Tue, 16 Jun 2020 09:28:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (105 records, 4 fields): 1 millis CompletedMACS2peakCalling