Job ID = 6367700 SRX = SRX395524 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:05 prefetch.2.10.7: 1) Downloading 'SRR1054248'... 2020-06-15T23:34:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:07 prefetch.2.10.7: 'SRR1054248' is valid 2020-06-15T23:35:07 prefetch.2.10.7: 1) 'SRR1054248' was downloaded successfully Read 5727694 spots for SRR1054248/SRR1054248.sra Written 5727694 spots for SRR1054248/SRR1054248.sra 2020-06-15T23:35:32 prefetch.2.10.7: 1) Downloading 'SRR1054249'... 2020-06-15T23:35:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:07 prefetch.2.10.7: 'SRR1054249' is valid 2020-06-15T23:36:07 prefetch.2.10.7: 1) 'SRR1054249' was downloaded successfully Read 5615844 spots for SRR1054249/SRR1054249.sra Written 5615844 spots for SRR1054249/SRR1054249.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: 00:01:43 11343538 reads; of these: 11343538 (100.00%) were unpaired; of these: 1234652 (10.88%) aligned 0 times 8464630 (74.62%) aligned exactly 1 time 1644256 (14.50%) aligned >1 times 89.12% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 927608 / 10108886 = 0.0918 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 08:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.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 08:40:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:33: 1000000 INFO @ Tue, 16 Jun 2020 08:40:38: 2000000 INFO @ Tue, 16 Jun 2020 08:40:42: 3000000 INFO @ Tue, 16 Jun 2020 08:40:47: 4000000 INFO @ Tue, 16 Jun 2020 08:40:52: 5000000 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 08:40:57: 6000000 INFO @ Tue, 16 Jun 2020 08:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.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 08:40:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:01: 7000000 INFO @ Tue, 16 Jun 2020 08:41:04: 1000000 INFO @ Tue, 16 Jun 2020 08:41:06: 8000000 INFO @ Tue, 16 Jun 2020 08:41:09: 2000000 INFO @ Tue, 16 Jun 2020 08:41:11: 9000000 INFO @ Tue, 16 Jun 2020 08:41:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:12: #1 total tags in treatment: 9181278 INFO @ Tue, 16 Jun 2020 08:41:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:12: #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 08:41:13: #1 tags after filtering in treatment: 9181278 INFO @ Tue, 16 Jun 2020 08:41:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:13: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 08:41:13: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:13: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:41:13: #2 alternative fragment length(s) may be 2,28,502,528,554,584 bps INFO @ Tue, 16 Jun 2020 08:41:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:13: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:13: #2 You may need to consider one of the other alternative d(s): 2,28,502,528,554,584 WARNING @ Tue, 16 Jun 2020 08:41:13: #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 08:41:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:15: 3000000 INFO @ Tue, 16 Jun 2020 08:41:20: 4000000 INFO @ Tue, 16 Jun 2020 08:41:25: 5000000 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 08:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.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 08:41:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:30: 6000000 INFO @ Tue, 16 Jun 2020 08:41:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:34: 1000000 INFO @ Tue, 16 Jun 2020 08:41:36: 7000000 INFO @ Tue, 16 Jun 2020 08:41:39: 2000000 INFO @ Tue, 16 Jun 2020 08:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:41: 8000000 INFO @ Tue, 16 Jun 2020 08:41:45: 3000000 INFO @ Tue, 16 Jun 2020 08:41:47: 9000000 INFO @ Tue, 16 Jun 2020 08:41:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:48: #1 total tags in treatment: 9181278 INFO @ Tue, 16 Jun 2020 08:41:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:48: #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 08:41:48: #1 tags after filtering in treatment: 9181278 INFO @ Tue, 16 Jun 2020 08:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:48: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 08:41:48: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:49: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:41:49: #2 alternative fragment length(s) may be 2,28,502,528,554,584 bps INFO @ Tue, 16 Jun 2020 08:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.10_model.r WARNING @ Tue, 16 Jun 2020 08:41:49: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:49: #2 You may need to consider one of the other alternative d(s): 2,28,502,528,554,584 WARNING @ Tue, 16 Jun 2020 08:41:49: #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 08:41:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:50: 4000000 INFO @ Tue, 16 Jun 2020 08:41:56: 5000000 INFO @ Tue, 16 Jun 2020 08:42:01: 6000000 INFO @ Tue, 16 Jun 2020 08:42:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:07: 7000000 INFO @ Tue, 16 Jun 2020 08:42:12: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:17: 9000000 INFO @ Tue, 16 Jun 2020 08:42:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:18: #1 total tags in treatment: 9181278 INFO @ Tue, 16 Jun 2020 08:42:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:18: #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 08:42:18: #1 tags after filtering in treatment: 9181278 INFO @ Tue, 16 Jun 2020 08:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:19: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 08:42:19: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:19: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 08:42:19: #2 alternative fragment length(s) may be 2,28,502,528,554,584 bps INFO @ Tue, 16 Jun 2020 08:42:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:19: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:19: #2 You may need to consider one of the other alternative d(s): 2,28,502,528,554,584 WARNING @ Tue, 16 Jun 2020 08:42:19: #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 08:42:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:42:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395524/SRX395524.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 millis CompletedMACS2peakCalling