Job ID = 6368075 SRX = SRX466538 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:02:00 prefetch.2.10.7: 1) Downloading 'SRR1163604'... 2020-06-16T00:02:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:21 prefetch.2.10.7: 1) 'SRR1163604' was downloaded successfully Read 13807720 spots for SRR1163604/SRR1163604.sra Written 13807720 spots for SRR1163604/SRR1163604.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: 00:02:42 13807720 reads; of these: 13807720 (100.00%) were unpaired; of these: 378492 (2.74%) aligned 0 times 10318435 (74.73%) aligned exactly 1 time 3110793 (22.53%) aligned >1 times 97.26% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 4574263 / 13429228 = 0.3406 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 09:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.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 09:10:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:02: 1000000 INFO @ Tue, 16 Jun 2020 09:11:07: 2000000 INFO @ Tue, 16 Jun 2020 09:11:13: 3000000 INFO @ Tue, 16 Jun 2020 09:11:19: 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 09:11:25: 5000000 INFO @ Tue, 16 Jun 2020 09:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.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 09:11:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:30: 6000000 INFO @ Tue, 16 Jun 2020 09:11:33: 1000000 INFO @ Tue, 16 Jun 2020 09:11:36: 7000000 INFO @ Tue, 16 Jun 2020 09:11:38: 2000000 INFO @ Tue, 16 Jun 2020 09:11:42: 8000000 INFO @ Tue, 16 Jun 2020 09:11:44: 3000000 INFO @ Tue, 16 Jun 2020 09:11:47: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:47: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:47: #1 total tags in treatment: 8854965 INFO @ Tue, 16 Jun 2020 09:11:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:47: #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 09:11:47: #1 tags after filtering in treatment: 8854965 INFO @ Tue, 16 Jun 2020 09:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:48: #2 number of paired peaks: 885 WARNING @ Tue, 16 Jun 2020 09:11:48: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:48: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:11:48: #2 alternative fragment length(s) may be 2,47,587 bps INFO @ Tue, 16 Jun 2020 09:11:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:48: #2 You may need to consider one of the other alternative d(s): 2,47,587 WARNING @ Tue, 16 Jun 2020 09:11:48: #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 09:11:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:50: 4000000 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 09:11:56: 5000000 INFO @ Tue, 16 Jun 2020 09:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.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 09:11:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:02: 6000000 INFO @ Tue, 16 Jun 2020 09:12:02: 1000000 INFO @ Tue, 16 Jun 2020 09:12:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:08: 7000000 INFO @ Tue, 16 Jun 2020 09:12:08: 2000000 INFO @ Tue, 16 Jun 2020 09:12:14: 8000000 INFO @ Tue, 16 Jun 2020 09:12:14: 3000000 INFO @ Tue, 16 Jun 2020 09:12:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:19: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:19: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:19: #1 total tags in treatment: 8854965 INFO @ Tue, 16 Jun 2020 09:12:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:19: #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 09:12:19: #1 tags after filtering in treatment: 8854965 INFO @ Tue, 16 Jun 2020 09:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:20: #2 number of paired peaks: 885 WARNING @ Tue, 16 Jun 2020 09:12:20: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:20: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:12:20: #2 alternative fragment length(s) may be 2,47,587 bps INFO @ Tue, 16 Jun 2020 09:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:20: #2 You may need to consider one of the other alternative d(s): 2,47,587 WARNING @ Tue, 16 Jun 2020 09:12:20: #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 09:12:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:20: 4000000 INFO @ Tue, 16 Jun 2020 09:12:26: 5000000 INFO @ Tue, 16 Jun 2020 09:12:32: 6000000 INFO @ Tue, 16 Jun 2020 09:12:38: 7000000 INFO @ Tue, 16 Jun 2020 09:12:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:44: 8000000 INFO @ Tue, 16 Jun 2020 09:12:49: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:49: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:49: #1 total tags in treatment: 8854965 INFO @ Tue, 16 Jun 2020 09:12:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:49: #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 09:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (524 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:49: #1 tags after filtering in treatment: 8854965 INFO @ Tue, 16 Jun 2020 09:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:50: #2 number of paired peaks: 885 WARNING @ Tue, 16 Jun 2020 09:12:50: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:50: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:12:50: #2 alternative fragment length(s) may be 2,47,587 bps INFO @ Tue, 16 Jun 2020 09:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:50: #2 You may need to consider one of the other alternative d(s): 2,47,587 WARNING @ Tue, 16 Jun 2020 09:12:50: #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 09:12:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466538/SRX466538.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling