Job ID = 6367615 SRX = SRX3411421 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR6311152'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:38 prefetch.2.10.7: 'SRR6311152' is valid 2020-06-15T23:32:38 prefetch.2.10.7: 1) 'SRR6311152' was downloaded successfully Read 6772794 spots for SRR6311152/SRR6311152.sra Written 6772794 spots for SRR6311152/SRR6311152.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: 00:01:05 6772794 reads; of these: 6772794 (100.00%) were unpaired; of these: 34994 (0.52%) aligned 0 times 5661228 (83.59%) aligned exactly 1 time 1076572 (15.90%) aligned >1 times 99.48% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 476268 / 6737800 = 0.0707 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 08:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.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 08:35:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:54: 1000000 INFO @ Tue, 16 Jun 2020 08:35:59: 2000000 INFO @ Tue, 16 Jun 2020 08:36:04: 3000000 INFO @ Tue, 16 Jun 2020 08:36:08: 4000000 INFO @ Tue, 16 Jun 2020 08:36:13: 5000000 INFO @ Tue, 16 Jun 2020 08:36:17: 6000000 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 08:36:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:18: #1 total tags in treatment: 6261532 INFO @ Tue, 16 Jun 2020 08:36:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:18: #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 08:36:19: #1 tags after filtering in treatment: 6261532 INFO @ Tue, 16 Jun 2020 08:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:19: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:36:19: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:19: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:36:19: #2 alternative fragment length(s) may be 3,31,546,573,596 bps INFO @ Tue, 16 Jun 2020 08:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:19: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:19: #2 You may need to consider one of the other alternative d(s): 3,31,546,573,596 WARNING @ Tue, 16 Jun 2020 08:36:19: #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 08:36:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.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 08:36:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:25: 1000000 INFO @ Tue, 16 Jun 2020 08:36:29: 2000000 INFO @ Tue, 16 Jun 2020 08:36:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:34: 3000000 INFO @ Tue, 16 Jun 2020 08:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:38: 4000000 INFO @ Tue, 16 Jun 2020 08:36:43: 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 08:36:48: 6000000 INFO @ Tue, 16 Jun 2020 08:36:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:49: #1 total tags in treatment: 6261532 INFO @ Tue, 16 Jun 2020 08:36:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:49: #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 08:36:49: #1 tags after filtering in treatment: 6261532 INFO @ Tue, 16 Jun 2020 08:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.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 08:36:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:50: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:36:50: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:50: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:36:50: #2 alternative fragment length(s) may be 3,31,546,573,596 bps INFO @ Tue, 16 Jun 2020 08:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:50: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:50: #2 You may need to consider one of the other alternative d(s): 3,31,546,573,596 WARNING @ Tue, 16 Jun 2020 08:36:50: #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 08:36:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:55: 1000000 INFO @ Tue, 16 Jun 2020 08:36:59: 2000000 INFO @ Tue, 16 Jun 2020 08:37:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:04: 3000000 INFO @ Tue, 16 Jun 2020 08:37:09: 4000000 INFO @ Tue, 16 Jun 2020 08:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:14: 5000000 INFO @ Tue, 16 Jun 2020 08:37:18: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:20: #1 total tags in treatment: 6261532 INFO @ Tue, 16 Jun 2020 08:37:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:20: #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 08:37:20: #1 tags after filtering in treatment: 6261532 INFO @ Tue, 16 Jun 2020 08:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:20: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:37:20: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:20: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:37:20: #2 alternative fragment length(s) may be 3,31,546,573,596 bps INFO @ Tue, 16 Jun 2020 08:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:20: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:20: #2 You may need to consider one of the other alternative d(s): 3,31,546,573,596 WARNING @ Tue, 16 Jun 2020 08:37:20: #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 08:37:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3411421/SRX3411421.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 1 millis CompletedMACS2peakCalling