Job ID = 6367743 SRX = SRX4082357 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:44 prefetch.2.10.7: 1) Downloading 'SRR7164175'... 2020-06-15T23:38:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:47 prefetch.2.10.7: 'SRR7164175' is valid 2020-06-15T23:40:47 prefetch.2.10.7: 1) 'SRR7164175' was downloaded successfully 2020-06-15T23:40:47 prefetch.2.10.7: 'SRR7164175' has 0 unresolved dependencies Read 11907573 spots for SRR7164175/SRR7164175.sra Written 11907573 spots for SRR7164175/SRR7164175.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: 00:02:30 11907573 reads; of these: 11907573 (100.00%) were unpaired; of these: 1545285 (12.98%) aligned 0 times 8939616 (75.08%) aligned exactly 1 time 1422672 (11.95%) aligned >1 times 87.02% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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 8 files... [bam_rmdupse_core] 2936916 / 10362288 = 0.2834 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 08:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.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 08:46:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:44: 1000000 INFO @ Tue, 16 Jun 2020 08:46:50: 2000000 INFO @ Tue, 16 Jun 2020 08:46:56: 3000000 INFO @ Tue, 16 Jun 2020 08:47:02: 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 08:47:08: 5000000 INFO @ Tue, 16 Jun 2020 08:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.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 08:47:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:14: 6000000 INFO @ Tue, 16 Jun 2020 08:47:14: 1000000 INFO @ Tue, 16 Jun 2020 08:47:20: 7000000 INFO @ Tue, 16 Jun 2020 08:47:20: 2000000 INFO @ Tue, 16 Jun 2020 08:47:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:47:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:47:23: #1 total tags in treatment: 7425372 INFO @ Tue, 16 Jun 2020 08:47:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:23: #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 08:47:23: #1 tags after filtering in treatment: 7425372 INFO @ Tue, 16 Jun 2020 08:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:23: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 08:47:23: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:23: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:47:23: #2 alternative fragment length(s) may be 4,48,482,598 bps INFO @ Tue, 16 Jun 2020 08:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.05_model.r WARNING @ Tue, 16 Jun 2020 08:47:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:23: #2 You may need to consider one of the other alternative d(s): 4,48,482,598 WARNING @ Tue, 16 Jun 2020 08:47:23: #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 08:47:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:27: 3000000 INFO @ Tue, 16 Jun 2020 08:47:33: 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 08:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.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 08:47:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:39: 5000000 INFO @ Tue, 16 Jun 2020 08:47:44: 1000000 INFO @ Tue, 16 Jun 2020 08:47:45: 6000000 INFO @ Tue, 16 Jun 2020 08:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.05_summits.bed INFO @ Tue, 16 Jun 2020 08:47:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:51: 2000000 INFO @ Tue, 16 Jun 2020 08:47:52: 7000000 INFO @ Tue, 16 Jun 2020 08:47:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:47:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:47:54: #1 total tags in treatment: 7425372 INFO @ Tue, 16 Jun 2020 08:47:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:54: #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 08:47:54: #1 tags after filtering in treatment: 7425372 INFO @ Tue, 16 Jun 2020 08:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:55: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 08:47:55: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:55: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:47:55: #2 alternative fragment length(s) may be 4,48,482,598 bps INFO @ Tue, 16 Jun 2020 08:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.10_model.r WARNING @ Tue, 16 Jun 2020 08:47:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:55: #2 You may need to consider one of the other alternative d(s): 4,48,482,598 WARNING @ Tue, 16 Jun 2020 08:47:55: #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 08:47:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:57: 3000000 INFO @ Tue, 16 Jun 2020 08:48:03: 4000000 INFO @ Tue, 16 Jun 2020 08:48:09: 5000000 INFO @ Tue, 16 Jun 2020 08:48:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:15: 6000000 INFO @ Tue, 16 Jun 2020 08:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:21: 7000000 INFO @ Tue, 16 Jun 2020 08:48:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:48:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:48:24: #1 total tags in treatment: 7425372 INFO @ Tue, 16 Jun 2020 08:48:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:24: #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 08:48:24: #1 tags after filtering in treatment: 7425372 INFO @ Tue, 16 Jun 2020 08:48:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:24: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 08:48:24: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:25: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:48:25: #2 alternative fragment length(s) may be 4,48,482,598 bps INFO @ Tue, 16 Jun 2020 08:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.20_model.r WARNING @ Tue, 16 Jun 2020 08:48:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:25: #2 You may need to consider one of the other alternative d(s): 4,48,482,598 WARNING @ Tue, 16 Jun 2020 08:48:25: #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 08:48:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082357/SRX4082357.20_summits.bed INFO @ Tue, 16 Jun 2020 08:48:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 1 millis CompletedMACS2peakCalling