Job ID = 5790652 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,021,546 reads read : 38,043,092 reads written : 19,021,546 reads 0-length : 19,021,546 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:33:02 19021546 reads; of these: 19021546 (100.00%) were unpaired; of these: 12232699 (64.31%) aligned 0 times 2468623 (12.98%) aligned exactly 1 time 4320224 (22.71%) aligned >1 times 35.69% overall alignment rate Time searching: 01:33:05 Overall time: 01:33:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 1145356 / 6788847 = 0.1687 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 @ Wed, 22 Apr 2020 06:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:46:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:46:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:46:56: 1000000 INFO @ Wed, 22 Apr 2020 06:47:03: 2000000 INFO @ Wed, 22 Apr 2020 06:47:10: 3000000 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 @ Wed, 22 Apr 2020 06:47:17: 4000000 INFO @ Wed, 22 Apr 2020 06:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:47:18: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:47:18: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:47:24: 5000000 INFO @ Wed, 22 Apr 2020 06:47:26: 1000000 INFO @ Wed, 22 Apr 2020 06:47:30: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:47:30: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:47:30: #1 total tags in treatment: 5643491 INFO @ Wed, 22 Apr 2020 06:47:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:47:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:47:30: #1 tags after filtering in treatment: 5643247 INFO @ Wed, 22 Apr 2020 06:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:47:30: #1 finished! INFO @ Wed, 22 Apr 2020 06:47:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:47:33: #2 number of paired peaks: 101590 INFO @ Wed, 22 Apr 2020 06:47:33: start model_add_line... INFO @ Wed, 22 Apr 2020 06:47:33: start X-correlation... INFO @ Wed, 22 Apr 2020 06:47:33: end of X-cor INFO @ Wed, 22 Apr 2020 06:47:33: #2 finished! INFO @ Wed, 22 Apr 2020 06:47:33: #2 predicted fragment length is 117 bps INFO @ Wed, 22 Apr 2020 06:47:33: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 22 Apr 2020 06:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.05_model.r WARNING @ Wed, 22 Apr 2020 06:47:33: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:47:33: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 22 Apr 2020 06:47:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:47:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:47:33: 2000000 INFO @ Wed, 22 Apr 2020 06:47:40: 3000000 INFO @ Wed, 22 Apr 2020 06:47:45: #3 Call peaks for each chromosome... 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 @ Wed, 22 Apr 2020 06:47:47: 4000000 INFO @ Wed, 22 Apr 2020 06:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:47:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:47:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.05_summits.bed INFO @ Wed, 22 Apr 2020 06:47:52: Done! pass1 - making usageList (87 chroms): 2 millis pass2 - checking and writing primary data (9211 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:47:55: 5000000 INFO @ Wed, 22 Apr 2020 06:47:57: 1000000 INFO @ Wed, 22 Apr 2020 06:48:00: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:48:00: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:48:00: #1 total tags in treatment: 5643491 INFO @ Wed, 22 Apr 2020 06:48:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:48:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:48:00: #1 tags after filtering in treatment: 5643247 INFO @ Wed, 22 Apr 2020 06:48:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:48:00: #1 finished! INFO @ Wed, 22 Apr 2020 06:48:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:48:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:48:03: #2 number of paired peaks: 101590 INFO @ Wed, 22 Apr 2020 06:48:03: start model_add_line... INFO @ Wed, 22 Apr 2020 06:48:03: start X-correlation... INFO @ Wed, 22 Apr 2020 06:48:03: end of X-cor INFO @ Wed, 22 Apr 2020 06:48:03: #2 finished! INFO @ Wed, 22 Apr 2020 06:48:03: #2 predicted fragment length is 117 bps INFO @ Wed, 22 Apr 2020 06:48:03: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 22 Apr 2020 06:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.10_model.r WARNING @ Wed, 22 Apr 2020 06:48:03: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:48:03: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 22 Apr 2020 06:48:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:48:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:48:05: 2000000 INFO @ Wed, 22 Apr 2020 06:48:12: 3000000 INFO @ Wed, 22 Apr 2020 06:48:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:48:19: 4000000 INFO @ Wed, 22 Apr 2020 06:48:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:48:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:48:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.10_summits.bed INFO @ Wed, 22 Apr 2020 06:48:22: Done! INFO @ Wed, 22 Apr 2020 06:48:26: 5000000 pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1230 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:48:30: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:48:30: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:48:30: #1 total tags in treatment: 5643491 INFO @ Wed, 22 Apr 2020 06:48:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:48:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:48:30: #1 tags after filtering in treatment: 5643247 INFO @ Wed, 22 Apr 2020 06:48:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:48:30: #1 finished! INFO @ Wed, 22 Apr 2020 06:48:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:48:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:48:33: #2 number of paired peaks: 101590 INFO @ Wed, 22 Apr 2020 06:48:33: start model_add_line... INFO @ Wed, 22 Apr 2020 06:48:33: start X-correlation... INFO @ Wed, 22 Apr 2020 06:48:33: end of X-cor INFO @ Wed, 22 Apr 2020 06:48:33: #2 finished! INFO @ Wed, 22 Apr 2020 06:48:33: #2 predicted fragment length is 117 bps INFO @ Wed, 22 Apr 2020 06:48:33: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 22 Apr 2020 06:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.20_model.r WARNING @ Wed, 22 Apr 2020 06:48:33: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:48:33: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 22 Apr 2020 06:48:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:48:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:48:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:48:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:48:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:48:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299295/SRX5299295.20_summits.bed INFO @ Wed, 22 Apr 2020 06:48:52: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。