Job ID = 5721199 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,108,107 reads read : 23,108,107 reads written : 23,108,107 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:19 23108107 reads; of these: 23108107 (100.00%) were unpaired; of these: 720681 (3.12%) aligned 0 times 15196867 (65.76%) aligned exactly 1 time 7190559 (31.12%) aligned >1 times 96.88% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3286804 / 22387426 = 0.1468 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 @ Thu, 16 Apr 2020 06:04:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:04:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:04:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:04:30: 1000000 INFO @ Thu, 16 Apr 2020 06:04:36: 2000000 INFO @ Thu, 16 Apr 2020 06:04:42: 3000000 INFO @ Thu, 16 Apr 2020 06:04:48: 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 @ Thu, 16 Apr 2020 06:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:04:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:04:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:04:54: 5000000 INFO @ Thu, 16 Apr 2020 06:04:59: 1000000 INFO @ Thu, 16 Apr 2020 06:05:00: 6000000 INFO @ Thu, 16 Apr 2020 06:05:05: 2000000 INFO @ Thu, 16 Apr 2020 06:05:06: 7000000 INFO @ Thu, 16 Apr 2020 06:05:11: 3000000 INFO @ Thu, 16 Apr 2020 06:05:12: 8000000 INFO @ Thu, 16 Apr 2020 06:05:17: 4000000 INFO @ Thu, 16 Apr 2020 06:05:18: 9000000 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 @ Thu, 16 Apr 2020 06:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:05:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:05:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:05:23: 5000000 INFO @ Thu, 16 Apr 2020 06:05:24: 10000000 INFO @ Thu, 16 Apr 2020 06:05:29: 6000000 INFO @ Thu, 16 Apr 2020 06:05:29: 1000000 INFO @ Thu, 16 Apr 2020 06:05:30: 11000000 INFO @ Thu, 16 Apr 2020 06:05:36: 7000000 INFO @ Thu, 16 Apr 2020 06:05:36: 2000000 INFO @ Thu, 16 Apr 2020 06:05:36: 12000000 INFO @ Thu, 16 Apr 2020 06:05:42: 8000000 INFO @ Thu, 16 Apr 2020 06:05:42: 3000000 INFO @ Thu, 16 Apr 2020 06:05:43: 13000000 INFO @ Thu, 16 Apr 2020 06:05:48: 9000000 INFO @ Thu, 16 Apr 2020 06:05:49: 4000000 INFO @ Thu, 16 Apr 2020 06:05:49: 14000000 INFO @ Thu, 16 Apr 2020 06:05:55: 10000000 INFO @ Thu, 16 Apr 2020 06:05:55: 5000000 INFO @ Thu, 16 Apr 2020 06:05:55: 15000000 INFO @ Thu, 16 Apr 2020 06:06:01: 11000000 INFO @ Thu, 16 Apr 2020 06:06:02: 6000000 INFO @ Thu, 16 Apr 2020 06:06:02: 16000000 INFO @ Thu, 16 Apr 2020 06:06:07: 12000000 INFO @ Thu, 16 Apr 2020 06:06:08: 17000000 INFO @ Thu, 16 Apr 2020 06:06:08: 7000000 INFO @ Thu, 16 Apr 2020 06:06:14: 13000000 INFO @ Thu, 16 Apr 2020 06:06:14: 18000000 INFO @ Thu, 16 Apr 2020 06:06:15: 8000000 INFO @ Thu, 16 Apr 2020 06:06:20: 14000000 INFO @ Thu, 16 Apr 2020 06:06:21: 19000000 INFO @ Thu, 16 Apr 2020 06:06:21: 9000000 INFO @ Thu, 16 Apr 2020 06:06:21: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:06:21: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:06:21: #1 total tags in treatment: 19100622 INFO @ Thu, 16 Apr 2020 06:06:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:06:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:06:22: #1 tags after filtering in treatment: 19100622 INFO @ Thu, 16 Apr 2020 06:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:06:22: #1 finished! INFO @ Thu, 16 Apr 2020 06:06:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:06:23: #2 number of paired peaks: 425 WARNING @ Thu, 16 Apr 2020 06:06:23: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 16 Apr 2020 06:06:23: start model_add_line... INFO @ Thu, 16 Apr 2020 06:06:23: start X-correlation... INFO @ Thu, 16 Apr 2020 06:06:23: end of X-cor INFO @ Thu, 16 Apr 2020 06:06:23: #2 finished! INFO @ Thu, 16 Apr 2020 06:06:23: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:06:23: #2 alternative fragment length(s) may be 4,48 bps INFO @ Thu, 16 Apr 2020 06:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.05_model.r WARNING @ Thu, 16 Apr 2020 06:06:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:06:23: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Thu, 16 Apr 2020 06:06:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:06:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:06:26: 15000000 INFO @ Thu, 16 Apr 2020 06:06:27: 10000000 INFO @ Thu, 16 Apr 2020 06:06:32: 16000000 INFO @ Thu, 16 Apr 2020 06:06:34: 11000000 INFO @ Thu, 16 Apr 2020 06:06:38: 17000000 INFO @ Thu, 16 Apr 2020 06:06:40: 12000000 INFO @ Thu, 16 Apr 2020 06:06:45: 18000000 INFO @ Thu, 16 Apr 2020 06:06:47: 13000000 INFO @ Thu, 16 Apr 2020 06:06:51: 19000000 INFO @ Thu, 16 Apr 2020 06:06:52: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:06:52: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:06:52: #1 total tags in treatment: 19100622 INFO @ Thu, 16 Apr 2020 06:06:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:06:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:06:52: #1 tags after filtering in treatment: 19100622 INFO @ Thu, 16 Apr 2020 06:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:06:52: #1 finished! INFO @ Thu, 16 Apr 2020 06:06:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:06:53: 14000000 INFO @ Thu, 16 Apr 2020 06:06:53: #2 number of paired peaks: 425 WARNING @ Thu, 16 Apr 2020 06:06:53: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 16 Apr 2020 06:06:53: start model_add_line... INFO @ Thu, 16 Apr 2020 06:06:53: start X-correlation... INFO @ Thu, 16 Apr 2020 06:06:53: end of X-cor INFO @ Thu, 16 Apr 2020 06:06:53: #2 finished! INFO @ Thu, 16 Apr 2020 06:06:53: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:06:53: #2 alternative fragment length(s) may be 4,48 bps INFO @ Thu, 16 Apr 2020 06:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.10_model.r WARNING @ Thu, 16 Apr 2020 06:06:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:06:53: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Thu, 16 Apr 2020 06:06:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:06:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:06:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:06:59: 15000000 INFO @ Thu, 16 Apr 2020 06:07:05: 16000000 INFO @ Thu, 16 Apr 2020 06:07:11: 17000000 INFO @ Thu, 16 Apr 2020 06:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.05_summits.bed INFO @ Thu, 16 Apr 2020 06:07:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3321 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:07:17: 18000000 INFO @ Thu, 16 Apr 2020 06:07:23: 19000000 INFO @ Thu, 16 Apr 2020 06:07:24: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:07:24: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:07:24: #1 total tags in treatment: 19100622 INFO @ Thu, 16 Apr 2020 06:07:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:07:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:07:24: #1 tags after filtering in treatment: 19100622 INFO @ Thu, 16 Apr 2020 06:07:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:07:24: #1 finished! INFO @ Thu, 16 Apr 2020 06:07:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:07:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:07:26: #2 number of paired peaks: 425 WARNING @ Thu, 16 Apr 2020 06:07:26: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 16 Apr 2020 06:07:26: start model_add_line... INFO @ Thu, 16 Apr 2020 06:07:26: start X-correlation... INFO @ Thu, 16 Apr 2020 06:07:26: end of X-cor INFO @ Thu, 16 Apr 2020 06:07:26: #2 finished! INFO @ Thu, 16 Apr 2020 06:07:26: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:07:26: #2 alternative fragment length(s) may be 4,48 bps INFO @ Thu, 16 Apr 2020 06:07:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.20_model.r WARNING @ Thu, 16 Apr 2020 06:07:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:07:26: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Thu, 16 Apr 2020 06:07:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:07:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:07:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.10_summits.bed INFO @ Thu, 16 Apr 2020 06:07:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2332 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:07:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827667/SRX6827667.20_summits.bed INFO @ Thu, 16 Apr 2020 06:08:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1245 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。