Job ID = 5720754 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,330,993 reads read : 30,661,986 reads written : 15,330,993 reads 0-length : 15,330,993 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: 00:06:09 15330993 reads; of these: 15330993 (100.00%) were unpaired; of these: 830251 (5.42%) aligned 0 times 10718027 (69.91%) aligned exactly 1 time 3782715 (24.67%) aligned >1 times 94.58% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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 8 files... [bam_rmdupse_core] 1320713 / 14500742 = 0.0911 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 01:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.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 01:28:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:28:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:28:50: 1000000 INFO @ Thu, 16 Apr 2020 01:28:56: 2000000 INFO @ Thu, 16 Apr 2020 01:29:03: 3000000 INFO @ Thu, 16 Apr 2020 01:29:09: 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 01:29:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.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 01:29:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:29:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:29:15: 5000000 INFO @ Thu, 16 Apr 2020 01:29:21: 1000000 INFO @ Thu, 16 Apr 2020 01:29:22: 6000000 INFO @ Thu, 16 Apr 2020 01:29:29: 2000000 INFO @ Thu, 16 Apr 2020 01:29:29: 7000000 INFO @ Thu, 16 Apr 2020 01:29:36: 3000000 INFO @ Thu, 16 Apr 2020 01:29:36: 8000000 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 01:29:43: 4000000 INFO @ Thu, 16 Apr 2020 01:29:43: 9000000 INFO @ Thu, 16 Apr 2020 01:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.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 01:29:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:29:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:29:50: 5000000 INFO @ Thu, 16 Apr 2020 01:29:50: 10000000 INFO @ Thu, 16 Apr 2020 01:29:50: 1000000 INFO @ Thu, 16 Apr 2020 01:29:57: 11000000 INFO @ Thu, 16 Apr 2020 01:29:57: 6000000 INFO @ Thu, 16 Apr 2020 01:29:57: 2000000 INFO @ Thu, 16 Apr 2020 01:30:04: 7000000 INFO @ Thu, 16 Apr 2020 01:30:04: 12000000 INFO @ Thu, 16 Apr 2020 01:30:05: 3000000 INFO @ Thu, 16 Apr 2020 01:30:11: 8000000 INFO @ Thu, 16 Apr 2020 01:30:11: 13000000 INFO @ Thu, 16 Apr 2020 01:30:12: 4000000 INFO @ Thu, 16 Apr 2020 01:30:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:30:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:30:12: #1 total tags in treatment: 13180029 INFO @ Thu, 16 Apr 2020 01:30:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:12: #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 01:30:12: #1 tags after filtering in treatment: 13180029 INFO @ Thu, 16 Apr 2020 01:30:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:12: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:13: #2 number of paired peaks: 654 WARNING @ Thu, 16 Apr 2020 01:30:13: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:13: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:13: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:13: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:13: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:13: #2 predicted fragment length is 81 bps INFO @ Thu, 16 Apr 2020 01:30:13: #2 alternative fragment length(s) may be 81 bps INFO @ Thu, 16 Apr 2020 01:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.05_model.r WARNING @ Thu, 16 Apr 2020 01:30:13: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:13: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Thu, 16 Apr 2020 01:30:13: #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 01:30:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:18: 9000000 INFO @ Thu, 16 Apr 2020 01:30:19: 5000000 INFO @ Thu, 16 Apr 2020 01:30:25: 10000000 INFO @ Thu, 16 Apr 2020 01:30:26: 6000000 INFO @ Thu, 16 Apr 2020 01:30:32: 11000000 INFO @ Thu, 16 Apr 2020 01:30:32: 7000000 INFO @ Thu, 16 Apr 2020 01:30:39: 12000000 INFO @ Thu, 16 Apr 2020 01:30:39: 8000000 INFO @ Thu, 16 Apr 2020 01:30:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:30:46: 13000000 INFO @ Thu, 16 Apr 2020 01:30:46: 9000000 INFO @ Thu, 16 Apr 2020 01:30:47: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:30:47: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:30:47: #1 total tags in treatment: 13180029 INFO @ Thu, 16 Apr 2020 01:30:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:47: #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 01:30:47: #1 tags after filtering in treatment: 13180029 INFO @ Thu, 16 Apr 2020 01:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:47: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:48: #2 number of paired peaks: 654 WARNING @ Thu, 16 Apr 2020 01:30:48: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:48: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:48: #2 predicted fragment length is 81 bps INFO @ Thu, 16 Apr 2020 01:30:48: #2 alternative fragment length(s) may be 81 bps INFO @ Thu, 16 Apr 2020 01:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.10_model.r WARNING @ Thu, 16 Apr 2020 01:30:48: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:48: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Thu, 16 Apr 2020 01:30:48: #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 01:30:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:52: 10000000 INFO @ Thu, 16 Apr 2020 01:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.05_summits.bed INFO @ Thu, 16 Apr 2020 01:30:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4189 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:30:59: 11000000 INFO @ Thu, 16 Apr 2020 01:31:05: 12000000 INFO @ Thu, 16 Apr 2020 01:31:11: 13000000 INFO @ Thu, 16 Apr 2020 01:31:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:31:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:31:12: #1 total tags in treatment: 13180029 INFO @ Thu, 16 Apr 2020 01:31:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:31:12: #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 01:31:13: #1 tags after filtering in treatment: 13180029 INFO @ Thu, 16 Apr 2020 01:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:31:13: #1 finished! INFO @ Thu, 16 Apr 2020 01:31:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:31:14: #2 number of paired peaks: 654 WARNING @ Thu, 16 Apr 2020 01:31:14: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Thu, 16 Apr 2020 01:31:14: start model_add_line... INFO @ Thu, 16 Apr 2020 01:31:14: start X-correlation... INFO @ Thu, 16 Apr 2020 01:31:14: end of X-cor INFO @ Thu, 16 Apr 2020 01:31:14: #2 finished! INFO @ Thu, 16 Apr 2020 01:31:14: #2 predicted fragment length is 81 bps INFO @ Thu, 16 Apr 2020 01:31:14: #2 alternative fragment length(s) may be 81 bps INFO @ Thu, 16 Apr 2020 01:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.20_model.r WARNING @ Thu, 16 Apr 2020 01:31:14: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:31:14: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Thu, 16 Apr 2020 01:31:14: #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 01:31:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:31:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.10_summits.bed INFO @ Thu, 16 Apr 2020 01:31:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2123 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:31:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226992/SRX5226992.20_summits.bed INFO @ Thu, 16 Apr 2020 01:31:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (816 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。