Job ID = 6529990 SRX = SRX5775914 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:10:24 25902420 reads; of these: 25902420 (100.00%) were unpaired; of these: 804408 (3.11%) aligned 0 times 18165665 (70.13%) aligned exactly 1 time 6932347 (26.76%) aligned >1 times 96.89% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10011641 / 25098012 = 0.3989 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, 30 Jun 2020 03:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.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 @ Tue, 30 Jun 2020 03:23:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:37: 1000000 INFO @ Tue, 30 Jun 2020 03:23:43: 2000000 INFO @ Tue, 30 Jun 2020 03:23:49: 3000000 INFO @ Tue, 30 Jun 2020 03:23:56: 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, 30 Jun 2020 03:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.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 @ Tue, 30 Jun 2020 03:24:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:24:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:24:03: 5000000 INFO @ Tue, 30 Jun 2020 03:24:08: 1000000 INFO @ Tue, 30 Jun 2020 03:24:10: 6000000 INFO @ Tue, 30 Jun 2020 03:24:15: 2000000 INFO @ Tue, 30 Jun 2020 03:24:17: 7000000 INFO @ Tue, 30 Jun 2020 03:24:22: 3000000 INFO @ Tue, 30 Jun 2020 03:24:23: 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 @ Tue, 30 Jun 2020 03:24:29: 4000000 INFO @ Tue, 30 Jun 2020 03:24:31: 9000000 INFO @ Tue, 30 Jun 2020 03:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.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 @ Tue, 30 Jun 2020 03:24:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:24:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:24:36: 5000000 INFO @ Tue, 30 Jun 2020 03:24:38: 10000000 INFO @ Tue, 30 Jun 2020 03:24:39: 1000000 INFO @ Tue, 30 Jun 2020 03:24:43: 6000000 INFO @ Tue, 30 Jun 2020 03:24:45: 11000000 INFO @ Tue, 30 Jun 2020 03:24:46: 2000000 INFO @ Tue, 30 Jun 2020 03:24:50: 7000000 INFO @ Tue, 30 Jun 2020 03:24:53: 12000000 INFO @ Tue, 30 Jun 2020 03:24:53: 3000000 INFO @ Tue, 30 Jun 2020 03:24:57: 8000000 INFO @ Tue, 30 Jun 2020 03:25:00: 13000000 INFO @ Tue, 30 Jun 2020 03:25:01: 4000000 INFO @ Tue, 30 Jun 2020 03:25:04: 9000000 INFO @ Tue, 30 Jun 2020 03:25:08: 14000000 INFO @ Tue, 30 Jun 2020 03:25:08: 5000000 INFO @ Tue, 30 Jun 2020 03:25:11: 10000000 INFO @ Tue, 30 Jun 2020 03:25:15: 6000000 INFO @ Tue, 30 Jun 2020 03:25:16: 15000000 INFO @ Tue, 30 Jun 2020 03:25:16: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:25:16: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:25:16: #1 total tags in treatment: 15086371 INFO @ Tue, 30 Jun 2020 03:25:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:25:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:25:17: #1 tags after filtering in treatment: 15086370 INFO @ Tue, 30 Jun 2020 03:25:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:25:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:25:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:25:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:25:18: #2 number of paired peaks: 851 WARNING @ Tue, 30 Jun 2020 03:25:18: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Tue, 30 Jun 2020 03:25:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:25:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:25:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:25:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:25:18: #2 predicted fragment length is 69 bps INFO @ Tue, 30 Jun 2020 03:25:18: #2 alternative fragment length(s) may be 3,69,547 bps INFO @ Tue, 30 Jun 2020 03:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.05_model.r WARNING @ Tue, 30 Jun 2020 03:25:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:25:18: #2 You may need to consider one of the other alternative d(s): 3,69,547 WARNING @ Tue, 30 Jun 2020 03:25:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:25:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:25:18: 11000000 INFO @ Tue, 30 Jun 2020 03:25:22: 7000000 INFO @ Tue, 30 Jun 2020 03:25:26: 12000000 INFO @ Tue, 30 Jun 2020 03:25:29: 8000000 INFO @ Tue, 30 Jun 2020 03:25:33: 13000000 INFO @ Tue, 30 Jun 2020 03:25:36: 9000000 INFO @ Tue, 30 Jun 2020 03:25:39: 14000000 INFO @ Tue, 30 Jun 2020 03:25:42: 10000000 INFO @ Tue, 30 Jun 2020 03:25:46: 15000000 INFO @ Tue, 30 Jun 2020 03:25:47: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:25:47: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:25:47: #1 total tags in treatment: 15086371 INFO @ Tue, 30 Jun 2020 03:25:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:25:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:25:48: #1 tags after filtering in treatment: 15086370 INFO @ Tue, 30 Jun 2020 03:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:25:48: #1 finished! INFO @ Tue, 30 Jun 2020 03:25:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:25:49: #2 number of paired peaks: 851 WARNING @ Tue, 30 Jun 2020 03:25:49: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Tue, 30 Jun 2020 03:25:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:25:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:25:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:25:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:25:49: #2 predicted fragment length is 69 bps INFO @ Tue, 30 Jun 2020 03:25:49: #2 alternative fragment length(s) may be 3,69,547 bps INFO @ Tue, 30 Jun 2020 03:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.10_model.r WARNING @ Tue, 30 Jun 2020 03:25:49: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:25:49: #2 You may need to consider one of the other alternative d(s): 3,69,547 WARNING @ Tue, 30 Jun 2020 03:25:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:25:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:25:49: 11000000 INFO @ Tue, 30 Jun 2020 03:25:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:25:56: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:26:02: 13000000 INFO @ Tue, 30 Jun 2020 03:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.05_summits.bed INFO @ Tue, 30 Jun 2020 03:26:07: Done! pass1 - making usageList (810 chroms): 1 millis pass2 - checking and writing primary data (2660 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:26:09: 14000000 INFO @ Tue, 30 Jun 2020 03:26:16: 15000000 INFO @ Tue, 30 Jun 2020 03:26:16: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:26:16: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:26:16: #1 total tags in treatment: 15086371 INFO @ Tue, 30 Jun 2020 03:26:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:26:17: #1 tags after filtering in treatment: 15086370 INFO @ Tue, 30 Jun 2020 03:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:18: #2 number of paired peaks: 851 WARNING @ Tue, 30 Jun 2020 03:26:18: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Tue, 30 Jun 2020 03:26:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:18: #2 predicted fragment length is 69 bps INFO @ Tue, 30 Jun 2020 03:26:18: #2 alternative fragment length(s) may be 3,69,547 bps INFO @ Tue, 30 Jun 2020 03:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.20_model.r WARNING @ Tue, 30 Jun 2020 03:26:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:18: #2 You may need to consider one of the other alternative d(s): 3,69,547 WARNING @ Tue, 30 Jun 2020 03:26:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:26:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.10_summits.bed INFO @ Tue, 30 Jun 2020 03:26:36: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (2026 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:26:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775914/SRX5775914.20_summits.bed INFO @ Tue, 30 Jun 2020 03:27:07: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1351 records, 4 fields): 16 millis CompletedMACS2peakCalling