Job ID = 6529264 SRX = SRX113310 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:01 24032472 reads; of these: 24032472 (100.00%) were unpaired; of these: 648841 (2.70%) aligned 0 times 16286173 (67.77%) aligned exactly 1 time 7097458 (29.53%) aligned >1 times 97.30% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 6306087 / 23383631 = 0.2697 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 02:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.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 02:00:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:52: 1000000 INFO @ Tue, 30 Jun 2020 02:00:59: 2000000 INFO @ Tue, 30 Jun 2020 02:01:05: 3000000 INFO @ Tue, 30 Jun 2020 02:01:11: 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 02:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.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 02:01:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:18: 5000000 INFO @ Tue, 30 Jun 2020 02:01:24: 1000000 INFO @ Tue, 30 Jun 2020 02:01:25: 6000000 INFO @ Tue, 30 Jun 2020 02:01:32: 7000000 INFO @ Tue, 30 Jun 2020 02:01:32: 2000000 INFO @ Tue, 30 Jun 2020 02:01:39: 8000000 INFO @ Tue, 30 Jun 2020 02:01:39: 3000000 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 02:01:46: 9000000 INFO @ Tue, 30 Jun 2020 02:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.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 02:01:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:47: 4000000 INFO @ Tue, 30 Jun 2020 02:01:54: 1000000 INFO @ Tue, 30 Jun 2020 02:01:54: 10000000 INFO @ Tue, 30 Jun 2020 02:01:55: 5000000 INFO @ Tue, 30 Jun 2020 02:02:01: 2000000 INFO @ Tue, 30 Jun 2020 02:02:01: 11000000 INFO @ Tue, 30 Jun 2020 02:02:03: 6000000 INFO @ Tue, 30 Jun 2020 02:02:08: 3000000 INFO @ Tue, 30 Jun 2020 02:02:08: 12000000 INFO @ Tue, 30 Jun 2020 02:02:10: 7000000 INFO @ Tue, 30 Jun 2020 02:02:15: 4000000 INFO @ Tue, 30 Jun 2020 02:02:15: 13000000 INFO @ Tue, 30 Jun 2020 02:02:18: 8000000 INFO @ Tue, 30 Jun 2020 02:02:22: 5000000 INFO @ Tue, 30 Jun 2020 02:02:23: 14000000 INFO @ Tue, 30 Jun 2020 02:02:25: 9000000 INFO @ Tue, 30 Jun 2020 02:02:29: 6000000 INFO @ Tue, 30 Jun 2020 02:02:30: 15000000 INFO @ Tue, 30 Jun 2020 02:02:33: 10000000 INFO @ Tue, 30 Jun 2020 02:02:37: 7000000 INFO @ Tue, 30 Jun 2020 02:02:37: 16000000 INFO @ Tue, 30 Jun 2020 02:02:41: 11000000 INFO @ Tue, 30 Jun 2020 02:02:44: 8000000 INFO @ Tue, 30 Jun 2020 02:02:45: 17000000 INFO @ Tue, 30 Jun 2020 02:02:46: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:02:46: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:02:46: #1 total tags in treatment: 17077544 INFO @ Tue, 30 Jun 2020 02:02:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:46: #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 02:02:46: #1 tags after filtering in treatment: 17077543 INFO @ Tue, 30 Jun 2020 02:02:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:46: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:48: #2 number of paired peaks: 144 WARNING @ Tue, 30 Jun 2020 02:02:48: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:48: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:48: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:48: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:48: #2 predicted fragment length is 30 bps INFO @ Tue, 30 Jun 2020 02:02:48: #2 alternative fragment length(s) may be 3,30,54,497 bps INFO @ Tue, 30 Jun 2020 02:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.05_model.r WARNING @ Tue, 30 Jun 2020 02:02:48: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:02:48: #2 You may need to consider one of the other alternative d(s): 3,30,54,497 WARNING @ Tue, 30 Jun 2020 02:02:48: #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 02:02:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:48: 12000000 INFO @ Tue, 30 Jun 2020 02:02:51: 9000000 INFO @ Tue, 30 Jun 2020 02:02:56: 13000000 INFO @ Tue, 30 Jun 2020 02:02:58: 10000000 INFO @ Tue, 30 Jun 2020 02:03:04: 14000000 INFO @ Tue, 30 Jun 2020 02:03:05: 11000000 INFO @ Tue, 30 Jun 2020 02:03:12: 15000000 INFO @ Tue, 30 Jun 2020 02:03:13: 12000000 INFO @ Tue, 30 Jun 2020 02:03:20: 16000000 INFO @ Tue, 30 Jun 2020 02:03:20: 13000000 INFO @ Tue, 30 Jun 2020 02:03:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:03:28: 14000000 INFO @ Tue, 30 Jun 2020 02:03:28: 17000000 INFO @ Tue, 30 Jun 2020 02:03:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:03:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:03:29: #1 total tags in treatment: 17077544 INFO @ Tue, 30 Jun 2020 02:03:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:29: #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 02:03:29: #1 tags after filtering in treatment: 17077543 INFO @ Tue, 30 Jun 2020 02:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:31: #2 number of paired peaks: 144 WARNING @ Tue, 30 Jun 2020 02:03:31: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:31: #2 predicted fragment length is 30 bps INFO @ Tue, 30 Jun 2020 02:03:31: #2 alternative fragment length(s) may be 3,30,54,497 bps INFO @ Tue, 30 Jun 2020 02:03:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.10_model.r WARNING @ Tue, 30 Jun 2020 02:03:31: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:31: #2 You may need to consider one of the other alternative d(s): 3,30,54,497 WARNING @ Tue, 30 Jun 2020 02:03:31: #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 02:03:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:34: 15000000 INFO @ Tue, 30 Jun 2020 02:03:40: 16000000 INFO @ Tue, 30 Jun 2020 02:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.05_summits.bed INFO @ Tue, 30 Jun 2020 02:03:43: Done! pass1 - making usageList (489 chroms): 1 millis pass2 - checking and writing primary data (1337 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:03:47: 17000000 INFO @ Tue, 30 Jun 2020 02:03:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:03:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:03:48: #1 total tags in treatment: 17077544 INFO @ Tue, 30 Jun 2020 02:03:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:48: #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 02:03:48: #1 tags after filtering in treatment: 17077543 INFO @ Tue, 30 Jun 2020 02:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:50: #2 number of paired peaks: 144 WARNING @ Tue, 30 Jun 2020 02:03:50: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:50: #2 predicted fragment length is 30 bps INFO @ Tue, 30 Jun 2020 02:03:50: #2 alternative fragment length(s) may be 3,30,54,497 bps INFO @ Tue, 30 Jun 2020 02:03:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.20_model.r WARNING @ Tue, 30 Jun 2020 02:03:50: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:50: #2 You may need to consider one of the other alternative d(s): 3,30,54,497 WARNING @ Tue, 30 Jun 2020 02:03:50: #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 02:03:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:04:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.10_summits.bed INFO @ Tue, 30 Jun 2020 02:04:25: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113310/SRX113310.20_summits.bed INFO @ Tue, 30 Jun 2020 02:04:44: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 4 millis CompletedMACS2peakCalling