Job ID = 6529261 SRX = SRX111811 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: 00:04:33 16119953 reads; of these: 16119953 (100.00%) were unpaired; of these: 1631735 (10.12%) aligned 0 times 10173487 (63.11%) aligned exactly 1 time 4314731 (26.77%) aligned >1 times 89.88% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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 8 files... [bam_rmdupse_core] 3405650 / 14488218 = 0.2351 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 01:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.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 01:56:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:29: 1000000 INFO @ Tue, 30 Jun 2020 01:56:35: 2000000 INFO @ Tue, 30 Jun 2020 01:56:41: 3000000 INFO @ Tue, 30 Jun 2020 01:56:46: 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 01:56:52: 5000000 INFO @ Tue, 30 Jun 2020 01:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.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 01:56:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:59: 6000000 INFO @ Tue, 30 Jun 2020 01:56:59: 1000000 INFO @ Tue, 30 Jun 2020 01:57:05: 7000000 INFO @ Tue, 30 Jun 2020 01:57:05: 2000000 INFO @ Tue, 30 Jun 2020 01:57:11: 8000000 INFO @ Tue, 30 Jun 2020 01:57:11: 3000000 INFO @ Tue, 30 Jun 2020 01:57:17: 4000000 INFO @ Tue, 30 Jun 2020 01:57:17: 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 @ Tue, 30 Jun 2020 01:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.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 01:57:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:24: 5000000 INFO @ Tue, 30 Jun 2020 01:57:24: 10000000 INFO @ Tue, 30 Jun 2020 01:57:30: 1000000 INFO @ Tue, 30 Jun 2020 01:57:30: 6000000 INFO @ Tue, 30 Jun 2020 01:57:30: 11000000 INFO @ Tue, 30 Jun 2020 01:57:31: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:57:31: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:57:31: #1 total tags in treatment: 11082568 INFO @ Tue, 30 Jun 2020 01:57:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:31: #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 01:57:31: #1 tags after filtering in treatment: 11082490 INFO @ Tue, 30 Jun 2020 01:57:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:31: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:32: #2 number of paired peaks: 382 WARNING @ Tue, 30 Jun 2020 01:57:32: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:32: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:32: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:32: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:32: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:32: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 01:57:32: #2 alternative fragment length(s) may be 4,14,44,545,567 bps INFO @ Tue, 30 Jun 2020 01:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:32: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:32: #2 You may need to consider one of the other alternative d(s): 4,14,44,545,567 WARNING @ Tue, 30 Jun 2020 01:57:32: #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 01:57:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:36: 7000000 INFO @ Tue, 30 Jun 2020 01:57:36: 2000000 INFO @ Tue, 30 Jun 2020 01:57:42: 8000000 INFO @ Tue, 30 Jun 2020 01:57:42: 3000000 INFO @ Tue, 30 Jun 2020 01:57:48: 9000000 INFO @ Tue, 30 Jun 2020 01:57:49: 4000000 INFO @ Tue, 30 Jun 2020 01:57:54: 10000000 INFO @ Tue, 30 Jun 2020 01:57:55: 5000000 INFO @ Tue, 30 Jun 2020 01:57:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:01: 11000000 INFO @ Tue, 30 Jun 2020 01:58:01: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:58:01: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:58:01: #1 total tags in treatment: 11082568 INFO @ Tue, 30 Jun 2020 01:58:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:01: #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 01:58:01: 6000000 INFO @ Tue, 30 Jun 2020 01:58:02: #1 tags after filtering in treatment: 11082490 INFO @ Tue, 30 Jun 2020 01:58:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:02: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:03: #2 number of paired peaks: 382 WARNING @ Tue, 30 Jun 2020 01:58:03: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:03: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:03: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:03: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:03: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:03: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 01:58:03: #2 alternative fragment length(s) may be 4,14,44,545,567 bps INFO @ Tue, 30 Jun 2020 01:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.10_model.r WARNING @ Tue, 30 Jun 2020 01:58:03: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:03: #2 You may need to consider one of the other alternative d(s): 4,14,44,545,567 WARNING @ Tue, 30 Jun 2020 01:58:03: #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 01:58:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:07: 7000000 INFO @ Tue, 30 Jun 2020 01:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:11: Done! pass1 - making usageList (578 chroms): 2 millis pass2 - checking and writing primary data (2730 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:13: 8000000 INFO @ Tue, 30 Jun 2020 01:58:20: 9000000 INFO @ Tue, 30 Jun 2020 01:58:26: 10000000 INFO @ Tue, 30 Jun 2020 01:58:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:58:32: 11000000 INFO @ Tue, 30 Jun 2020 01:58:33: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:58:33: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:58:33: #1 total tags in treatment: 11082568 INFO @ Tue, 30 Jun 2020 01:58:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:33: #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 01:58:33: #1 tags after filtering in treatment: 11082490 INFO @ Tue, 30 Jun 2020 01:58:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:33: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:34: #2 number of paired peaks: 382 WARNING @ Tue, 30 Jun 2020 01:58:34: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:34: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:34: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:34: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:34: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:34: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 01:58:34: #2 alternative fragment length(s) may be 4,14,44,545,567 bps INFO @ Tue, 30 Jun 2020 01:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:34: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:34: #2 You may need to consider one of the other alternative d(s): 4,14,44,545,567 WARNING @ Tue, 30 Jun 2020 01:58:34: #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 01:58:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.10_summits.bed INFO @ Tue, 30 Jun 2020 01:58:42: Done! pass1 - making usageList (440 chroms): 1 millis pass2 - checking and writing primary data (1151 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111811/SRX111811.20_summits.bed INFO @ Tue, 30 Jun 2020 01:59:12: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 4 millis CompletedMACS2peakCalling