Job ID = 6529815 SRX = SRX495184 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: 00:01:03 5177634 reads; of these: 5177634 (100.00%) were unpaired; of these: 229920 (4.44%) aligned 0 times 4155266 (80.25%) aligned exactly 1 time 792448 (15.31%) aligned >1 times 95.56% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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_rmdupse_core] 504238 / 4947714 = 0.1019 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 02:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.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 02:56:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:56: 1000000 INFO @ Tue, 30 Jun 2020 02:57:03: 2000000 INFO @ Tue, 30 Jun 2020 02:57:10: 3000000 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 02:57:18: 4000000 INFO @ Tue, 30 Jun 2020 02:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.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 02:57:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:21: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:57:21: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:57:21: #1 total tags in treatment: 4443476 INFO @ Tue, 30 Jun 2020 02:57:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:21: #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 02:57:22: #1 tags after filtering in treatment: 4443426 INFO @ Tue, 30 Jun 2020 02:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:22: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 02:57:22: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:22: #2 predicted fragment length is 72 bps INFO @ Tue, 30 Jun 2020 02:57:22: #2 alternative fragment length(s) may be 4,36,72,88,185,375,421,513,539,561,592 bps INFO @ Tue, 30 Jun 2020 02:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.05_model.r WARNING @ Tue, 30 Jun 2020 02:57:22: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:22: #2 You may need to consider one of the other alternative d(s): 4,36,72,88,185,375,421,513,539,561,592 WARNING @ Tue, 30 Jun 2020 02:57:22: #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 02:57:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:26: 1000000 INFO @ Tue, 30 Jun 2020 02:57:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:33: 2000000 INFO @ Tue, 30 Jun 2020 02:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.05_summits.bed INFO @ Tue, 30 Jun 2020 02:57:36: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:57:40: 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 02:57:48: 4000000 INFO @ Tue, 30 Jun 2020 02:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.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 02:57:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:51: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:57:51: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:57:51: #1 total tags in treatment: 4443476 INFO @ Tue, 30 Jun 2020 02:57:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:51: #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 02:57:52: #1 tags after filtering in treatment: 4443426 INFO @ Tue, 30 Jun 2020 02:57:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:52: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 02:57:52: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:52: #2 predicted fragment length is 72 bps INFO @ Tue, 30 Jun 2020 02:57:52: #2 alternative fragment length(s) may be 4,36,72,88,185,375,421,513,539,561,592 bps INFO @ Tue, 30 Jun 2020 02:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.10_model.r WARNING @ Tue, 30 Jun 2020 02:57:52: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:52: #2 You may need to consider one of the other alternative d(s): 4,36,72,88,185,375,421,513,539,561,592 WARNING @ Tue, 30 Jun 2020 02:57:52: #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 02:57:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:55: 1000000 INFO @ Tue, 30 Jun 2020 02:58:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:02: 2000000 INFO @ Tue, 30 Jun 2020 02:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.10_summits.bed INFO @ Tue, 30 Jun 2020 02:58:06: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:58:08: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:58:16: 4000000 INFO @ Tue, 30 Jun 2020 02:58:19: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:58:19: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:58:19: #1 total tags in treatment: 4443476 INFO @ Tue, 30 Jun 2020 02:58:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:19: #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 02:58:19: #1 tags after filtering in treatment: 4443426 INFO @ Tue, 30 Jun 2020 02:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:20: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 02:58:20: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:20: #2 predicted fragment length is 72 bps INFO @ Tue, 30 Jun 2020 02:58:20: #2 alternative fragment length(s) may be 4,36,72,88,185,375,421,513,539,561,592 bps INFO @ Tue, 30 Jun 2020 02:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.20_model.r WARNING @ Tue, 30 Jun 2020 02:58:20: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:20: #2 You may need to consider one of the other alternative d(s): 4,36,72,88,185,375,421,513,539,561,592 WARNING @ Tue, 30 Jun 2020 02:58:20: #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 02:58:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:58:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495184/SRX495184.20_summits.bed INFO @ Tue, 30 Jun 2020 02:58:34: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 2 millis CompletedMACS2peakCalling