Job ID = 6626593 SRX = SRX1532035 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:15 9079503 reads; of these: 9079503 (100.00%) were unpaired; of these: 558352 (6.15%) aligned 0 times 6010907 (66.20%) aligned exactly 1 time 2510244 (27.65%) aligned >1 times 93.85% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 613471 / 8521151 = 0.0720 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, 14 Jul 2020 07:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.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, 14 Jul 2020 07:47:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:47:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:47:34: 1000000 INFO @ Tue, 14 Jul 2020 07:47:39: 2000000 INFO @ Tue, 14 Jul 2020 07:47:45: 3000000 INFO @ Tue, 14 Jul 2020 07:47:50: 4000000 INFO @ Tue, 14 Jul 2020 07:47:55: 5000000 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, 14 Jul 2020 07:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.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, 14 Jul 2020 07:47:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:47:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:48:01: 6000000 INFO @ Tue, 14 Jul 2020 07:48:04: 1000000 INFO @ Tue, 14 Jul 2020 07:48:08: 7000000 INFO @ Tue, 14 Jul 2020 07:48:10: 2000000 INFO @ Tue, 14 Jul 2020 07:48:13: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:48:13: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:48:13: #1 total tags in treatment: 7907680 INFO @ Tue, 14 Jul 2020 07:48:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:48:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:48:13: #1 tags after filtering in treatment: 7907566 INFO @ Tue, 14 Jul 2020 07:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:48:13: #1 finished! INFO @ Tue, 14 Jul 2020 07:48:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:48:14: #2 number of paired peaks: 1840 INFO @ Tue, 14 Jul 2020 07:48:14: start model_add_line... INFO @ Tue, 14 Jul 2020 07:48:14: start X-correlation... INFO @ Tue, 14 Jul 2020 07:48:14: end of X-cor INFO @ Tue, 14 Jul 2020 07:48:14: #2 finished! INFO @ Tue, 14 Jul 2020 07:48:14: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 07:48:14: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 14 Jul 2020 07:48:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.05_model.r WARNING @ Tue, 14 Jul 2020 07:48:14: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:48:14: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 14 Jul 2020 07:48:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:48:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:48:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:48:16: 3000000 INFO @ Tue, 14 Jul 2020 07:48:22: 4000000 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, 14 Jul 2020 07:48:28: 5000000 INFO @ Tue, 14 Jul 2020 07:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.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, 14 Jul 2020 07:48:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:48:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:48:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:48:34: 6000000 INFO @ Tue, 14 Jul 2020 07:48:35: 1000000 INFO @ Tue, 14 Jul 2020 07:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.05_summits.bed INFO @ Tue, 14 Jul 2020 07:48:39: Done! pass1 - making usageList (517 chroms): 1 millis pass2 - checking and writing primary data (2385 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:48:41: 7000000 INFO @ Tue, 14 Jul 2020 07:48:41: 2000000 INFO @ Tue, 14 Jul 2020 07:48:47: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:48:47: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:48:47: #1 total tags in treatment: 7907680 INFO @ Tue, 14 Jul 2020 07:48:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:48:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:48:47: #1 tags after filtering in treatment: 7907566 INFO @ Tue, 14 Jul 2020 07:48:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:48:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:48:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:48:48: 3000000 INFO @ Tue, 14 Jul 2020 07:48:48: #2 number of paired peaks: 1840 INFO @ Tue, 14 Jul 2020 07:48:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:48:48: start X-correlation... INFO @ Tue, 14 Jul 2020 07:48:48: end of X-cor INFO @ Tue, 14 Jul 2020 07:48:48: #2 finished! INFO @ Tue, 14 Jul 2020 07:48:48: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 07:48:48: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 14 Jul 2020 07:48:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.10_model.r WARNING @ Tue, 14 Jul 2020 07:48:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:48:48: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 14 Jul 2020 07:48:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:48:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:48:54: 4000000 INFO @ Tue, 14 Jul 2020 07:49:00: 5000000 INFO @ Tue, 14 Jul 2020 07:49:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:49:12: 7000000 INFO @ Tue, 14 Jul 2020 07:49:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:49:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:49:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.10_summits.bed INFO @ Tue, 14 Jul 2020 07:49:13: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (1587 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:49:17: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:49:17: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:49:17: #1 total tags in treatment: 7907680 INFO @ Tue, 14 Jul 2020 07:49:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:49:18: #1 tags after filtering in treatment: 7907566 INFO @ Tue, 14 Jul 2020 07:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:49:18: #1 finished! INFO @ Tue, 14 Jul 2020 07:49:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:49:18: #2 number of paired peaks: 1840 INFO @ Tue, 14 Jul 2020 07:49:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:49:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:49:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:49:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:49:18: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 07:49:18: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 14 Jul 2020 07:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.20_model.r WARNING @ Tue, 14 Jul 2020 07:49:18: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:49:18: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 14 Jul 2020 07:49:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:49:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:49:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:49:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1532035/SRX1532035.20_summits.bed INFO @ Tue, 14 Jul 2020 07:49:43: Done! pass1 - making usageList (227 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 7 millis CompletedMACS2peakCalling