Job ID = 6529475 SRX = SRX287717 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: 00:04:23 17419333 reads; of these: 17419333 (100.00%) were unpaired; of these: 1130333 (6.49%) aligned 0 times 13260333 (76.12%) aligned exactly 1 time 3028667 (17.39%) aligned >1 times 93.51% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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 8 files... [bam_rmdupse_core] 1479529 / 16289000 = 0.0908 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 02:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.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 02:11:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:11:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:11:07: 1000000 INFO @ Tue, 30 Jun 2020 02:11:12: 2000000 INFO @ Tue, 30 Jun 2020 02:11:17: 3000000 INFO @ Tue, 30 Jun 2020 02:11:23: 4000000 INFO @ Tue, 30 Jun 2020 02:11:28: 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, 30 Jun 2020 02:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.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 02:11:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:11:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:11:33: 6000000 INFO @ Tue, 30 Jun 2020 02:11:37: 1000000 INFO @ Tue, 30 Jun 2020 02:11:39: 7000000 INFO @ Tue, 30 Jun 2020 02:11:43: 2000000 INFO @ Tue, 30 Jun 2020 02:11:45: 8000000 INFO @ Tue, 30 Jun 2020 02:11:49: 3000000 INFO @ Tue, 30 Jun 2020 02:11:50: 9000000 INFO @ Tue, 30 Jun 2020 02:11:55: 4000000 INFO @ Tue, 30 Jun 2020 02:11:56: 10000000 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 02:12:00: 5000000 INFO @ Tue, 30 Jun 2020 02:12:02: 11000000 INFO @ Tue, 30 Jun 2020 02:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.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 02:12:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:06: 6000000 INFO @ Tue, 30 Jun 2020 02:12:07: 1000000 INFO @ Tue, 30 Jun 2020 02:12:07: 12000000 INFO @ Tue, 30 Jun 2020 02:12:12: 7000000 INFO @ Tue, 30 Jun 2020 02:12:13: 2000000 INFO @ Tue, 30 Jun 2020 02:12:14: 13000000 INFO @ Tue, 30 Jun 2020 02:12:19: 8000000 INFO @ Tue, 30 Jun 2020 02:12:19: 3000000 INFO @ Tue, 30 Jun 2020 02:12:19: 14000000 INFO @ Tue, 30 Jun 2020 02:12:24: 4000000 INFO @ Tue, 30 Jun 2020 02:12:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:12:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:12:25: #1 total tags in treatment: 14809471 INFO @ Tue, 30 Jun 2020 02:12:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:25: #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 02:12:25: 9000000 INFO @ Tue, 30 Jun 2020 02:12:25: #1 tags after filtering in treatment: 14809464 INFO @ Tue, 30 Jun 2020 02:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:26: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:12:26: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:26: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:12:26: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 30 Jun 2020 02:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.05_model.r WARNING @ Tue, 30 Jun 2020 02:12:26: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:12:26: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 30 Jun 2020 02:12:26: #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 02:12:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:30: 5000000 INFO @ Tue, 30 Jun 2020 02:12:31: 10000000 INFO @ Tue, 30 Jun 2020 02:12:36: 6000000 INFO @ Tue, 30 Jun 2020 02:12:36: 11000000 INFO @ Tue, 30 Jun 2020 02:12:41: 7000000 INFO @ Tue, 30 Jun 2020 02:12:42: 12000000 INFO @ Tue, 30 Jun 2020 02:12:47: 8000000 INFO @ Tue, 30 Jun 2020 02:12:48: 13000000 INFO @ Tue, 30 Jun 2020 02:12:52: 9000000 INFO @ Tue, 30 Jun 2020 02:12:54: 14000000 INFO @ Tue, 30 Jun 2020 02:12:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:12:58: 10000000 INFO @ Tue, 30 Jun 2020 02:12:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:12:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:12:59: #1 total tags in treatment: 14809471 INFO @ Tue, 30 Jun 2020 02:12:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:59: #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 02:12:59: #1 tags after filtering in treatment: 14809464 INFO @ Tue, 30 Jun 2020 02:12:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:59: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:00: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:13:00: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:00: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:00: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:00: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:00: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:13:00: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 30 Jun 2020 02:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.10_model.r WARNING @ Tue, 30 Jun 2020 02:13:00: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:13:00: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 30 Jun 2020 02:13:00: #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 02:13:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:03: 11000000 INFO @ Tue, 30 Jun 2020 02:13:09: 12000000 INFO @ Tue, 30 Jun 2020 02:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.05_summits.bed INFO @ Tue, 30 Jun 2020 02:13:11: Done! pass1 - making usageList (460 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:13:14: 13000000 INFO @ Tue, 30 Jun 2020 02:13:19: 14000000 INFO @ Tue, 30 Jun 2020 02:13:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:24: #1 total tags in treatment: 14809471 INFO @ Tue, 30 Jun 2020 02:13:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:24: #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 02:13:24: #1 tags after filtering in treatment: 14809464 INFO @ Tue, 30 Jun 2020 02:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:25: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:13:25: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:25: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:13:25: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 30 Jun 2020 02:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.20_model.r WARNING @ Tue, 30 Jun 2020 02:13:25: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:13:25: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 30 Jun 2020 02:13:25: #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 02:13:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.10_summits.bed INFO @ Tue, 30 Jun 2020 02:13:42: Done! pass1 - making usageList (311 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:13:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287717/SRX287717.20_summits.bed INFO @ Tue, 30 Jun 2020 02:14:07: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 6 millis CompletedMACS2peakCalling