Job ID = 6529382 SRX = SRX2325644 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: 00:06:43 17220406 reads; of these: 17220406 (100.00%) were unpaired; of these: 746289 (4.33%) aligned 0 times 13569760 (78.80%) aligned exactly 1 time 2904357 (16.87%) aligned >1 times 95.67% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 1831250 / 16474117 = 0.1112 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 02:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.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 02:08:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:08:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:08:50: 1000000 INFO @ Tue, 30 Jun 2020 02:08:56: 2000000 INFO @ Tue, 30 Jun 2020 02:09:02: 3000000 INFO @ Tue, 30 Jun 2020 02:09:08: 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 02:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.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 02:09:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:15: 5000000 INFO @ Tue, 30 Jun 2020 02:09:18: 1000000 INFO @ Tue, 30 Jun 2020 02:09:21: 6000000 INFO @ Tue, 30 Jun 2020 02:09:25: 2000000 INFO @ Tue, 30 Jun 2020 02:09:27: 7000000 INFO @ Tue, 30 Jun 2020 02:09:32: 3000000 INFO @ Tue, 30 Jun 2020 02:09:34: 8000000 INFO @ Tue, 30 Jun 2020 02:09:39: 4000000 INFO @ Tue, 30 Jun 2020 02:09:40: 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 02:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.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 02:09:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:45: 5000000 INFO @ Tue, 30 Jun 2020 02:09:46: 10000000 INFO @ Tue, 30 Jun 2020 02:09:48: 1000000 INFO @ Tue, 30 Jun 2020 02:09:52: 6000000 INFO @ Tue, 30 Jun 2020 02:09:53: 11000000 INFO @ Tue, 30 Jun 2020 02:09:54: 2000000 INFO @ Tue, 30 Jun 2020 02:09:58: 7000000 INFO @ Tue, 30 Jun 2020 02:09:59: 12000000 INFO @ Tue, 30 Jun 2020 02:10:00: 3000000 INFO @ Tue, 30 Jun 2020 02:10:05: 8000000 INFO @ Tue, 30 Jun 2020 02:10:06: 4000000 INFO @ Tue, 30 Jun 2020 02:10:06: 13000000 INFO @ Tue, 30 Jun 2020 02:10:11: 5000000 INFO @ Tue, 30 Jun 2020 02:10:12: 9000000 INFO @ Tue, 30 Jun 2020 02:10:12: 14000000 INFO @ Tue, 30 Jun 2020 02:10:17: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:10:17: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:10:17: #1 total tags in treatment: 14642867 INFO @ Tue, 30 Jun 2020 02:10:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:10:17: #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 02:10:17: #1 tags after filtering in treatment: 14642841 INFO @ Tue, 30 Jun 2020 02:10:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:10:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:10:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:10:17: 6000000 INFO @ Tue, 30 Jun 2020 02:10:18: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 02:10:18: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 02:10:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:10:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:10:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:10:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:10:18: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:10:18: #2 alternative fragment length(s) may be 99,591 bps INFO @ Tue, 30 Jun 2020 02:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.05_model.r WARNING @ Tue, 30 Jun 2020 02:10:18: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:10:18: #2 You may need to consider one of the other alternative d(s): 99,591 WARNING @ Tue, 30 Jun 2020 02:10:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:10:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:10:18: 10000000 INFO @ Tue, 30 Jun 2020 02:10:23: 7000000 INFO @ Tue, 30 Jun 2020 02:10:25: 11000000 INFO @ Tue, 30 Jun 2020 02:10:29: 8000000 INFO @ Tue, 30 Jun 2020 02:10:31: 12000000 INFO @ Tue, 30 Jun 2020 02:10:35: 9000000 INFO @ Tue, 30 Jun 2020 02:10:38: 13000000 INFO @ Tue, 30 Jun 2020 02:10:41: 10000000 INFO @ Tue, 30 Jun 2020 02:10:45: 14000000 INFO @ Tue, 30 Jun 2020 02:10:47: 11000000 INFO @ Tue, 30 Jun 2020 02:10:49: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:10:49: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:10:49: #1 total tags in treatment: 14642867 INFO @ Tue, 30 Jun 2020 02:10:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:10:49: #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 02:10:50: #1 tags after filtering in treatment: 14642841 INFO @ Tue, 30 Jun 2020 02:10:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:10:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:10:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:10:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:10:51: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 02:10:51: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 02:10:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:10:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:10:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:10:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:10:51: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:10:51: #2 alternative fragment length(s) may be 99,591 bps INFO @ Tue, 30 Jun 2020 02:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.10_model.r WARNING @ Tue, 30 Jun 2020 02:10:51: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:10:51: #2 You may need to consider one of the other alternative d(s): 99,591 WARNING @ Tue, 30 Jun 2020 02:10:51: #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 02:10:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:10:52: 12000000 INFO @ Tue, 30 Jun 2020 02:10:58: 13000000 INFO @ Tue, 30 Jun 2020 02:11:04: 14000000 INFO @ Tue, 30 Jun 2020 02:11:08: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:11:08: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:11:08: #1 total tags in treatment: 14642867 INFO @ Tue, 30 Jun 2020 02:11:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:11:08: #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 02:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.05_summits.bed INFO @ Tue, 30 Jun 2020 02:11:08: Done! pass1 - making usageList (253 chroms): 1 millis INFO @ Tue, 30 Jun 2020 02:11:08: #1 tags after filtering in treatment: 14642841 INFO @ Tue, 30 Jun 2020 02:11:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:11:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:11:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:11:08: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (757 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:11:09: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 02:11:09: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 02:11:09: start model_add_line... INFO @ Tue, 30 Jun 2020 02:11:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:11:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:11:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:11:10: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:11:10: #2 alternative fragment length(s) may be 99,591 bps INFO @ Tue, 30 Jun 2020 02:11:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.20_model.r WARNING @ Tue, 30 Jun 2020 02:11:10: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:11:10: #2 You may need to consider one of the other alternative d(s): 99,591 WARNING @ Tue, 30 Jun 2020 02:11:10: #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 02:11:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:11:10: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:11:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.10_summits.bed INFO @ Tue, 30 Jun 2020 02:11:40: Done! pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:11:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:11:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:11:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:11:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325644/SRX2325644.20_summits.bed INFO @ Tue, 30 Jun 2020 02:11:58: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 6 millis CompletedMACS2peakCalling