Job ID = 6529843 SRX = SRX511126 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: 00:04:15 10401617 reads; of these: 10401617 (100.00%) were unpaired; of these: 209833 (2.02%) aligned 0 times 8068973 (77.57%) aligned exactly 1 time 2122811 (20.41%) aligned >1 times 97.98% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 739780 / 10191784 = 0.0726 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 03:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.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 03:10:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:06: 1000000 INFO @ Tue, 30 Jun 2020 03:11:15: 2000000 INFO @ Tue, 30 Jun 2020 03:11:23: 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 03:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.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 03:11:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:32: 4000000 INFO @ Tue, 30 Jun 2020 03:11:37: 1000000 INFO @ Tue, 30 Jun 2020 03:11:41: 5000000 INFO @ Tue, 30 Jun 2020 03:11:46: 2000000 INFO @ Tue, 30 Jun 2020 03:11:50: 6000000 INFO @ Tue, 30 Jun 2020 03:11:54: 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 03:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.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 03:11:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:00: 7000000 INFO @ Tue, 30 Jun 2020 03:12:03: 4000000 INFO @ Tue, 30 Jun 2020 03:12:07: 1000000 INFO @ Tue, 30 Jun 2020 03:12:10: 8000000 INFO @ Tue, 30 Jun 2020 03:12:12: 5000000 INFO @ Tue, 30 Jun 2020 03:12:16: 2000000 INFO @ Tue, 30 Jun 2020 03:12:19: 9000000 INFO @ Tue, 30 Jun 2020 03:12:21: 6000000 INFO @ Tue, 30 Jun 2020 03:12:24: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:12:24: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:12:24: #1 total tags in treatment: 9452004 INFO @ Tue, 30 Jun 2020 03:12:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:24: #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 03:12:24: #1 tags after filtering in treatment: 9451979 INFO @ Tue, 30 Jun 2020 03:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:24: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:25: #2 number of paired peaks: 280 WARNING @ Tue, 30 Jun 2020 03:12:25: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:25: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:25: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:25: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:25: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:25: #2 predicted fragment length is 91 bps INFO @ Tue, 30 Jun 2020 03:12:25: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 30 Jun 2020 03:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.05_model.r WARNING @ Tue, 30 Jun 2020 03:12:25: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:25: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 30 Jun 2020 03:12:25: #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 03:12:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:25: 3000000 INFO @ Tue, 30 Jun 2020 03:12:30: 7000000 INFO @ Tue, 30 Jun 2020 03:12:33: 4000000 INFO @ Tue, 30 Jun 2020 03:12:39: 8000000 INFO @ Tue, 30 Jun 2020 03:12:41: 5000000 INFO @ Tue, 30 Jun 2020 03:12:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:47: 9000000 INFO @ Tue, 30 Jun 2020 03:12:50: 6000000 INFO @ Tue, 30 Jun 2020 03:12:51: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:12:51: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:12:51: #1 total tags in treatment: 9452004 INFO @ Tue, 30 Jun 2020 03:12:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:51: #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 03:12:52: #1 tags after filtering in treatment: 9451979 INFO @ Tue, 30 Jun 2020 03:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:52: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:53: #2 number of paired peaks: 280 WARNING @ Tue, 30 Jun 2020 03:12:53: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:53: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:53: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:53: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:53: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:53: #2 predicted fragment length is 91 bps INFO @ Tue, 30 Jun 2020 03:12:53: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 30 Jun 2020 03:12:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:53: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:53: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 30 Jun 2020 03:12:53: #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 03:12:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.05_summits.bed INFO @ Tue, 30 Jun 2020 03:12:57: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (1575 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:57: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:13:06: 8000000 INFO @ Tue, 30 Jun 2020 03:13:13: 9000000 INFO @ Tue, 30 Jun 2020 03:13:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:17: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:13:17: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:13:17: #1 total tags in treatment: 9452004 INFO @ Tue, 30 Jun 2020 03:13:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:17: #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 03:13:17: #1 tags after filtering in treatment: 9451979 INFO @ Tue, 30 Jun 2020 03:13:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:18: #2 number of paired peaks: 280 WARNING @ Tue, 30 Jun 2020 03:13:18: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:18: #2 predicted fragment length is 91 bps INFO @ Tue, 30 Jun 2020 03:13:18: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 30 Jun 2020 03:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:18: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:18: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 30 Jun 2020 03:13:18: #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 03:13:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:13:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.10_summits.bed INFO @ Tue, 30 Jun 2020 03:13:27: Done! pass1 - making usageList (322 chroms): 1 millis pass2 - checking and writing primary data (686 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511126/SRX511126.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:52: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 7 millis CompletedMACS2peakCalling