Job ID = 6529731 SRX = SRX4510352 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: 00:07:41 20295569 reads; of these: 20295569 (100.00%) were unpaired; of these: 7748693 (38.18%) aligned 0 times 10694133 (52.69%) aligned exactly 1 time 1852743 (9.13%) aligned >1 times 61.82% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 1903081 / 12546876 = 0.1517 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 02:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.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 02:34:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:16: 1000000 INFO @ Tue, 30 Jun 2020 02:34:22: 2000000 INFO @ Tue, 30 Jun 2020 02:34:27: 3000000 INFO @ Tue, 30 Jun 2020 02:34:33: 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 02:34:39: 5000000 INFO @ Tue, 30 Jun 2020 02:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.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 02:34:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:44: 6000000 INFO @ Tue, 30 Jun 2020 02:34:47: 1000000 INFO @ Tue, 30 Jun 2020 02:34:50: 7000000 INFO @ Tue, 30 Jun 2020 02:34:53: 2000000 INFO @ Tue, 30 Jun 2020 02:34:56: 8000000 INFO @ Tue, 30 Jun 2020 02:34:59: 3000000 INFO @ Tue, 30 Jun 2020 02:35:03: 9000000 INFO @ Tue, 30 Jun 2020 02:35:05: 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, 30 Jun 2020 02:35:08: 10000000 INFO @ Tue, 30 Jun 2020 02:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.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 02:35:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:11: 5000000 INFO @ Tue, 30 Jun 2020 02:35:12: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:35:12: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:35:12: #1 total tags in treatment: 10643795 INFO @ Tue, 30 Jun 2020 02:35:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:12: #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 02:35:13: #1 tags after filtering in treatment: 10643629 INFO @ Tue, 30 Jun 2020 02:35:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:13: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:14: #2 number of paired peaks: 164 WARNING @ Tue, 30 Jun 2020 02:35:14: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:14: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:14: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:14: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:14: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:14: #2 predicted fragment length is 98 bps INFO @ Tue, 30 Jun 2020 02:35:14: #2 alternative fragment length(s) may be 4,98,549 bps INFO @ Tue, 30 Jun 2020 02:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.05_model.r WARNING @ Tue, 30 Jun 2020 02:35:14: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:35:14: #2 You may need to consider one of the other alternative d(s): 4,98,549 WARNING @ Tue, 30 Jun 2020 02:35:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:35:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:16: 1000000 INFO @ Tue, 30 Jun 2020 02:35:17: 6000000 INFO @ Tue, 30 Jun 2020 02:35:22: 2000000 INFO @ Tue, 30 Jun 2020 02:35:23: 7000000 INFO @ Tue, 30 Jun 2020 02:35:28: 3000000 INFO @ Tue, 30 Jun 2020 02:35:30: 8000000 INFO @ Tue, 30 Jun 2020 02:35:34: 4000000 INFO @ Tue, 30 Jun 2020 02:35:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:36: 9000000 INFO @ Tue, 30 Jun 2020 02:35:40: 5000000 INFO @ Tue, 30 Jun 2020 02:35:42: 10000000 INFO @ Tue, 30 Jun 2020 02:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.05_summits.bed INFO @ Tue, 30 Jun 2020 02:35:45: Done! pass1 - making usageList (376 chroms): 1 millis pass2 - checking and writing primary data (978 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:46: 6000000 INFO @ Tue, 30 Jun 2020 02:35:46: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:35:46: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:35:46: #1 total tags in treatment: 10643795 INFO @ Tue, 30 Jun 2020 02:35:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:46: #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 02:35:47: #1 tags after filtering in treatment: 10643629 INFO @ Tue, 30 Jun 2020 02:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:47: #2 number of paired peaks: 164 WARNING @ Tue, 30 Jun 2020 02:35:47: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:47: #2 predicted fragment length is 98 bps INFO @ Tue, 30 Jun 2020 02:35:47: #2 alternative fragment length(s) may be 4,98,549 bps INFO @ Tue, 30 Jun 2020 02:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.10_model.r WARNING @ Tue, 30 Jun 2020 02:35:47: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:35:47: #2 You may need to consider one of the other alternative d(s): 4,98,549 WARNING @ Tue, 30 Jun 2020 02:35:47: #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 02:35:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:51: 7000000 INFO @ Tue, 30 Jun 2020 02:35:57: 8000000 INFO @ Tue, 30 Jun 2020 02:36:03: 9000000 INFO @ Tue, 30 Jun 2020 02:36:09: 10000000 INFO @ Tue, 30 Jun 2020 02:36:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:36:13: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:36:13: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:36:13: #1 total tags in treatment: 10643795 INFO @ Tue, 30 Jun 2020 02:36:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:36:13: #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 02:36:13: #1 tags after filtering in treatment: 10643629 INFO @ Tue, 30 Jun 2020 02:36:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:36:13: #1 finished! INFO @ Tue, 30 Jun 2020 02:36:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:36:14: #2 number of paired peaks: 164 WARNING @ Tue, 30 Jun 2020 02:36:14: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 30 Jun 2020 02:36:14: start model_add_line... INFO @ Tue, 30 Jun 2020 02:36:14: start X-correlation... INFO @ Tue, 30 Jun 2020 02:36:14: end of X-cor INFO @ Tue, 30 Jun 2020 02:36:14: #2 finished! INFO @ Tue, 30 Jun 2020 02:36:14: #2 predicted fragment length is 98 bps INFO @ Tue, 30 Jun 2020 02:36:14: #2 alternative fragment length(s) may be 4,98,549 bps INFO @ Tue, 30 Jun 2020 02:36:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.20_model.r WARNING @ Tue, 30 Jun 2020 02:36:14: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:36:14: #2 You may need to consider one of the other alternative d(s): 4,98,549 WARNING @ Tue, 30 Jun 2020 02:36:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:36:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:36:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.10_summits.bed INFO @ Tue, 30 Jun 2020 02:36:20: Done! pass1 - making usageList (291 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:36:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510352/SRX4510352.20_summits.bed INFO @ Tue, 30 Jun 2020 02:36:44: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (265 records, 4 fields): 9 millis CompletedMACS2peakCalling