Job ID = 6529765 SRX = SRX474526 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: 00:03:27 11861106 reads; of these: 11861106 (100.00%) were unpaired; of these: 260306 (2.19%) aligned 0 times 7889163 (66.51%) aligned exactly 1 time 3711637 (31.29%) aligned >1 times 97.81% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 833964 / 11600800 = 0.0719 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 02:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.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 02:35:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:42: 1000000 INFO @ Tue, 30 Jun 2020 02:35:48: 2000000 INFO @ Tue, 30 Jun 2020 02:35:53: 3000000 INFO @ Tue, 30 Jun 2020 02:35:59: 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 02:36:05: 5000000 INFO @ Tue, 30 Jun 2020 02:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.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 02:36:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:11: 6000000 INFO @ Tue, 30 Jun 2020 02:36:12: 1000000 INFO @ Tue, 30 Jun 2020 02:36:17: 7000000 INFO @ Tue, 30 Jun 2020 02:36:19: 2000000 INFO @ Tue, 30 Jun 2020 02:36:23: 8000000 INFO @ Tue, 30 Jun 2020 02:36:25: 3000000 INFO @ Tue, 30 Jun 2020 02:36:29: 9000000 INFO @ Tue, 30 Jun 2020 02:36:30: 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 02:36:35: 10000000 INFO @ Tue, 30 Jun 2020 02:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.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 02:36:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:37: 5000000 INFO @ Tue, 30 Jun 2020 02:36:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:36:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:36:40: #1 total tags in treatment: 10766836 INFO @ Tue, 30 Jun 2020 02:36:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:36:40: #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 02:36:41: #1 tags after filtering in treatment: 10766836 INFO @ Tue, 30 Jun 2020 02:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:36:41: #1 finished! INFO @ Tue, 30 Jun 2020 02:36:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:36:42: #2 number of paired peaks: 738 WARNING @ Tue, 30 Jun 2020 02:36:42: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Tue, 30 Jun 2020 02:36:42: start model_add_line... INFO @ Tue, 30 Jun 2020 02:36:42: start X-correlation... INFO @ Tue, 30 Jun 2020 02:36:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:36:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:36:42: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:36:42: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 02:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.05_model.r WARNING @ Tue, 30 Jun 2020 02:36:42: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:36:42: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 02:36:42: #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 02:36:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:36:42: 1000000 INFO @ Tue, 30 Jun 2020 02:36:43: 6000000 INFO @ Tue, 30 Jun 2020 02:36:48: 2000000 INFO @ Tue, 30 Jun 2020 02:36:49: 7000000 INFO @ Tue, 30 Jun 2020 02:36:54: 3000000 INFO @ Tue, 30 Jun 2020 02:36:55: 8000000 INFO @ Tue, 30 Jun 2020 02:37:00: 4000000 INFO @ Tue, 30 Jun 2020 02:37:02: 9000000 INFO @ Tue, 30 Jun 2020 02:37:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:37:06: 5000000 INFO @ Tue, 30 Jun 2020 02:37:08: 10000000 INFO @ Tue, 30 Jun 2020 02:37:12: 6000000 INFO @ Tue, 30 Jun 2020 02:37:13: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:37:13: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:37:13: #1 total tags in treatment: 10766836 INFO @ Tue, 30 Jun 2020 02:37:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:13: #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 02:37:14: #1 tags after filtering in treatment: 10766836 INFO @ Tue, 30 Jun 2020 02:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:15: #2 number of paired peaks: 738 WARNING @ Tue, 30 Jun 2020 02:37:15: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:15: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:15: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:15: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:15: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:15: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:37:15: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 02:37:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.10_model.r WARNING @ Tue, 30 Jun 2020 02:37:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:15: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 02:37:15: #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 02:37:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.05_summits.bed INFO @ Tue, 30 Jun 2020 02:37:18: Done! pass1 - making usageList (625 chroms): 1 millis pass2 - checking and writing primary data (2638 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:37:18: 7000000 INFO @ Tue, 30 Jun 2020 02:37:24: 8000000 INFO @ Tue, 30 Jun 2020 02:37:31: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:37:37: 10000000 INFO @ Tue, 30 Jun 2020 02:37:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:37:42: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:37:42: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:37:42: #1 total tags in treatment: 10766836 INFO @ Tue, 30 Jun 2020 02:37:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:42: #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 02:37:42: #1 tags after filtering in treatment: 10766836 INFO @ Tue, 30 Jun 2020 02:37:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:43: #2 number of paired peaks: 738 WARNING @ Tue, 30 Jun 2020 02:37:43: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:43: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:37:43: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 02:37:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.20_model.r WARNING @ Tue, 30 Jun 2020 02:37:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:43: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 02:37:43: #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 02:37:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.10_summits.bed INFO @ Tue, 30 Jun 2020 02:37:50: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (1962 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:38:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474526/SRX474526.20_summits.bed INFO @ Tue, 30 Jun 2020 02:38:19: Done! pass1 - making usageList (316 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 13 millis CompletedMACS2peakCalling