Job ID = 6529855 SRX = SRX5287829 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: 00:09:08 22858962 reads; of these: 22858962 (100.00%) were unpaired; of these: 688395 (3.01%) aligned 0 times 16872227 (73.81%) aligned exactly 1 time 5298340 (23.18%) aligned >1 times 96.99% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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 12 files... [bam_rmdupse_core] 2588854 / 22170567 = 0.1168 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 03:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.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 03:10:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:28: 1000000 INFO @ Tue, 30 Jun 2020 03:10:35: 2000000 INFO @ Tue, 30 Jun 2020 03:10:43: 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 03:10:50: 4000000 INFO @ Tue, 30 Jun 2020 03:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.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 03:10:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:58: 5000000 INFO @ Tue, 30 Jun 2020 03:10:58: 1000000 INFO @ Tue, 30 Jun 2020 03:11:06: 6000000 INFO @ Tue, 30 Jun 2020 03:11:06: 2000000 INFO @ Tue, 30 Jun 2020 03:11:15: 7000000 INFO @ Tue, 30 Jun 2020 03:11:15: 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 03:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.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 03:11:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:23: 8000000 INFO @ Tue, 30 Jun 2020 03:11:23: 4000000 INFO @ Tue, 30 Jun 2020 03:11:29: 1000000 INFO @ Tue, 30 Jun 2020 03:11:31: 9000000 INFO @ Tue, 30 Jun 2020 03:11:31: 5000000 INFO @ Tue, 30 Jun 2020 03:11:37: 2000000 INFO @ Tue, 30 Jun 2020 03:11:39: 10000000 INFO @ Tue, 30 Jun 2020 03:11:39: 6000000 INFO @ Tue, 30 Jun 2020 03:11:46: 3000000 INFO @ Tue, 30 Jun 2020 03:11:48: 11000000 INFO @ Tue, 30 Jun 2020 03:11:48: 7000000 INFO @ Tue, 30 Jun 2020 03:11:54: 4000000 INFO @ Tue, 30 Jun 2020 03:11:56: 8000000 INFO @ Tue, 30 Jun 2020 03:11:56: 12000000 INFO @ Tue, 30 Jun 2020 03:12:03: 5000000 INFO @ Tue, 30 Jun 2020 03:12:04: 9000000 INFO @ Tue, 30 Jun 2020 03:12:04: 13000000 INFO @ Tue, 30 Jun 2020 03:12:11: 6000000 INFO @ Tue, 30 Jun 2020 03:12:12: 10000000 INFO @ Tue, 30 Jun 2020 03:12:13: 14000000 INFO @ Tue, 30 Jun 2020 03:12:19: 7000000 INFO @ Tue, 30 Jun 2020 03:12:20: 11000000 INFO @ Tue, 30 Jun 2020 03:12:21: 15000000 INFO @ Tue, 30 Jun 2020 03:12:27: 8000000 INFO @ Tue, 30 Jun 2020 03:12:28: 12000000 INFO @ Tue, 30 Jun 2020 03:12:30: 16000000 INFO @ Tue, 30 Jun 2020 03:12:35: 9000000 INFO @ Tue, 30 Jun 2020 03:12:36: 13000000 INFO @ Tue, 30 Jun 2020 03:12:38: 17000000 INFO @ Tue, 30 Jun 2020 03:12:43: 10000000 INFO @ Tue, 30 Jun 2020 03:12:44: 14000000 INFO @ Tue, 30 Jun 2020 03:12:46: 18000000 INFO @ Tue, 30 Jun 2020 03:12:50: 11000000 INFO @ Tue, 30 Jun 2020 03:12:52: 15000000 INFO @ Tue, 30 Jun 2020 03:12:54: 19000000 INFO @ Tue, 30 Jun 2020 03:12:58: 12000000 INFO @ Tue, 30 Jun 2020 03:12:59: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:12:59: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:12:59: #1 total tags in treatment: 19581713 INFO @ Tue, 30 Jun 2020 03:12:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:59: #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 03:13:00: #1 tags after filtering in treatment: 19581711 INFO @ Tue, 30 Jun 2020 03:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:00: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:01: 16000000 INFO @ Tue, 30 Jun 2020 03:13:01: #2 number of paired peaks: 321 WARNING @ Tue, 30 Jun 2020 03:13:01: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:01: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:13:01: #2 alternative fragment length(s) may be 3,67 bps INFO @ Tue, 30 Jun 2020 03:13:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.05_model.r WARNING @ Tue, 30 Jun 2020 03:13:01: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:01: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Tue, 30 Jun 2020 03:13:01: #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 03:13:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:13:09: 17000000 INFO @ Tue, 30 Jun 2020 03:13:13: 14000000 INFO @ Tue, 30 Jun 2020 03:13:17: 18000000 INFO @ Tue, 30 Jun 2020 03:13:21: 15000000 INFO @ Tue, 30 Jun 2020 03:13:25: 19000000 INFO @ Tue, 30 Jun 2020 03:13:29: 16000000 INFO @ Tue, 30 Jun 2020 03:13:30: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:13:30: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:13:30: #1 total tags in treatment: 19581713 INFO @ Tue, 30 Jun 2020 03:13:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:30: #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 03:13:31: #1 tags after filtering in treatment: 19581711 INFO @ Tue, 30 Jun 2020 03:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:31: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:32: #2 number of paired peaks: 321 WARNING @ Tue, 30 Jun 2020 03:13:32: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:32: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:32: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:32: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:32: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:32: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:13:32: #2 alternative fragment length(s) may be 3,67 bps INFO @ Tue, 30 Jun 2020 03:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.10_model.r WARNING @ Tue, 30 Jun 2020 03:13:32: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:32: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Tue, 30 Jun 2020 03:13:32: #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 03:13:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:36: 17000000 INFO @ Tue, 30 Jun 2020 03:13:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:44: 18000000 INFO @ Tue, 30 Jun 2020 03:13:51: 19000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:13:55: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:13:55: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:13:55: #1 total tags in treatment: 19581713 INFO @ Tue, 30 Jun 2020 03:13:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:55: #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 03:13:55: #1 tags after filtering in treatment: 19581711 INFO @ Tue, 30 Jun 2020 03:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:57: #2 number of paired peaks: 321 WARNING @ Tue, 30 Jun 2020 03:13:57: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:57: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:13:57: #2 alternative fragment length(s) may be 3,67 bps INFO @ Tue, 30 Jun 2020 03:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:57: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:57: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Tue, 30 Jun 2020 03:13:57: #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 03:13:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.05_summits.bed INFO @ Tue, 30 Jun 2020 03:14:02: Done! pass1 - making usageList (669 chroms): 1 millis pass2 - checking and writing primary data (2332 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.10_summits.bed INFO @ Tue, 30 Jun 2020 03:14:32: Done! pass1 - making usageList (574 chroms): 1 millis pass2 - checking and writing primary data (1704 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287829/SRX5287829.20_summits.bed INFO @ Tue, 30 Jun 2020 03:14:55: Done! pass1 - making usageList (415 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 14 millis CompletedMACS2peakCalling