Job ID = 6529650 SRX = SRX3723038 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: 00:12:58 49519079 reads; of these: 49519079 (100.00%) were unpaired; of these: 20061715 (40.51%) aligned 0 times 21483654 (43.38%) aligned exactly 1 time 7973710 (16.10%) aligned >1 times 59.49% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 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] 7069758 / 29457364 = 0.2400 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 02:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.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 02:45:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:07: 1000000 INFO @ Tue, 30 Jun 2020 02:45:13: 2000000 INFO @ Tue, 30 Jun 2020 02:45:19: 3000000 INFO @ Tue, 30 Jun 2020 02:45:26: 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 02:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.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 02:45:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:33: 5000000 INFO @ Tue, 30 Jun 2020 02:45:38: 1000000 INFO @ Tue, 30 Jun 2020 02:45:40: 6000000 INFO @ Tue, 30 Jun 2020 02:45:46: 2000000 INFO @ Tue, 30 Jun 2020 02:45:48: 7000000 INFO @ Tue, 30 Jun 2020 02:45:53: 3000000 INFO @ Tue, 30 Jun 2020 02:45:56: 8000000 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 02:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.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 02:46:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:01: 4000000 INFO @ Tue, 30 Jun 2020 02:46:03: 9000000 INFO @ Tue, 30 Jun 2020 02:46:08: 1000000 INFO @ Tue, 30 Jun 2020 02:46:08: 5000000 INFO @ Tue, 30 Jun 2020 02:46:11: 10000000 INFO @ Tue, 30 Jun 2020 02:46:16: 2000000 INFO @ Tue, 30 Jun 2020 02:46:16: 6000000 INFO @ Tue, 30 Jun 2020 02:46:19: 11000000 INFO @ Tue, 30 Jun 2020 02:46:23: 3000000 INFO @ Tue, 30 Jun 2020 02:46:24: 7000000 INFO @ Tue, 30 Jun 2020 02:46:26: 12000000 INFO @ Tue, 30 Jun 2020 02:46:31: 4000000 INFO @ Tue, 30 Jun 2020 02:46:31: 8000000 INFO @ Tue, 30 Jun 2020 02:46:34: 13000000 INFO @ Tue, 30 Jun 2020 02:46:39: 9000000 INFO @ Tue, 30 Jun 2020 02:46:39: 5000000 INFO @ Tue, 30 Jun 2020 02:46:42: 14000000 INFO @ Tue, 30 Jun 2020 02:46:46: 10000000 INFO @ Tue, 30 Jun 2020 02:46:47: 6000000 INFO @ Tue, 30 Jun 2020 02:46:50: 15000000 INFO @ Tue, 30 Jun 2020 02:46:54: 11000000 INFO @ Tue, 30 Jun 2020 02:46:54: 7000000 INFO @ Tue, 30 Jun 2020 02:46:58: 16000000 INFO @ Tue, 30 Jun 2020 02:47:02: 12000000 INFO @ Tue, 30 Jun 2020 02:47:02: 8000000 INFO @ Tue, 30 Jun 2020 02:47:05: 17000000 INFO @ Tue, 30 Jun 2020 02:47:10: 13000000 INFO @ Tue, 30 Jun 2020 02:47:10: 9000000 INFO @ Tue, 30 Jun 2020 02:47:13: 18000000 INFO @ Tue, 30 Jun 2020 02:47:17: 14000000 INFO @ Tue, 30 Jun 2020 02:47:18: 10000000 INFO @ Tue, 30 Jun 2020 02:47:21: 19000000 INFO @ Tue, 30 Jun 2020 02:47:25: 15000000 INFO @ Tue, 30 Jun 2020 02:47:25: 11000000 INFO @ Tue, 30 Jun 2020 02:47:29: 20000000 INFO @ Tue, 30 Jun 2020 02:47:32: 16000000 INFO @ Tue, 30 Jun 2020 02:47:33: 12000000 INFO @ Tue, 30 Jun 2020 02:47:37: 21000000 INFO @ Tue, 30 Jun 2020 02:47:40: 17000000 INFO @ Tue, 30 Jun 2020 02:47:41: 13000000 INFO @ Tue, 30 Jun 2020 02:47:45: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:47:48: 18000000 INFO @ Tue, 30 Jun 2020 02:47:49: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 02:47:49: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 02:47:49: #1 total tags in treatment: 22387606 INFO @ Tue, 30 Jun 2020 02:47:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:49: #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 02:47:49: 14000000 INFO @ Tue, 30 Jun 2020 02:47:49: #1 tags after filtering in treatment: 22387604 INFO @ Tue, 30 Jun 2020 02:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:51: #2 number of paired peaks: 305 WARNING @ Tue, 30 Jun 2020 02:47:51: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:51: #2 predicted fragment length is 82 bps INFO @ Tue, 30 Jun 2020 02:47:51: #2 alternative fragment length(s) may be 4,82,597 bps INFO @ Tue, 30 Jun 2020 02:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:51: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:51: #2 You may need to consider one of the other alternative d(s): 4,82,597 WARNING @ Tue, 30 Jun 2020 02:47:51: #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 02:47:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:56: 19000000 INFO @ Tue, 30 Jun 2020 02:47:57: 15000000 INFO @ Tue, 30 Jun 2020 02:48:04: 20000000 INFO @ Tue, 30 Jun 2020 02:48:05: 16000000 INFO @ Tue, 30 Jun 2020 02:48:11: 21000000 INFO @ Tue, 30 Jun 2020 02:48:12: 17000000 INFO @ Tue, 30 Jun 2020 02:48:19: 22000000 INFO @ Tue, 30 Jun 2020 02:48:20: 18000000 INFO @ Tue, 30 Jun 2020 02:48:22: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 02:48:22: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 02:48:22: #1 total tags in treatment: 22387606 INFO @ Tue, 30 Jun 2020 02:48:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:22: #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 02:48:23: #1 tags after filtering in treatment: 22387604 INFO @ Tue, 30 Jun 2020 02:48:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:24: #2 number of paired peaks: 305 WARNING @ Tue, 30 Jun 2020 02:48:24: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:25: #2 predicted fragment length is 82 bps INFO @ Tue, 30 Jun 2020 02:48:25: #2 alternative fragment length(s) may be 4,82,597 bps INFO @ Tue, 30 Jun 2020 02:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:25: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:25: #2 You may need to consider one of the other alternative d(s): 4,82,597 WARNING @ Tue, 30 Jun 2020 02:48:25: #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 02:48:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:28: 19000000 INFO @ Tue, 30 Jun 2020 02:48:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:35: 20000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:48:42: 21000000 INFO @ Tue, 30 Jun 2020 02:48:50: 22000000 INFO @ Tue, 30 Jun 2020 02:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.05_summits.bed INFO @ Tue, 30 Jun 2020 02:48:50: Done! pass1 - making usageList (870 chroms): 1 millis pass2 - checking and writing primary data (3885 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:53: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 02:48:53: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 02:48:53: #1 total tags in treatment: 22387606 INFO @ Tue, 30 Jun 2020 02:48:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:53: #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 02:48:53: #1 tags after filtering in treatment: 22387604 INFO @ Tue, 30 Jun 2020 02:48:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:55: #2 number of paired peaks: 305 WARNING @ Tue, 30 Jun 2020 02:48:55: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:55: #2 predicted fragment length is 82 bps INFO @ Tue, 30 Jun 2020 02:48:55: #2 alternative fragment length(s) may be 4,82,597 bps INFO @ Tue, 30 Jun 2020 02:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:55: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:55: #2 You may need to consider one of the other alternative d(s): 4,82,597 WARNING @ Tue, 30 Jun 2020 02:48:55: #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 02:48:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.10_summits.bed INFO @ Tue, 30 Jun 2020 02:49:24: Done! pass1 - making usageList (720 chroms): 1 millis pass2 - checking and writing primary data (2372 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3723038/SRX3723038.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:54: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (1262 records, 4 fields): 16 millis CompletedMACS2peakCalling