Job ID = 6529947 SRX = SRX5431041 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: 00:05:15 20512187 reads; of these: 20512187 (100.00%) were unpaired; of these: 999582 (4.87%) aligned 0 times 15389705 (75.03%) aligned exactly 1 time 4122900 (20.10%) aligned >1 times 95.13% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 2244675 / 19512605 = 0.1150 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 03:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.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 03:09:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:41: 1000000 INFO @ Tue, 30 Jun 2020 03:09:47: 2000000 INFO @ Tue, 30 Jun 2020 03:09:54: 3000000 INFO @ Tue, 30 Jun 2020 03:10:01: 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 03:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.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 03:10:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:08: 5000000 INFO @ Tue, 30 Jun 2020 03:10:11: 1000000 INFO @ Tue, 30 Jun 2020 03:10:15: 6000000 INFO @ Tue, 30 Jun 2020 03:10:17: 2000000 INFO @ Tue, 30 Jun 2020 03:10:22: 7000000 INFO @ Tue, 30 Jun 2020 03:10:24: 3000000 INFO @ Tue, 30 Jun 2020 03:10:29: 8000000 INFO @ Tue, 30 Jun 2020 03:10:30: 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 03:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.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 03:10:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:36: 9000000 INFO @ Tue, 30 Jun 2020 03:10:37: 5000000 INFO @ Tue, 30 Jun 2020 03:10:41: 1000000 INFO @ Tue, 30 Jun 2020 03:10:44: 10000000 INFO @ Tue, 30 Jun 2020 03:10:44: 6000000 INFO @ Tue, 30 Jun 2020 03:10:48: 2000000 INFO @ Tue, 30 Jun 2020 03:10:51: 11000000 INFO @ Tue, 30 Jun 2020 03:10:51: 7000000 INFO @ Tue, 30 Jun 2020 03:10:55: 3000000 INFO @ Tue, 30 Jun 2020 03:10:58: 8000000 INFO @ Tue, 30 Jun 2020 03:10:58: 12000000 INFO @ Tue, 30 Jun 2020 03:11:01: 4000000 INFO @ Tue, 30 Jun 2020 03:11:05: 9000000 INFO @ Tue, 30 Jun 2020 03:11:05: 13000000 INFO @ Tue, 30 Jun 2020 03:11:08: 5000000 INFO @ Tue, 30 Jun 2020 03:11:11: 10000000 INFO @ Tue, 30 Jun 2020 03:11:12: 14000000 INFO @ Tue, 30 Jun 2020 03:11:15: 6000000 INFO @ Tue, 30 Jun 2020 03:11:18: 11000000 INFO @ Tue, 30 Jun 2020 03:11:20: 15000000 INFO @ Tue, 30 Jun 2020 03:11:22: 7000000 INFO @ Tue, 30 Jun 2020 03:11:25: 12000000 INFO @ Tue, 30 Jun 2020 03:11:27: 16000000 INFO @ Tue, 30 Jun 2020 03:11:28: 8000000 INFO @ Tue, 30 Jun 2020 03:11:32: 13000000 INFO @ Tue, 30 Jun 2020 03:11:35: 17000000 INFO @ Tue, 30 Jun 2020 03:11:35: 9000000 INFO @ Tue, 30 Jun 2020 03:11:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:37: #1 total tags in treatment: 17267930 INFO @ Tue, 30 Jun 2020 03:11:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:37: #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 03:11:37: #1 tags after filtering in treatment: 17267930 INFO @ Tue, 30 Jun 2020 03:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:38: #2 number of paired peaks: 303 WARNING @ Tue, 30 Jun 2020 03:11:38: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:38: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:39: 14000000 INFO @ Tue, 30 Jun 2020 03:11:39: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:39: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:39: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:39: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:11:39: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 30 Jun 2020 03:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:39: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 30 Jun 2020 03:11:39: #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 03:11:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:41: 10000000 INFO @ Tue, 30 Jun 2020 03:11:45: 15000000 INFO @ Tue, 30 Jun 2020 03:11:47: 11000000 INFO @ Tue, 30 Jun 2020 03:11:51: 16000000 INFO @ Tue, 30 Jun 2020 03:11:54: 12000000 INFO @ Tue, 30 Jun 2020 03:11:58: 17000000 INFO @ Tue, 30 Jun 2020 03:12:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:00: #1 total tags in treatment: 17267930 INFO @ Tue, 30 Jun 2020 03:12:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:00: #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 03:12:00: 13000000 INFO @ Tue, 30 Jun 2020 03:12:00: #1 tags after filtering in treatment: 17267930 INFO @ Tue, 30 Jun 2020 03:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:00: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:01: #2 number of paired peaks: 303 WARNING @ Tue, 30 Jun 2020 03:12:01: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:02: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:02: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:12:02: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 30 Jun 2020 03:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:02: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 30 Jun 2020 03:12:02: #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 03:12:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:06: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:12: 15000000 INFO @ Tue, 30 Jun 2020 03:12:17: 16000000 INFO @ Tue, 30 Jun 2020 03:12:23: 17000000 INFO @ Tue, 30 Jun 2020 03:12:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:25: #1 total tags in treatment: 17267930 INFO @ Tue, 30 Jun 2020 03:12:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:25: #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 03:12:25: #1 tags after filtering in treatment: 17267930 INFO @ Tue, 30 Jun 2020 03:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:25: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.05_summits.bed INFO @ Tue, 30 Jun 2020 03:12:26: Done! pass1 - making usageList (595 chroms): 2 millis pass2 - checking and writing primary data (4493 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:26: #2 number of paired peaks: 303 WARNING @ Tue, 30 Jun 2020 03:12:26: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:26: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:27: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:27: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:27: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:27: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:12:27: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 30 Jun 2020 03:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:27: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 30 Jun 2020 03:12:27: #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 03:12:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:51: Done! pass1 - making usageList (463 chroms): 1 millis pass2 - checking and writing primary data (1739 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431041/SRX5431041.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:17: Done! pass1 - making usageList (285 chroms): 0 millis pass2 - checking and writing primary data (576 records, 4 fields): 9 millis CompletedMACS2peakCalling