Job ID = 6530039 SRX = SRX6468504 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: 00:06:45 26072395 reads; of these: 26072395 (100.00%) were unpaired; of these: 2567664 (9.85%) aligned 0 times 16611934 (63.71%) aligned exactly 1 time 6892797 (26.44%) aligned >1 times 90.15% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 8606300 / 23504731 = 0.3662 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 03:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.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 03:19:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:24: 1000000 INFO @ Tue, 30 Jun 2020 03:19:29: 2000000 INFO @ Tue, 30 Jun 2020 03:19:35: 3000000 INFO @ Tue, 30 Jun 2020 03:19:40: 4000000 INFO @ Tue, 30 Jun 2020 03:19:45: 5000000 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 03:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.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 03:19:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:51: 6000000 INFO @ Tue, 30 Jun 2020 03:19:55: 1000000 INFO @ Tue, 30 Jun 2020 03:19:58: 7000000 INFO @ Tue, 30 Jun 2020 03:20:02: 2000000 INFO @ Tue, 30 Jun 2020 03:20:04: 8000000 INFO @ Tue, 30 Jun 2020 03:20:09: 3000000 INFO @ Tue, 30 Jun 2020 03:20:10: 9000000 INFO @ Tue, 30 Jun 2020 03:20:16: 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 03:20:17: 10000000 INFO @ Tue, 30 Jun 2020 03:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.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 03:20:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:22: 5000000 INFO @ Tue, 30 Jun 2020 03:20:23: 11000000 INFO @ Tue, 30 Jun 2020 03:20:25: 1000000 INFO @ Tue, 30 Jun 2020 03:20:29: 6000000 INFO @ Tue, 30 Jun 2020 03:20:30: 12000000 INFO @ Tue, 30 Jun 2020 03:20:32: 2000000 INFO @ Tue, 30 Jun 2020 03:20:36: 7000000 INFO @ Tue, 30 Jun 2020 03:20:37: 13000000 INFO @ Tue, 30 Jun 2020 03:20:39: 3000000 INFO @ Tue, 30 Jun 2020 03:20:43: 14000000 INFO @ Tue, 30 Jun 2020 03:20:43: 8000000 INFO @ Tue, 30 Jun 2020 03:20:46: 4000000 INFO @ Tue, 30 Jun 2020 03:20:49: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:20:49: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:20:49: #1 total tags in treatment: 14898431 INFO @ Tue, 30 Jun 2020 03:20:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:20:49: #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 03:20:50: #1 tags after filtering in treatment: 14898431 INFO @ Tue, 30 Jun 2020 03:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:20:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:20:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:20:50: 9000000 INFO @ Tue, 30 Jun 2020 03:20:51: #2 number of paired peaks: 132 WARNING @ Tue, 30 Jun 2020 03:20:51: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 30 Jun 2020 03:20:51: start model_add_line... INFO @ Tue, 30 Jun 2020 03:20:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:20:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:20:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:20:51: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:20:51: #2 alternative fragment length(s) may be 1,45 bps INFO @ Tue, 30 Jun 2020 03:20:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.05_model.r WARNING @ Tue, 30 Jun 2020 03:20:51: #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 03:20:51: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Tue, 30 Jun 2020 03:20:51: #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 03:20:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:20:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:20:53: 5000000 INFO @ Tue, 30 Jun 2020 03:20:57: 10000000 INFO @ Tue, 30 Jun 2020 03:21:00: 6000000 INFO @ Tue, 30 Jun 2020 03:21:04: 11000000 INFO @ Tue, 30 Jun 2020 03:21:07: 7000000 INFO @ Tue, 30 Jun 2020 03:21:12: 12000000 INFO @ Tue, 30 Jun 2020 03:21:13: 8000000 INFO @ Tue, 30 Jun 2020 03:21:19: 13000000 INFO @ Tue, 30 Jun 2020 03:21:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:21:26: 14000000 INFO @ Tue, 30 Jun 2020 03:21:27: 10000000 INFO @ Tue, 30 Jun 2020 03:21:32: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:21:32: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:21:32: #1 total tags in treatment: 14898431 INFO @ Tue, 30 Jun 2020 03:21:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:32: #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 03:21:33: #1 tags after filtering in treatment: 14898431 INFO @ Tue, 30 Jun 2020 03:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.05_summits.bed INFO @ Tue, 30 Jun 2020 03:21:33: Done! pass1 - making usageList (542 chroms): 1 millis pass2 - checking and writing primary data (2009 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:21:34: #2 number of paired peaks: 132 WARNING @ Tue, 30 Jun 2020 03:21:34: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:34: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:21:34: #2 alternative fragment length(s) may be 1,45 bps INFO @ Tue, 30 Jun 2020 03:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.10_model.r WARNING @ Tue, 30 Jun 2020 03:21:34: #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 03:21:34: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Tue, 30 Jun 2020 03:21:34: #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 03:21:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:34: 11000000 INFO @ Tue, 30 Jun 2020 03:21:41: 12000000 INFO @ Tue, 30 Jun 2020 03:21:48: 13000000 INFO @ Tue, 30 Jun 2020 03:21:54: 14000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:22:00: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:22:00: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:22:00: #1 total tags in treatment: 14898431 INFO @ Tue, 30 Jun 2020 03:22:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:00: #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 03:22:01: #1 tags after filtering in treatment: 14898431 INFO @ Tue, 30 Jun 2020 03:22:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:02: #2 number of paired peaks: 132 WARNING @ Tue, 30 Jun 2020 03:22:02: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:02: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:02: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:02: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:22:02: #2 alternative fragment length(s) may be 1,45 bps INFO @ Tue, 30 Jun 2020 03:22:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.20_model.r WARNING @ Tue, 30 Jun 2020 03:22:02: #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 03:22:02: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Tue, 30 Jun 2020 03:22:02: #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 03:22:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.10_summits.bed INFO @ Tue, 30 Jun 2020 03:22:16: Done! pass1 - making usageList (353 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468504/SRX6468504.20_summits.bed INFO @ Tue, 30 Jun 2020 03:22:43: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 4 millis CompletedMACS2peakCalling