Job ID = 10166616 SRX = SRX7723715 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: 00:07:53 23112749 reads; of these: 23112749 (100.00%) were unpaired; of these: 2402938 (10.40%) aligned 0 times 15478013 (66.97%) aligned exactly 1 time 5231798 (22.64%) aligned >1 times 89.60% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 2086015 / 20709811 = 0.1007 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 @ Thu, 08 Oct 2020 22:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.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 @ Thu, 08 Oct 2020 22:07:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:07:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:07:51: 1000000 INFO @ Thu, 08 Oct 2020 22:07:56: 2000000 INFO @ Thu, 08 Oct 2020 22:08:02: 3000000 INFO @ Thu, 08 Oct 2020 22:08:08: 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 @ Thu, 08 Oct 2020 22:08:14: 5000000 INFO @ Thu, 08 Oct 2020 22:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.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 @ Thu, 08 Oct 2020 22:08:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:08:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:08:21: 6000000 INFO @ Thu, 08 Oct 2020 22:08:21: 1000000 INFO @ Thu, 08 Oct 2020 22:08:28: 7000000 INFO @ Thu, 08 Oct 2020 22:08:28: 2000000 INFO @ Thu, 08 Oct 2020 22:08:34: 8000000 INFO @ Thu, 08 Oct 2020 22:08:35: 3000000 INFO @ Thu, 08 Oct 2020 22:08:41: 9000000 INFO @ Thu, 08 Oct 2020 22:08:42: 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 @ Thu, 08 Oct 2020 22:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.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 @ Thu, 08 Oct 2020 22:08:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:08:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:08:48: 10000000 INFO @ Thu, 08 Oct 2020 22:08:49: 5000000 INFO @ Thu, 08 Oct 2020 22:08:53: 1000000 INFO @ Thu, 08 Oct 2020 22:08:56: 11000000 INFO @ Thu, 08 Oct 2020 22:08:57: 6000000 INFO @ Thu, 08 Oct 2020 22:09:01: 2000000 INFO @ Thu, 08 Oct 2020 22:09:03: 12000000 INFO @ Thu, 08 Oct 2020 22:09:04: 7000000 INFO @ Thu, 08 Oct 2020 22:09:09: 3000000 INFO @ Thu, 08 Oct 2020 22:09:11: 13000000 INFO @ Thu, 08 Oct 2020 22:09:12: 8000000 INFO @ Thu, 08 Oct 2020 22:09:18: 4000000 INFO @ Thu, 08 Oct 2020 22:09:18: 14000000 INFO @ Thu, 08 Oct 2020 22:09:19: 9000000 INFO @ Thu, 08 Oct 2020 22:09:26: 5000000 INFO @ Thu, 08 Oct 2020 22:09:26: 15000000 INFO @ Thu, 08 Oct 2020 22:09:27: 10000000 INFO @ Thu, 08 Oct 2020 22:09:34: 6000000 INFO @ Thu, 08 Oct 2020 22:09:34: 16000000 INFO @ Thu, 08 Oct 2020 22:09:35: 11000000 INFO @ Thu, 08 Oct 2020 22:09:41: 17000000 INFO @ Thu, 08 Oct 2020 22:09:42: 7000000 INFO @ Thu, 08 Oct 2020 22:09:42: 12000000 INFO @ Thu, 08 Oct 2020 22:09:49: 18000000 INFO @ Thu, 08 Oct 2020 22:09:50: 13000000 INFO @ Thu, 08 Oct 2020 22:09:50: 8000000 INFO @ Thu, 08 Oct 2020 22:09:54: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:09:54: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:09:54: #1 total tags in treatment: 18623796 INFO @ Thu, 08 Oct 2020 22:09:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:09:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:09:54: #1 tags after filtering in treatment: 18623677 INFO @ Thu, 08 Oct 2020 22:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:09:54: #1 finished! INFO @ Thu, 08 Oct 2020 22:09:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:09:56: #2 number of paired peaks: 714 WARNING @ Thu, 08 Oct 2020 22:09:56: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Thu, 08 Oct 2020 22:09:56: start model_add_line... INFO @ Thu, 08 Oct 2020 22:09:56: start X-correlation... INFO @ Thu, 08 Oct 2020 22:09:56: end of X-cor INFO @ Thu, 08 Oct 2020 22:09:56: #2 finished! INFO @ Thu, 08 Oct 2020 22:09:56: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 22:09:56: #2 alternative fragment length(s) may be 3,65,565 bps INFO @ Thu, 08 Oct 2020 22:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.05_model.r WARNING @ Thu, 08 Oct 2020 22:09:56: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:09:56: #2 You may need to consider one of the other alternative d(s): 3,65,565 WARNING @ Thu, 08 Oct 2020 22:09:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:09:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:09:57: 14000000 INFO @ Thu, 08 Oct 2020 22:09:58: 9000000 INFO @ Thu, 08 Oct 2020 22:10:05: 15000000 INFO @ Thu, 08 Oct 2020 22:10:06: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 22:10:12: 16000000 INFO @ Thu, 08 Oct 2020 22:10:14: 11000000 INFO @ Thu, 08 Oct 2020 22:10:20: 17000000 INFO @ Thu, 08 Oct 2020 22:10:22: 12000000 INFO @ Thu, 08 Oct 2020 22:10:27: 18000000 INFO @ Thu, 08 Oct 2020 22:10:30: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:10:30: 13000000 INFO @ Thu, 08 Oct 2020 22:10:32: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:10:32: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:10:32: #1 total tags in treatment: 18623796 INFO @ Thu, 08 Oct 2020 22:10:32: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:10:33: #1 tags after filtering in treatment: 18623677 INFO @ Thu, 08 Oct 2020 22:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:10:33: #1 finished! INFO @ Thu, 08 Oct 2020 22:10:33: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:10:34: #2 number of paired peaks: 714 WARNING @ Thu, 08 Oct 2020 22:10:34: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Thu, 08 Oct 2020 22:10:34: start model_add_line... INFO @ Thu, 08 Oct 2020 22:10:34: start X-correlation... INFO @ Thu, 08 Oct 2020 22:10:34: end of X-cor INFO @ Thu, 08 Oct 2020 22:10:34: #2 finished! INFO @ Thu, 08 Oct 2020 22:10:34: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 22:10:34: #2 alternative fragment length(s) may be 3,65,565 bps INFO @ Thu, 08 Oct 2020 22:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.10_model.r WARNING @ Thu, 08 Oct 2020 22:10:34: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:10:34: #2 You may need to consider one of the other alternative d(s): 3,65,565 WARNING @ Thu, 08 Oct 2020 22:10:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:10:34: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:10:38: 14000000 INFO @ Thu, 08 Oct 2020 22:10:45: 15000000 INFO @ Thu, 08 Oct 2020 22:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.05_peaks.xls INFO @ Thu, 08 Oct 2020 22:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.05_summits.bed INFO @ Thu, 08 Oct 2020 22:10:46: Done! pass1 - making usageList (682 chroms): 2 millis pass2 - checking and writing primary data (2551 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 22:10:52: 16000000 INFO @ Thu, 08 Oct 2020 22:10:59: 17000000 INFO @ Thu, 08 Oct 2020 22:11:07: 18000000 INFO @ Thu, 08 Oct 2020 22:11:08: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:11:11: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:11:11: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:11:11: #1 total tags in treatment: 18623796 INFO @ Thu, 08 Oct 2020 22:11:11: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:11:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:11:12: #1 tags after filtering in treatment: 18623677 INFO @ Thu, 08 Oct 2020 22:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:11:12: #1 finished! INFO @ Thu, 08 Oct 2020 22:11:12: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:11:13: #2 number of paired peaks: 714 WARNING @ Thu, 08 Oct 2020 22:11:13: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Thu, 08 Oct 2020 22:11:13: start model_add_line... INFO @ Thu, 08 Oct 2020 22:11:13: start X-correlation... INFO @ Thu, 08 Oct 2020 22:11:13: end of X-cor INFO @ Thu, 08 Oct 2020 22:11:13: #2 finished! INFO @ Thu, 08 Oct 2020 22:11:13: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 22:11:13: #2 alternative fragment length(s) may be 3,65,565 bps INFO @ Thu, 08 Oct 2020 22:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.20_model.r WARNING @ Thu, 08 Oct 2020 22:11:13: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:11:13: #2 You may need to consider one of the other alternative d(s): 3,65,565 WARNING @ Thu, 08 Oct 2020 22:11:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:11:13: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.10_peaks.xls INFO @ Thu, 08 Oct 2020 22:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:11:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.10_summits.bed INFO @ Thu, 08 Oct 2020 22:11:24: Done! pass1 - making usageList (616 chroms): 1 millis pass2 - checking and writing primary data (2008 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:11:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.20_peaks.xls INFO @ Thu, 08 Oct 2020 22:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723715/SRX7723715.20_summits.bed INFO @ Thu, 08 Oct 2020 22:12:04: Done! pass1 - making usageList (534 chroms): 1 millis pass2 - checking and writing primary data (1512 records, 4 fields): 16 millis CompletedMACS2peakCalling