Job ID = 6529866 SRX = SRX5343103 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: 00:03:47 13384207 reads; of these: 13384207 (100.00%) were unpaired; of these: 717459 (5.36%) aligned 0 times 10542974 (78.77%) aligned exactly 1 time 2123774 (15.87%) aligned >1 times 94.64% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 1022275 / 12666748 = 0.0807 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 02:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.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 02:48:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:34: 1000000 INFO @ Tue, 30 Jun 2020 02:48:41: 2000000 INFO @ Tue, 30 Jun 2020 02:48:47: 3000000 INFO @ Tue, 30 Jun 2020 02:48:54: 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 02:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.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 02:48:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:01: 5000000 INFO @ Tue, 30 Jun 2020 02:49:04: 1000000 INFO @ Tue, 30 Jun 2020 02:49:08: 6000000 INFO @ Tue, 30 Jun 2020 02:49:12: 2000000 INFO @ Tue, 30 Jun 2020 02:49:15: 7000000 INFO @ Tue, 30 Jun 2020 02:49:19: 3000000 INFO @ Tue, 30 Jun 2020 02:49:23: 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 02:49:27: 4000000 INFO @ Tue, 30 Jun 2020 02:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.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 02:49:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:30: 9000000 INFO @ Tue, 30 Jun 2020 02:49:34: 5000000 INFO @ Tue, 30 Jun 2020 02:49:34: 1000000 INFO @ Tue, 30 Jun 2020 02:49:37: 10000000 INFO @ Tue, 30 Jun 2020 02:49:42: 6000000 INFO @ Tue, 30 Jun 2020 02:49:42: 2000000 INFO @ Tue, 30 Jun 2020 02:49:45: 11000000 INFO @ Tue, 30 Jun 2020 02:49:49: 7000000 INFO @ Tue, 30 Jun 2020 02:49:49: 3000000 INFO @ Tue, 30 Jun 2020 02:49:50: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 02:49:50: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 02:49:50: #1 total tags in treatment: 11644473 INFO @ Tue, 30 Jun 2020 02:49:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:50: #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 02:49:50: #1 tags after filtering in treatment: 11644470 INFO @ Tue, 30 Jun 2020 02:49:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:51: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:49:51: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:51: #2 predicted fragment length is 68 bps INFO @ Tue, 30 Jun 2020 02:49:51: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 30 Jun 2020 02:49:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:51: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 30 Jun 2020 02:49:51: #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 02:49:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:56: 8000000 INFO @ Tue, 30 Jun 2020 02:49:56: 4000000 INFO @ Tue, 30 Jun 2020 02:50:03: 9000000 INFO @ Tue, 30 Jun 2020 02:50:04: 5000000 INFO @ Tue, 30 Jun 2020 02:50:11: 6000000 INFO @ Tue, 30 Jun 2020 02:50:11: 10000000 INFO @ Tue, 30 Jun 2020 02:50:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:18: 7000000 INFO @ Tue, 30 Jun 2020 02:50:18: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:50:23: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 02:50:23: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 02:50:23: #1 total tags in treatment: 11644473 INFO @ Tue, 30 Jun 2020 02:50:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:23: #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 02:50:24: #1 tags after filtering in treatment: 11644470 INFO @ Tue, 30 Jun 2020 02:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:24: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:50:24: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:24: #2 predicted fragment length is 68 bps INFO @ Tue, 30 Jun 2020 02:50:24: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 30 Jun 2020 02:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:24: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:24: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 30 Jun 2020 02:50:24: #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 02:50:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:25: 8000000 INFO @ Tue, 30 Jun 2020 02:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:26: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (825 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:32: 9000000 INFO @ Tue, 30 Jun 2020 02:50:39: 10000000 INFO @ Tue, 30 Jun 2020 02:50:45: 11000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:50:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:50: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 02:50:50: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 02:50:50: #1 total tags in treatment: 11644473 INFO @ Tue, 30 Jun 2020 02:50:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:50: #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 02:50:50: #1 tags after filtering in treatment: 11644470 INFO @ Tue, 30 Jun 2020 02:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:51: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:50:51: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:51: #2 predicted fragment length is 68 bps INFO @ Tue, 30 Jun 2020 02:50:51: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 30 Jun 2020 02:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:51: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 30 Jun 2020 02:50:51: #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 02:50:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.10_summits.bed INFO @ Tue, 30 Jun 2020 02:51:00: Done! pass1 - making usageList (181 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343103/SRX5343103.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:25: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 4 millis CompletedMACS2peakCalling