Job ID = 6626918 SRX = SRX7262568 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: 00:15:38 88583966 reads; of these: 88583966 (100.00%) were unpaired; of these: 81288926 (91.76%) aligned 0 times 5488376 (6.20%) aligned exactly 1 time 1806664 (2.04%) aligned >1 times 8.24% overall alignment rate Time searching: 00:15:38 Overall time: 00:15:38 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_rmdupse_core] 816696 / 7295040 = 0.1120 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, 14 Jul 2020 09:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.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, 14 Jul 2020 09:16:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:16:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:17:05: 1000000 INFO @ Tue, 14 Jul 2020 09:17:11: 2000000 INFO @ Tue, 14 Jul 2020 09:17:18: 3000000 INFO @ Tue, 14 Jul 2020 09:17:24: 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, 14 Jul 2020 09:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.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, 14 Jul 2020 09:17:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:17:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:17:31: 5000000 INFO @ Tue, 14 Jul 2020 09:17:36: 1000000 INFO @ Tue, 14 Jul 2020 09:17:38: 6000000 INFO @ Tue, 14 Jul 2020 09:17:42: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:17:42: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:17:42: #1 total tags in treatment: 6478344 INFO @ Tue, 14 Jul 2020 09:17:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:17:42: #1 tags after filtering in treatment: 6478133 INFO @ Tue, 14 Jul 2020 09:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:17:42: #1 finished! INFO @ Tue, 14 Jul 2020 09:17:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:17:42: #2 number of paired peaks: 1735 INFO @ Tue, 14 Jul 2020 09:17:42: start model_add_line... INFO @ Tue, 14 Jul 2020 09:17:42: start X-correlation... INFO @ Tue, 14 Jul 2020 09:17:42: end of X-cor INFO @ Tue, 14 Jul 2020 09:17:42: #2 finished! INFO @ Tue, 14 Jul 2020 09:17:42: #2 predicted fragment length is 73 bps INFO @ Tue, 14 Jul 2020 09:17:42: #2 alternative fragment length(s) may be 3,73,503,598 bps INFO @ Tue, 14 Jul 2020 09:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.05_model.r WARNING @ Tue, 14 Jul 2020 09:17:42: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:17:42: #2 You may need to consider one of the other alternative d(s): 3,73,503,598 WARNING @ Tue, 14 Jul 2020 09:17:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:17:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:17:43: 2000000 INFO @ Tue, 14 Jul 2020 09:17:50: 3000000 INFO @ Tue, 14 Jul 2020 09:17:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:17:57: 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, 14 Jul 2020 09:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.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, 14 Jul 2020 09:17:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:17:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.05_summits.bed INFO @ Tue, 14 Jul 2020 09:18:03: Done! INFO @ Tue, 14 Jul 2020 09:18:04: 5000000 pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1583 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:18:06: 1000000 INFO @ Tue, 14 Jul 2020 09:18:11: 6000000 INFO @ Tue, 14 Jul 2020 09:18:13: 2000000 INFO @ Tue, 14 Jul 2020 09:18:15: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:18:15: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:18:15: #1 total tags in treatment: 6478344 INFO @ Tue, 14 Jul 2020 09:18:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:18:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:18:15: #1 tags after filtering in treatment: 6478133 INFO @ Tue, 14 Jul 2020 09:18:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:18:15: #1 finished! INFO @ Tue, 14 Jul 2020 09:18:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:18:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:18:15: #2 number of paired peaks: 1735 INFO @ Tue, 14 Jul 2020 09:18:15: start model_add_line... INFO @ Tue, 14 Jul 2020 09:18:15: start X-correlation... INFO @ Tue, 14 Jul 2020 09:18:15: end of X-cor INFO @ Tue, 14 Jul 2020 09:18:15: #2 finished! INFO @ Tue, 14 Jul 2020 09:18:15: #2 predicted fragment length is 73 bps INFO @ Tue, 14 Jul 2020 09:18:15: #2 alternative fragment length(s) may be 3,73,503,598 bps INFO @ Tue, 14 Jul 2020 09:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.10_model.r WARNING @ Tue, 14 Jul 2020 09:18:15: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:18:15: #2 You may need to consider one of the other alternative d(s): 3,73,503,598 WARNING @ Tue, 14 Jul 2020 09:18:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:18:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:18:20: 3000000 INFO @ Tue, 14 Jul 2020 09:18:27: 4000000 INFO @ Tue, 14 Jul 2020 09:18:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:18:34: 5000000 INFO @ Tue, 14 Jul 2020 09:18:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:18:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:18:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.10_summits.bed INFO @ Tue, 14 Jul 2020 09:18:36: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:18:40: 6000000 INFO @ Tue, 14 Jul 2020 09:18:44: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:18:44: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:18:44: #1 total tags in treatment: 6478344 INFO @ Tue, 14 Jul 2020 09:18:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:18:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:18:44: #1 tags after filtering in treatment: 6478133 INFO @ Tue, 14 Jul 2020 09:18:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:18:44: #1 finished! INFO @ Tue, 14 Jul 2020 09:18:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:18:44: #2 number of paired peaks: 1735 INFO @ Tue, 14 Jul 2020 09:18:44: start model_add_line... INFO @ Tue, 14 Jul 2020 09:18:44: start X-correlation... INFO @ Tue, 14 Jul 2020 09:18:44: end of X-cor INFO @ Tue, 14 Jul 2020 09:18:44: #2 finished! INFO @ Tue, 14 Jul 2020 09:18:44: #2 predicted fragment length is 73 bps INFO @ Tue, 14 Jul 2020 09:18:44: #2 alternative fragment length(s) may be 3,73,503,598 bps INFO @ Tue, 14 Jul 2020 09:18:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.20_model.r WARNING @ Tue, 14 Jul 2020 09:18:44: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:18:44: #2 You may need to consider one of the other alternative d(s): 3,73,503,598 WARNING @ Tue, 14 Jul 2020 09:18:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:18:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:18:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:18:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7262568/SRX7262568.20_summits.bed INFO @ Tue, 14 Jul 2020 09:19:05: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 5 millis CompletedMACS2peakCalling