Job ID = 6456163 SRX = SRX3270986 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:59 prefetch.2.10.7: 1) Downloading 'SRR6159397'... 2020-06-21T10:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:32 prefetch.2.10.7: 1) 'SRR6159397' was downloaded successfully Read 22465717 spots for SRR6159397/SRR6159397.sra Written 22465717 spots for SRR6159397/SRR6159397.sra 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: 00:08:07 22465717 reads; of these: 22465717 (100.00%) were unpaired; of these: 1386222 (6.17%) aligned 0 times 10710076 (47.67%) aligned exactly 1 time 10369419 (46.16%) aligned >1 times 93.83% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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] 8381509 / 21079495 = 0.3976 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 @ Sun, 21 Jun 2020 19:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.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 @ Sun, 21 Jun 2020 19:55:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:22: 1000000 INFO @ Sun, 21 Jun 2020 19:55:29: 2000000 INFO @ Sun, 21 Jun 2020 19:55:36: 3000000 INFO @ Sun, 21 Jun 2020 19:55:42: 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 @ Sun, 21 Jun 2020 19:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.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 @ Sun, 21 Jun 2020 19:55:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:49: 5000000 INFO @ Sun, 21 Jun 2020 19:55:52: 1000000 INFO @ Sun, 21 Jun 2020 19:55:56: 6000000 INFO @ Sun, 21 Jun 2020 19:55:59: 2000000 INFO @ Sun, 21 Jun 2020 19:56:03: 7000000 INFO @ Sun, 21 Jun 2020 19:56:06: 3000000 INFO @ Sun, 21 Jun 2020 19:56:09: 8000000 INFO @ Sun, 21 Jun 2020 19:56:12: 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 @ Sun, 21 Jun 2020 19:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.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 @ Sun, 21 Jun 2020 19:56:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:16: 9000000 INFO @ Sun, 21 Jun 2020 19:56:19: 5000000 INFO @ Sun, 21 Jun 2020 19:56:22: 1000000 INFO @ Sun, 21 Jun 2020 19:56:24: 10000000 INFO @ Sun, 21 Jun 2020 19:56:25: 6000000 INFO @ Sun, 21 Jun 2020 19:56:29: 2000000 INFO @ Sun, 21 Jun 2020 19:56:30: 11000000 INFO @ Sun, 21 Jun 2020 19:56:32: 7000000 INFO @ Sun, 21 Jun 2020 19:56:36: 3000000 INFO @ Sun, 21 Jun 2020 19:56:38: 12000000 INFO @ Sun, 21 Jun 2020 19:56:39: 8000000 INFO @ Sun, 21 Jun 2020 19:56:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:56:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:56:43: #1 total tags in treatment: 12697986 INFO @ Sun, 21 Jun 2020 19:56:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:56:43: 4000000 INFO @ Sun, 21 Jun 2020 19:56:44: #1 tags after filtering in treatment: 12697986 INFO @ Sun, 21 Jun 2020 19:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:45: #2 number of paired peaks: 1819 INFO @ Sun, 21 Jun 2020 19:56:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:45: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:56:45: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 21 Jun 2020 19:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.05_model.r WARNING @ Sun, 21 Jun 2020 19:56:45: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:45: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 21 Jun 2020 19:56:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:56:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:46: 9000000 INFO @ Sun, 21 Jun 2020 19:56:50: 5000000 INFO @ Sun, 21 Jun 2020 19:56:53: 10000000 INFO @ Sun, 21 Jun 2020 19:56:56: 6000000 INFO @ Sun, 21 Jun 2020 19:57:00: 11000000 INFO @ Sun, 21 Jun 2020 19:57:02: 7000000 INFO @ Sun, 21 Jun 2020 19:57:06: 12000000 INFO @ Sun, 21 Jun 2020 19:57:08: 8000000 INFO @ Sun, 21 Jun 2020 19:57:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:57:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:57:11: #1 total tags in treatment: 12697986 INFO @ Sun, 21 Jun 2020 19:57:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:57:11: #1 tags after filtering in treatment: 12697986 INFO @ Sun, 21 Jun 2020 19:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:12: #2 number of paired peaks: 1819 INFO @ Sun, 21 Jun 2020 19:57:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:13: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:57:13: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 21 Jun 2020 19:57:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.10_model.r WARNING @ Sun, 21 Jun 2020 19:57:13: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:13: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 21 Jun 2020 19:57:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:57:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:14: 9000000 INFO @ Sun, 21 Jun 2020 19:57:21: 10000000 INFO @ Sun, 21 Jun 2020 19:57:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.05_summits.bed INFO @ Sun, 21 Jun 2020 19:57:22: Done! pass1 - making usageList (1122 chroms): 2 millis pass2 - checking and writing primary data (4588 records, 4 fields): 63 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:57:27: 11000000 INFO @ Sun, 21 Jun 2020 19:57:33: 12000000 INFO @ Sun, 21 Jun 2020 19:57:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:57:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:57:37: #1 total tags in treatment: 12697986 INFO @ Sun, 21 Jun 2020 19:57:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:57:37: #1 tags after filtering in treatment: 12697986 INFO @ Sun, 21 Jun 2020 19:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:39: #2 number of paired peaks: 1819 INFO @ Sun, 21 Jun 2020 19:57:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:39: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:57:39: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 21 Jun 2020 19:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.20_model.r WARNING @ Sun, 21 Jun 2020 19:57:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:39: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 21 Jun 2020 19:57:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:57:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.10_summits.bed INFO @ Sun, 21 Jun 2020 19:57:48: Done! pass1 - making usageList (862 chroms): 1 millis pass2 - checking and writing primary data (2830 records, 4 fields): 48 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:58:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270986/SRX3270986.20_summits.bed INFO @ Sun, 21 Jun 2020 19:58:15: Done! pass1 - making usageList (551 chroms): 2 millis pass2 - checking and writing primary data (1719 records, 4 fields): 31 millis CompletedMACS2peakCalling