Job ID = 6456958 SRX = SRX4158182 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:07:42 prefetch.2.10.7: 1) Downloading 'SRR7253462'... 2020-06-21T11:07:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:47 prefetch.2.10.7: 1) 'SRR7253462' was downloaded successfully Read 13828807 spots for SRR7253462/SRR7253462.sra Written 13828807 spots for SRR7253462/SRR7253462.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: 00:03:47 13828807 reads; of these: 13828807 (100.00%) were unpaired; of these: 459567 (3.32%) aligned 0 times 8000355 (57.85%) aligned exactly 1 time 5368885 (38.82%) aligned >1 times 96.68% 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] 1778796 / 13369240 = 0.1331 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 20:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.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 20:17:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:17:52: 1000000 INFO @ Sun, 21 Jun 2020 20:17:57: 2000000 INFO @ Sun, 21 Jun 2020 20:18:03: 3000000 INFO @ Sun, 21 Jun 2020 20:18:08: 4000000 INFO @ Sun, 21 Jun 2020 20:18:13: 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 @ Sun, 21 Jun 2020 20:18:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.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 20:18:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:18: 6000000 INFO @ Sun, 21 Jun 2020 20:18:23: 1000000 INFO @ Sun, 21 Jun 2020 20:18:23: 7000000 INFO @ Sun, 21 Jun 2020 20:18:28: 2000000 INFO @ Sun, 21 Jun 2020 20:18:29: 8000000 INFO @ Sun, 21 Jun 2020 20:18:34: 3000000 INFO @ Sun, 21 Jun 2020 20:18:34: 9000000 INFO @ Sun, 21 Jun 2020 20:18:39: 4000000 INFO @ Sun, 21 Jun 2020 20:18:40: 10000000 INFO @ Sun, 21 Jun 2020 20:18:44: 5000000 INFO @ Sun, 21 Jun 2020 20:18:45: 11000000 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 20:18:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.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 20:18:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:48: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:18:48: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:18:48: #1 total tags in treatment: 11590444 INFO @ Sun, 21 Jun 2020 20:18:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:48: #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 20:18:49: #1 tags after filtering in treatment: 11590386 INFO @ Sun, 21 Jun 2020 20:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:50: 6000000 INFO @ Sun, 21 Jun 2020 20:18:50: #2 number of paired peaks: 1000 INFO @ Sun, 21 Jun 2020 20:18:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:50: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 20:18:50: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 20:18:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.05_model.r WARNING @ Sun, 21 Jun 2020 20:18:50: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:18:50: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 20:18:50: #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 20:18:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:18:53: 1000000 INFO @ Sun, 21 Jun 2020 20:18:55: 7000000 INFO @ Sun, 21 Jun 2020 20:18:58: 2000000 INFO @ Sun, 21 Jun 2020 20:19:00: 8000000 INFO @ Sun, 21 Jun 2020 20:19:03: 3000000 INFO @ Sun, 21 Jun 2020 20:19:06: 9000000 INFO @ Sun, 21 Jun 2020 20:19:09: 4000000 INFO @ Sun, 21 Jun 2020 20:19:11: 10000000 INFO @ Sun, 21 Jun 2020 20:19:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:14: 5000000 INFO @ Sun, 21 Jun 2020 20:19:17: 11000000 INFO @ Sun, 21 Jun 2020 20:19:19: 6000000 INFO @ Sun, 21 Jun 2020 20:19:20: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:19:20: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:19:20: #1 total tags in treatment: 11590444 INFO @ Sun, 21 Jun 2020 20:19:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:20: #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 20:19:20: #1 tags after filtering in treatment: 11590386 INFO @ Sun, 21 Jun 2020 20:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:21: #2 number of paired peaks: 1000 INFO @ Sun, 21 Jun 2020 20:19:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:21: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 20:19:21: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 20:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.10_model.r WARNING @ Sun, 21 Jun 2020 20:19:21: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:19:21: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 20:19:21: #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 20:19:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:25: 7000000 INFO @ Sun, 21 Jun 2020 20:19:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.05_summits.bed INFO @ Sun, 21 Jun 2020 20:19:26: Done! pass1 - making usageList (521 chroms): 2 millis pass2 - checking and writing primary data (2389 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:19:30: 8000000 INFO @ Sun, 21 Jun 2020 20:19:35: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:19:40: 10000000 INFO @ Sun, 21 Jun 2020 20:19:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:45: 11000000 INFO @ Sun, 21 Jun 2020 20:19:48: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:19:48: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:19:48: #1 total tags in treatment: 11590444 INFO @ Sun, 21 Jun 2020 20:19:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:48: #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 20:19:49: #1 tags after filtering in treatment: 11590386 INFO @ Sun, 21 Jun 2020 20:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:50: #2 number of paired peaks: 1000 INFO @ Sun, 21 Jun 2020 20:19:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:50: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 20:19:50: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 20:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.20_model.r WARNING @ Sun, 21 Jun 2020 20:19:50: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:19:50: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 20:19:50: #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 20:19:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.10_summits.bed INFO @ Sun, 21 Jun 2020 20:19:56: Done! pass1 - making usageList (306 chroms): 1 millis pass2 - checking and writing primary data (1177 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:20:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158182/SRX4158182.20_summits.bed INFO @ Sun, 21 Jun 2020 20:20:27: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 7 millis CompletedMACS2peakCalling