Job ID = 6458027 SRX = SRX4941151 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:10:35 prefetch.2.10.7: 1) Downloading 'SRR8114854'... 2020-06-21T12:10:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:12 prefetch.2.10.7: 1) 'SRR8114854' was downloaded successfully 2020-06-21T12:13:12 prefetch.2.10.7: 'SRR8114854' has 0 unresolved dependencies Read 20294177 spots for SRR8114854/SRR8114854.sra Written 20294177 spots for SRR8114854/SRR8114854.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: 00:08:33 20294177 reads; of these: 20294177 (100.00%) were unpaired; of these: 9309953 (45.87%) aligned 0 times 4417292 (21.77%) aligned exactly 1 time 6566932 (32.36%) aligned >1 times 54.13% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 6491832 / 10984224 = 0.5910 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 21:26:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.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 21:26:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:25: 1000000 INFO @ Sun, 21 Jun 2020 21:26:31: 2000000 INFO @ Sun, 21 Jun 2020 21:26:37: 3000000 INFO @ Sun, 21 Jun 2020 21:26:44: 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 21:26:47: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:26:47: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:26:47: #1 total tags in treatment: 4492392 INFO @ Sun, 21 Jun 2020 21:26:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:47: #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 21:26:48: #1 tags after filtering in treatment: 4492179 INFO @ Sun, 21 Jun 2020 21:26:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:48: #2 number of paired peaks: 2791 INFO @ Sun, 21 Jun 2020 21:26:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:48: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 21:26:48: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 21:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.05_model.r WARNING @ Sun, 21 Jun 2020 21:26:48: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:48: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sun, 21 Jun 2020 21:26:48: #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 21:26:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.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 21:26:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:55: 1000000 INFO @ Sun, 21 Jun 2020 21:26:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:01: 2000000 INFO @ Sun, 21 Jun 2020 21:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.05_summits.bed INFO @ Sun, 21 Jun 2020 21:27:04: Done! pass1 - making usageList (583 chroms): 2 millis pass2 - checking and writing primary data (2450 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:27:07: 3000000 INFO @ Sun, 21 Jun 2020 21:27:14: 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 21:27:17: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:27:17: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:27:17: #1 total tags in treatment: 4492392 INFO @ Sun, 21 Jun 2020 21:27:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:17: #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 21:27:17: #1 tags after filtering in treatment: 4492179 INFO @ Sun, 21 Jun 2020 21:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:18: #2 number of paired peaks: 2791 INFO @ Sun, 21 Jun 2020 21:27:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:18: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 21:27:18: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 21:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.10_model.r WARNING @ Sun, 21 Jun 2020 21:27:18: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:27:18: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sun, 21 Jun 2020 21:27:18: #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 21:27:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.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 21:27:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:25: 1000000 INFO @ Sun, 21 Jun 2020 21:27:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:31: 2000000 INFO @ Sun, 21 Jun 2020 21:27:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.10_summits.bed INFO @ Sun, 21 Jun 2020 21:27:33: Done! pass1 - making usageList (518 chroms): 3 millis pass2 - checking and writing primary data (1640 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:27:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:27:44: 4000000 INFO @ Sun, 21 Jun 2020 21:27:47: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:27:47: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:27:47: #1 total tags in treatment: 4492392 INFO @ Sun, 21 Jun 2020 21:27:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:47: #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 21:27:48: #1 tags after filtering in treatment: 4492179 INFO @ Sun, 21 Jun 2020 21:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:48: #2 number of paired peaks: 2791 INFO @ Sun, 21 Jun 2020 21:27:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:48: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 21:27:48: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 21:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.20_model.r WARNING @ Sun, 21 Jun 2020 21:27:48: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:27:48: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sun, 21 Jun 2020 21:27:48: #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 21:27:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:27:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4941151/SRX4941151.20_summits.bed INFO @ Sun, 21 Jun 2020 21:28:04: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 12 millis CompletedMACS2peakCalling