Job ID = 6458417 SRX = SRX5226976 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:24:24 prefetch.2.10.7: 1) Downloading 'SRR8417891'... 2020-06-21T12:24:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:25:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:25:22 prefetch.2.10.7: 'SRR8417891' is valid 2020-06-21T12:25:22 prefetch.2.10.7: 1) 'SRR8417891' was downloaded successfully 2020-06-21T12:25:22 prefetch.2.10.7: 'SRR8417891' has 0 unresolved dependencies Read 4392408 spots for SRR8417891/SRR8417891.sra Written 4392408 spots for SRR8417891/SRR8417891.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: 00:01:59 4392408 reads; of these: 4392408 (100.00%) were unpaired; of these: 462264 (10.52%) aligned 0 times 2691770 (61.28%) aligned exactly 1 time 1238374 (28.19%) aligned >1 times 89.48% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 384961 / 3930144 = 0.0980 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 21:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.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 21:29:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:32: 1000000 INFO @ Sun, 21 Jun 2020 21:29:38: 2000000 INFO @ Sun, 21 Jun 2020 21:29:45: 3000000 INFO @ Sun, 21 Jun 2020 21:29:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:29:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:29:48: #1 total tags in treatment: 3545183 INFO @ Sun, 21 Jun 2020 21:29:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:48: #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 21:29:48: #1 tags after filtering in treatment: 3544930 INFO @ Sun, 21 Jun 2020 21:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:49: #2 number of paired peaks: 1652 INFO @ Sun, 21 Jun 2020 21:29:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:49: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:29:49: #2 alternative fragment length(s) may be 91,563,570 bps INFO @ Sun, 21 Jun 2020 21:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:49: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:49: #2 You may need to consider one of the other alternative d(s): 91,563,570 WARNING @ Sun, 21 Jun 2020 21:29:49: #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 21:29:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:49: #3 Pre-compute pvalue-qvalue table... 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 21:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.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 21:29:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:01: 1000000 INFO @ Sun, 21 Jun 2020 21:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:01: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (1205 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:07: 2000000 INFO @ Sun, 21 Jun 2020 21:30:14: 3000000 INFO @ Sun, 21 Jun 2020 21:30:17: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:30:17: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:30:17: #1 total tags in treatment: 3545183 INFO @ Sun, 21 Jun 2020 21:30:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:17: #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 21:30:17: #1 tags after filtering in treatment: 3544930 INFO @ Sun, 21 Jun 2020 21:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:18: #2 number of paired peaks: 1652 INFO @ Sun, 21 Jun 2020 21:30:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:18: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:30:18: #2 alternative fragment length(s) may be 91,563,570 bps INFO @ Sun, 21 Jun 2020 21:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.10_model.r WARNING @ Sun, 21 Jun 2020 21:30:18: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:18: #2 You may need to consider one of the other alternative d(s): 91,563,570 WARNING @ Sun, 21 Jun 2020 21:30:18: #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 21:30:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:18: #3 Pre-compute pvalue-qvalue table... 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 21:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.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 21:30:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.10_summits.bed INFO @ Sun, 21 Jun 2020 21:30:30: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (573 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:32: 1000000 INFO @ Sun, 21 Jun 2020 21:30:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:47: 3000000 INFO @ Sun, 21 Jun 2020 21:30:51: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:30:51: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:30:51: #1 total tags in treatment: 3545183 INFO @ Sun, 21 Jun 2020 21:30:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:51: #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 21:30:52: #1 tags after filtering in treatment: 3544930 INFO @ Sun, 21 Jun 2020 21:30:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:52: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:30:52: #2 number of paired peaks: 1652 INFO @ Sun, 21 Jun 2020 21:30:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:52: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:30:52: #2 alternative fragment length(s) may be 91,563,570 bps INFO @ Sun, 21 Jun 2020 21:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:52: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:52: #2 You may need to consider one of the other alternative d(s): 91,563,570 WARNING @ Sun, 21 Jun 2020 21:30:52: #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 21:30:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226976/SRX5226976.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:04: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 5 millis CompletedMACS2peakCalling