Job ID = 6456206 SRX = SRX330997 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:34 prefetch.2.10.7: 1) Downloading 'SRR947211'... 2020-06-21T10:33:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:02 prefetch.2.10.7: 'SRR947211' is valid 2020-06-21T10:34:02 prefetch.2.10.7: 1) 'SRR947211' was downloaded successfully Read 3024052 spots for SRR947211/SRR947211.sra Written 3024052 spots for SRR947211/SRR947211.sra 2020-06-21T10:34:21 prefetch.2.10.7: 1) Downloading 'SRR947212'... 2020-06-21T10:34:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:56 prefetch.2.10.7: 'SRR947212' is valid 2020-06-21T10:34:56 prefetch.2.10.7: 1) 'SRR947212' was downloaded successfully Read 5101822 spots for SRR947212/SRR947212.sra Written 5101822 spots for SRR947212/SRR947212.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: 00:01:19 8125874 reads; of these: 8125874 (100.00%) were unpaired; of these: 2210900 (27.21%) aligned 0 times 4262936 (52.46%) aligned exactly 1 time 1652038 (20.33%) aligned >1 times 72.79% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 568724 / 5914974 = 0.0961 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 19:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.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 19:38:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:10: 1000000 INFO @ Sun, 21 Jun 2020 19:38:14: 2000000 INFO @ Sun, 21 Jun 2020 19:38:18: 3000000 INFO @ Sun, 21 Jun 2020 19:38:23: 4000000 INFO @ Sun, 21 Jun 2020 19:38:28: 5000000 INFO @ Sun, 21 Jun 2020 19:38:29: #1 tag size is determined as 28 bps INFO @ Sun, 21 Jun 2020 19:38:29: #1 tag size = 28 INFO @ Sun, 21 Jun 2020 19:38:29: #1 total tags in treatment: 5346250 INFO @ Sun, 21 Jun 2020 19:38:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:29: #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 19:38:30: #1 tags after filtering in treatment: 5346092 INFO @ Sun, 21 Jun 2020 19:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:30: #2 number of paired peaks: 1049 INFO @ Sun, 21 Jun 2020 19:38:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:30: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:38:30: #2 alternative fragment length(s) may be 54,507,540 bps INFO @ Sun, 21 Jun 2020 19:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.05_model.r WARNING @ Sun, 21 Jun 2020 19:38:30: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:30: #2 You may need to consider one of the other alternative d(s): 54,507,540 WARNING @ Sun, 21 Jun 2020 19:38:30: #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 19:38:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:30: #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 19:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.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 19:38:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:40: 1000000 INFO @ Sun, 21 Jun 2020 19:38:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:44: 2000000 INFO @ Sun, 21 Jun 2020 19:38:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:48: Done! pass1 - making usageList (284 chroms): 1 millis pass2 - checking and writing primary data (1974 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:49: 3000000 INFO @ Sun, 21 Jun 2020 19:38:53: 4000000 INFO @ Sun, 21 Jun 2020 19:38:58: 5000000 INFO @ Sun, 21 Jun 2020 19:39:00: #1 tag size is determined as 28 bps INFO @ Sun, 21 Jun 2020 19:39:00: #1 tag size = 28 INFO @ Sun, 21 Jun 2020 19:39:00: #1 total tags in treatment: 5346250 INFO @ Sun, 21 Jun 2020 19:39:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:00: #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 19:39:00: #1 tags after filtering in treatment: 5346092 INFO @ Sun, 21 Jun 2020 19:39:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:01: #2 number of paired peaks: 1049 INFO @ Sun, 21 Jun 2020 19:39:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:01: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:39:01: #2 alternative fragment length(s) may be 54,507,540 bps INFO @ Sun, 21 Jun 2020 19:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.10_model.r WARNING @ Sun, 21 Jun 2020 19:39:01: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:01: #2 You may need to consider one of the other alternative d(s): 54,507,540 WARNING @ Sun, 21 Jun 2020 19:39:01: #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 19:39:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:01: #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 19:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.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 19:39:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:10: 1000000 INFO @ Sun, 21 Jun 2020 19:39:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:15: 2000000 INFO @ Sun, 21 Jun 2020 19:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.10_summits.bed INFO @ Sun, 21 Jun 2020 19:39:20: Done! pass1 - making usageList (213 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:20: 3000000 INFO @ Sun, 21 Jun 2020 19:39:25: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:39:31: 5000000 INFO @ Sun, 21 Jun 2020 19:39:33: #1 tag size is determined as 28 bps INFO @ Sun, 21 Jun 2020 19:39:33: #1 tag size = 28 INFO @ Sun, 21 Jun 2020 19:39:33: #1 total tags in treatment: 5346250 INFO @ Sun, 21 Jun 2020 19:39:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:33: #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 19:39:33: #1 tags after filtering in treatment: 5346092 INFO @ Sun, 21 Jun 2020 19:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:33: #2 number of paired peaks: 1049 INFO @ Sun, 21 Jun 2020 19:39:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:34: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:39:34: #2 alternative fragment length(s) may be 54,507,540 bps INFO @ Sun, 21 Jun 2020 19:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.20_model.r WARNING @ Sun, 21 Jun 2020 19:39:34: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:34: #2 You may need to consider one of the other alternative d(s): 54,507,540 WARNING @ Sun, 21 Jun 2020 19:39:34: #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 19:39:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX330997/SRX330997.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:52: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 3 millis CompletedMACS2peakCalling