Job ID = 6456004 SRX = SRX315135 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:23:36 prefetch.2.10.7: 1) Downloading 'SRR922191'... 2020-06-21T10:23:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:05 prefetch.2.10.7: 'SRR922191' is valid 2020-06-21T10:26:05 prefetch.2.10.7: 1) 'SRR922191' was downloaded successfully 2020-06-21T10:26:05 prefetch.2.10.7: 'SRR922191' has 0 unresolved dependencies Read 4607828 spots for SRR922191/SRR922191.sra Written 4607828 spots for SRR922191/SRR922191.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:12 4607828 reads; of these: 4607828 (100.00%) were unpaired; of these: 399413 (8.67%) aligned 0 times 3307410 (71.78%) aligned exactly 1 time 901005 (19.55%) aligned >1 times 91.33% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 1243174 / 4208415 = 0.2954 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 19:32:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.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 19:32:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:30: 1000000 INFO @ Sun, 21 Jun 2020 19:32:38: 2000000 INFO @ Sun, 21 Jun 2020 19:32:47: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 19:32:47: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 19:32:47: #1 total tags in treatment: 2965241 INFO @ Sun, 21 Jun 2020 19:32:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:47: #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 19:32:47: #1 tags after filtering in treatment: 2964931 INFO @ Sun, 21 Jun 2020 19:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:48: #2 number of paired peaks: 4821 INFO @ Sun, 21 Jun 2020 19:32:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:48: #2 predicted fragment length is 209 bps INFO @ Sun, 21 Jun 2020 19:32:48: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 21 Jun 2020 19:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.05_model.r WARNING @ Sun, 21 Jun 2020 19:32:48: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:32:48: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sun, 21 Jun 2020 19:32:48: #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 19:32:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:48: #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 19:32:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.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 19:32:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:59: 1000000 INFO @ Sun, 21 Jun 2020 19:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.05_summits.bed INFO @ Sun, 21 Jun 2020 19:33:01: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (5447 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:08: 2000000 INFO @ Sun, 21 Jun 2020 19:33:16: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 19:33:16: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 19:33:16: #1 total tags in treatment: 2965241 INFO @ Sun, 21 Jun 2020 19:33:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:16: #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 19:33:17: #1 tags after filtering in treatment: 2964931 INFO @ Sun, 21 Jun 2020 19:33:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:17: #2 number of paired peaks: 4821 INFO @ Sun, 21 Jun 2020 19:33:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:17: #2 predicted fragment length is 209 bps INFO @ Sun, 21 Jun 2020 19:33:17: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 21 Jun 2020 19:33:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.10_model.r WARNING @ Sun, 21 Jun 2020 19:33:17: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:17: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sun, 21 Jun 2020 19:33:17: #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 19:33:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:17: #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 19:33:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.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 19:33:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:29: 1000000 INFO @ Sun, 21 Jun 2020 19:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.10_summits.bed INFO @ Sun, 21 Jun 2020 19:33:30: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (4114 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:33:40: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:33:51: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 19:33:51: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 19:33:51: #1 total tags in treatment: 2965241 INFO @ Sun, 21 Jun 2020 19:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:51: #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 19:33:52: #1 tags after filtering in treatment: 2964931 INFO @ Sun, 21 Jun 2020 19:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:52: #2 number of paired peaks: 4821 INFO @ Sun, 21 Jun 2020 19:33:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:52: #2 predicted fragment length is 209 bps INFO @ Sun, 21 Jun 2020 19:33:52: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 21 Jun 2020 19:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.20_model.r WARNING @ Sun, 21 Jun 2020 19:33:52: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:52: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sun, 21 Jun 2020 19:33:52: #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 19:33:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX315135/SRX315135.20_summits.bed INFO @ Sun, 21 Jun 2020 19:34:05: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (2819 records, 4 fields): 5 millis CompletedMACS2peakCalling