Job ID = 6453119 SRX = SRX1032418 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:17:18 prefetch.2.10.7: 1) Downloading 'SRR2031919'... 2020-06-21T08:17:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:18:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:18:09 prefetch.2.10.7: 'SRR2031919' is valid 2020-06-21T08:18:09 prefetch.2.10.7: 1) 'SRR2031919' was downloaded successfully Read 6380089 spots for SRR2031919/SRR2031919.sra Written 6380089 spots for SRR2031919/SRR2031919.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: 00:01:45 6380089 reads; of these: 6380089 (100.00%) were unpaired; of these: 298661 (4.68%) aligned 0 times 3819467 (59.87%) aligned exactly 1 time 2261961 (35.45%) aligned >1 times 95.32% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 676579 / 6081428 = 0.1113 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 17:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.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 17:22:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:24: 1000000 INFO @ Sun, 21 Jun 2020 17:22:30: 2000000 INFO @ Sun, 21 Jun 2020 17:22:35: 3000000 INFO @ Sun, 21 Jun 2020 17:22:41: 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 17:22:48: 5000000 INFO @ Sun, 21 Jun 2020 17:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.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 17:22:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:50: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 17:22:50: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 17:22:50: #1 total tags in treatment: 5404849 INFO @ Sun, 21 Jun 2020 17:22:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:50: #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 17:22:51: #1 tags after filtering in treatment: 5404847 INFO @ Sun, 21 Jun 2020 17:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:51: #2 number of paired peaks: 1039 INFO @ Sun, 21 Jun 2020 17:22:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:51: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 17:22:51: #2 alternative fragment length(s) may be 4,37 bps INFO @ Sun, 21 Jun 2020 17:22:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.05_model.r WARNING @ Sun, 21 Jun 2020 17:22:52: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:52: #2 You may need to consider one of the other alternative d(s): 4,37 WARNING @ Sun, 21 Jun 2020 17:22:52: #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 17:22:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:54: 1000000 INFO @ Sun, 21 Jun 2020 17:22:59: 2000000 INFO @ Sun, 21 Jun 2020 17:23:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:05: 3000000 INFO @ Sun, 21 Jun 2020 17:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:08: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (2404 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:11: 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 17:23:17: 5000000 INFO @ Sun, 21 Jun 2020 17:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.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 17:23:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:20: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 17:23:20: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 17:23:20: #1 total tags in treatment: 5404849 INFO @ Sun, 21 Jun 2020 17:23:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:20: #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 17:23:21: #1 tags after filtering in treatment: 5404847 INFO @ Sun, 21 Jun 2020 17:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:21: #2 number of paired peaks: 1039 INFO @ Sun, 21 Jun 2020 17:23:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:21: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 17:23:21: #2 alternative fragment length(s) may be 4,37 bps INFO @ Sun, 21 Jun 2020 17:23:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.10_model.r WARNING @ Sun, 21 Jun 2020 17:23:21: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:23:21: #2 You may need to consider one of the other alternative d(s): 4,37 WARNING @ Sun, 21 Jun 2020 17:23:21: #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 17:23:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:24: 1000000 INFO @ Sun, 21 Jun 2020 17:23:30: 2000000 INFO @ Sun, 21 Jun 2020 17:23:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:36: 3000000 INFO @ Sun, 21 Jun 2020 17:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.10_summits.bed INFO @ Sun, 21 Jun 2020 17:23:38: Done! pass1 - making usageList (345 chroms): 2 millis pass2 - checking and writing primary data (786 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:42: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:23:48: 5000000 INFO @ Sun, 21 Jun 2020 17:23:51: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 17:23:51: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 17:23:51: #1 total tags in treatment: 5404849 INFO @ Sun, 21 Jun 2020 17:23:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:51: #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 17:23:51: #1 tags after filtering in treatment: 5404847 INFO @ Sun, 21 Jun 2020 17:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:52: #2 number of paired peaks: 1039 INFO @ Sun, 21 Jun 2020 17:23:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:52: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 17:23:52: #2 alternative fragment length(s) may be 4,37 bps INFO @ Sun, 21 Jun 2020 17:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.20_model.r WARNING @ Sun, 21 Jun 2020 17:23:52: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:23:52: #2 You may need to consider one of the other alternative d(s): 4,37 WARNING @ Sun, 21 Jun 2020 17:23:52: #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 17:23:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:24:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032418/SRX1032418.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:08: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 8 millis CompletedMACS2peakCalling