Job ID = 6509074 SRX = SRX645117 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:10:58 prefetch.2.10.7: 1) Downloading 'SRR1505717'... 2020-06-26T15:10:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:15:10 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:15:10 prefetch.2.10.7: 1) 'SRR1505717' was downloaded successfully Read 22213587 spots for SRR1505717/SRR1505717.sra Written 22213587 spots for SRR1505717/SRR1505717.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: 00:06:18 22213587 reads; of these: 22213587 (100.00%) were unpaired; of these: 14963678 (67.36%) aligned 0 times 5986690 (26.95%) aligned exactly 1 time 1263219 (5.69%) aligned >1 times 32.64% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 3967269 / 7249909 = 0.5472 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 @ Sat, 27 Jun 2020 00:25:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.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 @ Sat, 27 Jun 2020 00:25:26: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:27: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:34: 1000000 INFO @ Sat, 27 Jun 2020 00:25:41: 2000000 INFO @ Sat, 27 Jun 2020 00:25:48: 3000000 INFO @ Sat, 27 Jun 2020 00:25:50: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:25:50: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:25:50: #1 total tags in treatment: 3282640 INFO @ Sat, 27 Jun 2020 00:25:50: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:25:50: #1 tags after filtering in treatment: 3282523 INFO @ Sat, 27 Jun 2020 00:25:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:25:50: #1 finished! INFO @ Sat, 27 Jun 2020 00:25:50: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:25:50: #2 number of paired peaks: 3937 INFO @ Sat, 27 Jun 2020 00:25:50: start model_add_line... INFO @ Sat, 27 Jun 2020 00:25:50: start X-correlation... INFO @ Sat, 27 Jun 2020 00:25:50: end of X-cor INFO @ Sat, 27 Jun 2020 00:25:50: #2 finished! INFO @ Sat, 27 Jun 2020 00:25:50: #2 predicted fragment length is 130 bps INFO @ Sat, 27 Jun 2020 00:25:50: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 27 Jun 2020 00:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.05_model.r WARNING @ Sat, 27 Jun 2020 00:25:50: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:25:50: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sat, 27 Jun 2020 00:25:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:25:50: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:25:50: #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 @ Sat, 27 Jun 2020 00:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.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 @ Sat, 27 Jun 2020 00:25:57: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:57: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:58: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.05_summits.bed INFO @ Sat, 27 Jun 2020 00:26:02: Done! pass1 - making usageList (444 chroms): 1 millis pass2 - checking and writing primary data (5289 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:26:05: 1000000 INFO @ Sat, 27 Jun 2020 00:26:13: 2000000 INFO @ Sat, 27 Jun 2020 00:26:22: 3000000 INFO @ Sat, 27 Jun 2020 00:26:25: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:26:25: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:26:25: #1 total tags in treatment: 3282640 INFO @ Sat, 27 Jun 2020 00:26:25: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 @ Sat, 27 Jun 2020 00:26:25: #1 tags after filtering in treatment: 3282523 INFO @ Sat, 27 Jun 2020 00:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:25: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:25: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:25: #2 number of paired peaks: 3937 INFO @ Sat, 27 Jun 2020 00:26:25: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:25: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:25: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:25: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:25: #2 predicted fragment length is 130 bps INFO @ Sat, 27 Jun 2020 00:26:25: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 27 Jun 2020 00:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.10_model.r WARNING @ Sat, 27 Jun 2020 00:26:25: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:26:25: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sat, 27 Jun 2020 00:26:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:26:25: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.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 @ Sat, 27 Jun 2020 00:26:27: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:26:27: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:26:33: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:26:35: 1000000 INFO @ Sat, 27 Jun 2020 00:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.10_summits.bed INFO @ Sat, 27 Jun 2020 00:26:37: Done! pass1 - making usageList (270 chroms): 1 millis pass2 - checking and writing primary data (2333 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:26:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:26:52: 3000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:26:55: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:26:55: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:26:55: #1 total tags in treatment: 3282640 INFO @ Sat, 27 Jun 2020 00:26:55: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:55: #1 tags after filtering in treatment: 3282523 INFO @ Sat, 27 Jun 2020 00:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:55: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:55: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:55: #2 number of paired peaks: 3937 INFO @ Sat, 27 Jun 2020 00:26:55: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:55: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:55: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:55: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:55: #2 predicted fragment length is 130 bps INFO @ Sat, 27 Jun 2020 00:26:55: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 27 Jun 2020 00:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.20_model.r WARNING @ Sat, 27 Jun 2020 00:26:55: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:26:55: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sat, 27 Jun 2020 00:26:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:26:55: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645117/SRX645117.20_summits.bed INFO @ Sat, 27 Jun 2020 00:27:07: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (495 records, 4 fields): 5 millis CompletedMACS2peakCalling