Job ID = 6454679 SRX = SRX2504295 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:23:44 prefetch.2.10.7: 1) Downloading 'SRR5188373'... 2020-06-21T09:23:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:24:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:24:03 prefetch.2.10.7: 'SRR5188373' is valid 2020-06-21T09:24:03 prefetch.2.10.7: 1) 'SRR5188373' was downloaded successfully 2020-06-21T09:24:08 prefetch.2.10.7: 'SRR5188373' has 0 unresolved dependencies Read 1489562 spots for SRR5188373/SRR5188373.sra Written 1489562 spots for SRR5188373/SRR5188373.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: 00:00:25 1489562 reads; of these: 1489562 (100.00%) were unpaired; of these: 2806 (0.19%) aligned 0 times 1414666 (94.97%) aligned exactly 1 time 72090 (4.84%) aligned >1 times 99.81% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 3052 / 1486756 = 0.0021 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 18:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.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 18:25:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:39: 1000000 INFO @ Sun, 21 Jun 2020 18:25:43: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:25:43: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:25:43: #1 total tags in treatment: 1483704 INFO @ Sun, 21 Jun 2020 18:25:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:25:43: #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 18:25:43: #1 tags after filtering in treatment: 1482896 INFO @ Sun, 21 Jun 2020 18:25:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:25:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:25:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:25:43: #2 number of paired peaks: 103 WARNING @ Sun, 21 Jun 2020 18:25:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Sun, 21 Jun 2020 18:25:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:25:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:25:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:25:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:25:43: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:25:43: #2 alternative fragment length(s) may be 53,313,373,521 bps INFO @ Sun, 21 Jun 2020 18:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.05_model.r WARNING @ Sun, 21 Jun 2020 18:25:43: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:25:43: #2 You may need to consider one of the other alternative d(s): 53,313,373,521 WARNING @ Sun, 21 Jun 2020 18:25:43: #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 18:25:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:25:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.05_summits.bed INFO @ Sun, 21 Jun 2020 18:25:49: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 18:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.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 18:26:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:11: 1000000 INFO @ Sun, 21 Jun 2020 18:26:15: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:26:15: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:26:15: #1 total tags in treatment: 1483704 INFO @ Sun, 21 Jun 2020 18:26:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:15: #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 18:26:16: #1 tags after filtering in treatment: 1482896 INFO @ Sun, 21 Jun 2020 18:26:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:16: #2 number of paired peaks: 103 WARNING @ Sun, 21 Jun 2020 18:26:16: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:16: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:26:16: #2 alternative fragment length(s) may be 53,313,373,521 bps INFO @ Sun, 21 Jun 2020 18:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.10_model.r WARNING @ Sun, 21 Jun 2020 18:26:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:16: #2 You may need to consider one of the other alternative d(s): 53,313,373,521 WARNING @ Sun, 21 Jun 2020 18:26:16: #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 18:26:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.10_summits.bed INFO @ Sun, 21 Jun 2020 18:26:21: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 18:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.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 18:26:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:39: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:26:43: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:26:43: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:26:43: #1 total tags in treatment: 1483704 INFO @ Sun, 21 Jun 2020 18:26:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:43: #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 18:26:43: #1 tags after filtering in treatment: 1482896 INFO @ Sun, 21 Jun 2020 18:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:43: #2 number of paired peaks: 103 WARNING @ Sun, 21 Jun 2020 18:26:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:43: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:26:43: #2 alternative fragment length(s) may be 53,313,373,521 bps INFO @ Sun, 21 Jun 2020 18:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.20_model.r WARNING @ Sun, 21 Jun 2020 18:26:43: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:43: #2 You may need to consider one of the other alternative d(s): 53,313,373,521 WARNING @ Sun, 21 Jun 2020 18:26:43: #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 18:26:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:26:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2504295/SRX2504295.20_summits.bed INFO @ Sun, 21 Jun 2020 18:26:48: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling