Job ID = 6456505 SRX = SRX3511953 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:14:24 prefetch.2.10.7: 1) Downloading 'SRR6418938'... 2020-06-21T11:14:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:13 prefetch.2.10.7: 'SRR6418938' is valid 2020-06-21T11:16:13 prefetch.2.10.7: 1) 'SRR6418938' was downloaded successfully 2020-06-21T11:16:13 prefetch.2.10.7: 'SRR6418938' has 0 unresolved dependencies Read 6329909 spots for SRR6418938/SRR6418938.sra Written 6329909 spots for SRR6418938/SRR6418938.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: 00:02:56 6329909 reads; of these: 6329909 (100.00%) were unpaired; of these: 655664 (10.36%) aligned 0 times 4053363 (64.04%) aligned exactly 1 time 1620882 (25.61%) aligned >1 times 89.64% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 663201 / 5674245 = 0.1169 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 20:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.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 20:22:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:07: 1000000 INFO @ Sun, 21 Jun 2020 20:22:14: 2000000 INFO @ Sun, 21 Jun 2020 20:22:21: 3000000 INFO @ Sun, 21 Jun 2020 20:22:28: 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 20:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.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 20:22:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:36: 5000000 INFO @ Sun, 21 Jun 2020 20:22:36: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:22:36: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:22:36: #1 total tags in treatment: 5011044 INFO @ Sun, 21 Jun 2020 20:22:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:22:36: #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 20:22:36: #1 tags after filtering in treatment: 5011028 INFO @ Sun, 21 Jun 2020 20:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:22:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:22:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:22:37: #2 number of paired peaks: 583 WARNING @ Sun, 21 Jun 2020 20:22:37: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sun, 21 Jun 2020 20:22:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:22:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:22:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:22:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:22:37: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 20:22:37: #2 alternative fragment length(s) may be 4,117,536,561,588 bps INFO @ Sun, 21 Jun 2020 20:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.05_model.r WARNING @ Sun, 21 Jun 2020 20:22:37: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:22:37: #2 You may need to consider one of the other alternative d(s): 4,117,536,561,588 WARNING @ Sun, 21 Jun 2020 20:22:37: #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 20:22:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:22:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:22:38: 1000000 INFO @ Sun, 21 Jun 2020 20:22:45: 2000000 INFO @ Sun, 21 Jun 2020 20:22:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:22:52: 3000000 INFO @ Sun, 21 Jun 2020 20:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.05_summits.bed INFO @ Sun, 21 Jun 2020 20:22:53: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (1089 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sun, 21 Jun 2020 20:22:59: 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 20:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.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 20:23:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:07: 5000000 INFO @ Sun, 21 Jun 2020 20:23:07: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:23:07: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:23:07: #1 total tags in treatment: 5011044 INFO @ Sun, 21 Jun 2020 20:23:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:07: #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 20:23:07: #1 tags after filtering in treatment: 5011028 INFO @ Sun, 21 Jun 2020 20:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:08: #2 number of paired peaks: 583 WARNING @ Sun, 21 Jun 2020 20:23:08: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sun, 21 Jun 2020 20:23:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:08: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 20:23:08: #2 alternative fragment length(s) may be 4,117,536,561,588 bps INFO @ Sun, 21 Jun 2020 20:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.10_model.r WARNING @ Sun, 21 Jun 2020 20:23:08: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:23:08: #2 You may need to consider one of the other alternative d(s): 4,117,536,561,588 WARNING @ Sun, 21 Jun 2020 20:23:08: #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 20:23:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:08: 1000000 INFO @ Sun, 21 Jun 2020 20:23:15: 2000000 INFO @ Sun, 21 Jun 2020 20:23:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:22: 3000000 INFO @ Sun, 21 Jun 2020 20:23:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.10_summits.bed INFO @ Sun, 21 Jun 2020 20:23:24: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:23:29: 4000000 INFO @ Sun, 21 Jun 2020 20:23:37: 5000000 INFO @ Sun, 21 Jun 2020 20:23:37: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:23:37: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:23:37: #1 total tags in treatment: 5011044 INFO @ Sun, 21 Jun 2020 20:23:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:37: #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 20:23:37: #1 tags after filtering in treatment: 5011028 INFO @ Sun, 21 Jun 2020 20:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:37: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:37: #2 number of paired peaks: 583 WARNING @ Sun, 21 Jun 2020 20:23:37: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sun, 21 Jun 2020 20:23:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:37: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 20:23:37: #2 alternative fragment length(s) may be 4,117,536,561,588 bps INFO @ Sun, 21 Jun 2020 20:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.20_model.r WARNING @ Sun, 21 Jun 2020 20:23:37: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:23:37: #2 You may need to consider one of the other alternative d(s): 4,117,536,561,588 WARNING @ Sun, 21 Jun 2020 20:23:37: #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 20:23:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:23:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511953/SRX3511953.20_summits.bed INFO @ Sun, 21 Jun 2020 20:23:54: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 5 millis CompletedMACS2peakCalling