Job ID = 6452933 SRX = SRX050600 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:48:30 prefetch.2.10.7: 1) Downloading 'SRR139082'... 2020-06-21T07:48:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:51:00 prefetch.2.10.7: 'SRR139082' is valid 2020-06-21T07:51:00 prefetch.2.10.7: 1) 'SRR139082' was downloaded successfully Read 8148551 spots for SRR139082/SRR139082.sra Written 8148551 spots for SRR139082/SRR139082.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 8148551 reads; of these: 8148551 (100.00%) were unpaired; of these: 403760 (4.95%) aligned 0 times 5638169 (69.19%) aligned exactly 1 time 2106622 (25.85%) aligned >1 times 95.05% 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] 954277 / 7744791 = 0.1232 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 16:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.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 16:55:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:55:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:55:11: 1000000 INFO @ Sun, 21 Jun 2020 16:55:15: 2000000 INFO @ Sun, 21 Jun 2020 16:55:19: 3000000 INFO @ Sun, 21 Jun 2020 16:55:24: 4000000 INFO @ Sun, 21 Jun 2020 16:55:28: 5000000 INFO @ Sun, 21 Jun 2020 16:55:33: 6000000 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 16:55:36: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:55:36: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:55:36: #1 total tags in treatment: 6790514 INFO @ Sun, 21 Jun 2020 16:55:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:55:36: #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 16:55:37: #1 tags after filtering in treatment: 6790513 INFO @ Sun, 21 Jun 2020 16:55:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:37: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.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 16:55:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:55:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:55:37: #2 number of paired peaks: 794 WARNING @ Sun, 21 Jun 2020 16:55:37: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Sun, 21 Jun 2020 16:55:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:37: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 16:55:37: #2 alternative fragment length(s) may be 4,31,566 bps INFO @ Sun, 21 Jun 2020 16:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.05_model.r WARNING @ Sun, 21 Jun 2020 16:55:37: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:55:37: #2 You may need to consider one of the other alternative d(s): 4,31,566 WARNING @ Sun, 21 Jun 2020 16:55:37: #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 16:55:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:55:41: 1000000 INFO @ Sun, 21 Jun 2020 16:55:45: 2000000 INFO @ Sun, 21 Jun 2020 16:55:49: 3000000 INFO @ Sun, 21 Jun 2020 16:55:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:54: 4000000 INFO @ Sun, 21 Jun 2020 16:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.05_summits.bed INFO @ Sun, 21 Jun 2020 16:55:57: Done! pass1 - making usageList (454 chroms): 2 millis pass2 - checking and writing primary data (2563 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:55:58: 5000000 INFO @ Sun, 21 Jun 2020 16:56:03: 6000000 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 16:56:06: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:56:06: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:56:06: #1 total tags in treatment: 6790514 INFO @ Sun, 21 Jun 2020 16:56:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:56:06: #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 16:56:06: #1 tags after filtering in treatment: 6790513 INFO @ Sun, 21 Jun 2020 16:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:56:06: #1 finished! INFO @ Sun, 21 Jun 2020 16:56:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.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 16:56:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:07: #2 number of paired peaks: 794 WARNING @ Sun, 21 Jun 2020 16:56:07: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Sun, 21 Jun 2020 16:56:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:56:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:56:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:56:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:56:07: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 16:56:07: #2 alternative fragment length(s) may be 4,31,566 bps INFO @ Sun, 21 Jun 2020 16:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.10_model.r WARNING @ Sun, 21 Jun 2020 16:56:07: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:56:07: #2 You may need to consider one of the other alternative d(s): 4,31,566 WARNING @ Sun, 21 Jun 2020 16:56:07: #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 16:56:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:56:11: 1000000 INFO @ Sun, 21 Jun 2020 16:56:15: 2000000 INFO @ Sun, 21 Jun 2020 16:56:19: 3000000 INFO @ Sun, 21 Jun 2020 16:56:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:56:24: 4000000 INFO @ Sun, 21 Jun 2020 16:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:56:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:56:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.10_summits.bed INFO @ Sun, 21 Jun 2020 16:56:27: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:56:28: 5000000 INFO @ Sun, 21 Jun 2020 16:56:32: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:56:36: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:56:36: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:56:36: #1 total tags in treatment: 6790514 INFO @ Sun, 21 Jun 2020 16:56:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:56:36: #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 16:56:36: #1 tags after filtering in treatment: 6790513 INFO @ Sun, 21 Jun 2020 16:56:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:56:36: #1 finished! INFO @ Sun, 21 Jun 2020 16:56:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:56:37: #2 number of paired peaks: 794 WARNING @ Sun, 21 Jun 2020 16:56:37: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Sun, 21 Jun 2020 16:56:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:56:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:56:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:56:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:56:37: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 16:56:37: #2 alternative fragment length(s) may be 4,31,566 bps INFO @ Sun, 21 Jun 2020 16:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.20_model.r WARNING @ Sun, 21 Jun 2020 16:56:37: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:56:37: #2 You may need to consider one of the other alternative d(s): 4,31,566 WARNING @ Sun, 21 Jun 2020 16:56:37: #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 16:56:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:56:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:56:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050600/SRX050600.20_summits.bed INFO @ Sun, 21 Jun 2020 16:56:57: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 3 millis CompletedMACS2peakCalling