Job ID = 6627448 SRX = SRX8521322 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:05:40 40938304 reads; of these: 40938304 (100.00%) were unpaired; of these: 36940588 (90.23%) aligned 0 times 3044792 (7.44%) aligned exactly 1 time 952924 (2.33%) aligned >1 times 9.77% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 461459 / 3997716 = 0.1154 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 @ Tue, 14 Jul 2020 11:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.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 @ Tue, 14 Jul 2020 11:39:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:39:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:39:24: 1000000 INFO @ Tue, 14 Jul 2020 11:39:29: 2000000 INFO @ Tue, 14 Jul 2020 11:39:35: 3000000 INFO @ Tue, 14 Jul 2020 11:39:38: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:39:38: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:39:38: #1 total tags in treatment: 3536257 INFO @ Tue, 14 Jul 2020 11:39:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:39:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:39:38: #1 tags after filtering in treatment: 3535997 INFO @ Tue, 14 Jul 2020 11:39:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:39:38: #1 finished! INFO @ Tue, 14 Jul 2020 11:39:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:39:39: #2 number of paired peaks: 799 WARNING @ Tue, 14 Jul 2020 11:39:39: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Tue, 14 Jul 2020 11:39:39: start model_add_line... INFO @ Tue, 14 Jul 2020 11:39:39: start X-correlation... INFO @ Tue, 14 Jul 2020 11:39:39: end of X-cor INFO @ Tue, 14 Jul 2020 11:39:39: #2 finished! INFO @ Tue, 14 Jul 2020 11:39:39: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 11:39:39: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 11:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.05_model.r WARNING @ Tue, 14 Jul 2020 11:39:39: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:39:39: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 11:39:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:39:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:39:47: #3 Call peaks for each chromosome... 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 @ Tue, 14 Jul 2020 11:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.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 @ Tue, 14 Jul 2020 11:39:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:39:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.05_summits.bed INFO @ Tue, 14 Jul 2020 11:39:51: Done! pass1 - making usageList (162 chroms): 0 millis pass2 - checking and writing primary data (830 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:39:55: 1000000 INFO @ Tue, 14 Jul 2020 11:40:01: 2000000 INFO @ Tue, 14 Jul 2020 11:40:07: 3000000 INFO @ Tue, 14 Jul 2020 11:40:11: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:40:11: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:40:11: #1 total tags in treatment: 3536257 INFO @ Tue, 14 Jul 2020 11:40:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:40:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:40:11: #1 tags after filtering in treatment: 3535997 INFO @ Tue, 14 Jul 2020 11:40:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:40:11: #1 finished! INFO @ Tue, 14 Jul 2020 11:40:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:40:12: #2 number of paired peaks: 799 WARNING @ Tue, 14 Jul 2020 11:40:12: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Tue, 14 Jul 2020 11:40:12: start model_add_line... INFO @ Tue, 14 Jul 2020 11:40:12: start X-correlation... INFO @ Tue, 14 Jul 2020 11:40:12: end of X-cor INFO @ Tue, 14 Jul 2020 11:40:12: #2 finished! INFO @ Tue, 14 Jul 2020 11:40:12: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 11:40:12: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 11:40:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.10_model.r WARNING @ Tue, 14 Jul 2020 11:40:12: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:40:12: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 11:40:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:40:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:40:12: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 14 Jul 2020 11:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.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 @ Tue, 14 Jul 2020 11:40:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:40:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:40:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.10_summits.bed INFO @ Tue, 14 Jul 2020 11:40:24: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:40:25: 1000000 INFO @ Tue, 14 Jul 2020 11:40:32: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:40:37: 3000000 INFO @ Tue, 14 Jul 2020 11:40:41: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:40:41: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:40:41: #1 total tags in treatment: 3536257 INFO @ Tue, 14 Jul 2020 11:40:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:40:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:40:41: #1 tags after filtering in treatment: 3535997 INFO @ Tue, 14 Jul 2020 11:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:40:41: #1 finished! INFO @ Tue, 14 Jul 2020 11:40:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:40:41: #2 number of paired peaks: 799 WARNING @ Tue, 14 Jul 2020 11:40:41: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Tue, 14 Jul 2020 11:40:41: start model_add_line... INFO @ Tue, 14 Jul 2020 11:40:41: start X-correlation... INFO @ Tue, 14 Jul 2020 11:40:41: end of X-cor INFO @ Tue, 14 Jul 2020 11:40:41: #2 finished! INFO @ Tue, 14 Jul 2020 11:40:41: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 11:40:41: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 11:40:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.20_model.r WARNING @ Tue, 14 Jul 2020 11:40:41: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:40:41: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 11:40:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:40:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:40:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:40:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521322/SRX8521322.20_summits.bed INFO @ Tue, 14 Jul 2020 11:40:53: Done! pass1 - making usageList (57 chroms): 0 millis pass2 - checking and writing primary data (89 records, 4 fields): 3 millis CompletedMACS2peakCalling