Job ID = 6627756 SRX = SRX8521403 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: 00:07:20 54172612 reads; of these: 54172612 (100.00%) were unpaired; of these: 48420278 (89.38%) aligned 0 times 4313282 (7.96%) aligned exactly 1 time 1439052 (2.66%) aligned >1 times 10.62% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 785207 / 5752334 = 0.1365 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 13:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.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 13:12:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:12:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:12:32: 1000000 INFO @ Tue, 14 Jul 2020 13:12:38: 2000000 INFO @ Tue, 14 Jul 2020 13:12:44: 3000000 INFO @ Tue, 14 Jul 2020 13:12:50: 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 @ Tue, 14 Jul 2020 13:12:56: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 13:12:56: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 13:12:56: #1 total tags in treatment: 4967127 INFO @ Tue, 14 Jul 2020 13:12:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:12:56: #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 13:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.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 13:12:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:12:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:12:56: #1 tags after filtering in treatment: 4966910 INFO @ Tue, 14 Jul 2020 13:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:12:56: #1 finished! INFO @ Tue, 14 Jul 2020 13:12:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:12:57: #2 number of paired peaks: 775 WARNING @ Tue, 14 Jul 2020 13:12:57: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Tue, 14 Jul 2020 13:12:57: start model_add_line... INFO @ Tue, 14 Jul 2020 13:12:57: start X-correlation... INFO @ Tue, 14 Jul 2020 13:12:57: end of X-cor INFO @ Tue, 14 Jul 2020 13:12:57: #2 finished! INFO @ Tue, 14 Jul 2020 13:12:57: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 13:12:57: #2 alternative fragment length(s) may be 60,546 bps INFO @ Tue, 14 Jul 2020 13:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.05_model.r WARNING @ Tue, 14 Jul 2020 13:12:57: #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 13:12:57: #2 You may need to consider one of the other alternative d(s): 60,546 WARNING @ Tue, 14 Jul 2020 13:12:57: #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 13:12:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:13:02: 1000000 INFO @ Tue, 14 Jul 2020 13:13:07: 2000000 INFO @ Tue, 14 Jul 2020 13:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:13:12: 3000000 INFO @ Tue, 14 Jul 2020 13:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.05_peaks.xls INFO @ Tue, 14 Jul 2020 13:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.05_summits.bed INFO @ Tue, 14 Jul 2020 13:13:13: Done! pass1 - making usageList (193 chroms): 1 millis pass2 - checking and writing primary data (997 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:13:17: 4000000 INFO @ Tue, 14 Jul 2020 13:13:23: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 13:13:23: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 13:13:23: #1 total tags in treatment: 4967127 INFO @ Tue, 14 Jul 2020 13:13:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:13:23: #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 13:13:24: #1 tags after filtering in treatment: 4966910 INFO @ Tue, 14 Jul 2020 13:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:13:24: #1 finished! INFO @ Tue, 14 Jul 2020 13:13:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:13:24: #2 number of paired peaks: 775 WARNING @ Tue, 14 Jul 2020 13:13:24: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Tue, 14 Jul 2020 13:13:24: start model_add_line... INFO @ Tue, 14 Jul 2020 13:13:24: start X-correlation... INFO @ Tue, 14 Jul 2020 13:13:24: end of X-cor INFO @ Tue, 14 Jul 2020 13:13:24: #2 finished! INFO @ Tue, 14 Jul 2020 13:13:24: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 13:13:24: #2 alternative fragment length(s) may be 60,546 bps INFO @ Tue, 14 Jul 2020 13:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.10_model.r WARNING @ Tue, 14 Jul 2020 13:13:24: #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 13:13:24: #2 You may need to consider one of the other alternative d(s): 60,546 WARNING @ Tue, 14 Jul 2020 13:13:24: #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 13:13:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:13:24: #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 13:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.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 13:13:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:13:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:13:32: 1000000 INFO @ Tue, 14 Jul 2020 13:13:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:13:38: 2000000 INFO @ Tue, 14 Jul 2020 13:13:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.10_peaks.xls INFO @ Tue, 14 Jul 2020 13:13:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:13:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.10_summits.bed INFO @ Tue, 14 Jul 2020 13:13:41: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:13:44: 3000000 INFO @ Tue, 14 Jul 2020 13:13:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 13:13:56: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 13:13:56: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 13:13:56: #1 total tags in treatment: 4967127 INFO @ Tue, 14 Jul 2020 13:13:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:13:56: #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 13:13:57: #1 tags after filtering in treatment: 4966910 INFO @ Tue, 14 Jul 2020 13:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:13:57: #1 finished! INFO @ Tue, 14 Jul 2020 13:13:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:13:57: #2 number of paired peaks: 775 WARNING @ Tue, 14 Jul 2020 13:13:57: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Tue, 14 Jul 2020 13:13:57: start model_add_line... INFO @ Tue, 14 Jul 2020 13:13:57: start X-correlation... INFO @ Tue, 14 Jul 2020 13:13:57: end of X-cor INFO @ Tue, 14 Jul 2020 13:13:57: #2 finished! INFO @ Tue, 14 Jul 2020 13:13:57: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 13:13:57: #2 alternative fragment length(s) may be 60,546 bps INFO @ Tue, 14 Jul 2020 13:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.20_model.r WARNING @ Tue, 14 Jul 2020 13:13:57: #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 13:13:57: #2 You may need to consider one of the other alternative d(s): 60,546 WARNING @ Tue, 14 Jul 2020 13:13:57: #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 13:13:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:13:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 13:14:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.20_peaks.xls INFO @ Tue, 14 Jul 2020 13:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521403/SRX8521403.20_summits.bed INFO @ Tue, 14 Jul 2020 13:14:13: Done! pass1 - making usageList (79 chroms): 0 millis pass2 - checking and writing primary data (138 records, 4 fields): 3 millis CompletedMACS2peakCalling