Job ID = 6627763 SRX = SRX8521400 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: 00:07:17 49211387 reads; of these: 49211387 (100.00%) were unpaired; of these: 39090683 (79.43%) aligned 0 times 7518114 (15.28%) aligned exactly 1 time 2602590 (5.29%) aligned >1 times 20.57% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 1758945 / 10120704 = 0.1738 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 13:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.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 13:16:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:16:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:16:29: 1000000 INFO @ Tue, 14 Jul 2020 13:16:36: 2000000 INFO @ Tue, 14 Jul 2020 13:16:42: 3000000 INFO @ Tue, 14 Jul 2020 13:16:48: 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 13:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.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 13:16:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:16:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:16:54: 5000000 INFO @ Tue, 14 Jul 2020 13:17:00: 1000000 INFO @ Tue, 14 Jul 2020 13:17:01: 6000000 INFO @ Tue, 14 Jul 2020 13:17:06: 2000000 INFO @ Tue, 14 Jul 2020 13:17:07: 7000000 INFO @ Tue, 14 Jul 2020 13:17:12: 3000000 INFO @ Tue, 14 Jul 2020 13:17:14: 8000000 INFO @ Tue, 14 Jul 2020 13:17:17: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 13:17:17: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 13:17:17: #1 total tags in treatment: 8361759 INFO @ Tue, 14 Jul 2020 13:17:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:17:17: #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 13:17:17: #1 tags after filtering in treatment: 8361614 INFO @ Tue, 14 Jul 2020 13:17:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:17:17: #1 finished! INFO @ Tue, 14 Jul 2020 13:17:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:17:17: #2 number of paired peaks: 458 WARNING @ Tue, 14 Jul 2020 13:17:17: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Tue, 14 Jul 2020 13:17:17: start model_add_line... INFO @ Tue, 14 Jul 2020 13:17:18: start X-correlation... INFO @ Tue, 14 Jul 2020 13:17:18: end of X-cor INFO @ Tue, 14 Jul 2020 13:17:18: #2 finished! INFO @ Tue, 14 Jul 2020 13:17:18: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 13:17:18: #2 alternative fragment length(s) may be 4,48,532,552,565 bps INFO @ Tue, 14 Jul 2020 13:17:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.05_model.r WARNING @ Tue, 14 Jul 2020 13:17:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:17:18: #2 You may need to consider one of the other alternative d(s): 4,48,532,552,565 WARNING @ Tue, 14 Jul 2020 13:17:18: #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 13:17:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:17:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:17:19: 4000000 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 13:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.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 13:17:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:17:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:17:25: 5000000 INFO @ Tue, 14 Jul 2020 13:17:30: 1000000 INFO @ Tue, 14 Jul 2020 13:17:31: 6000000 INFO @ Tue, 14 Jul 2020 13:17:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:17:36: 2000000 INFO @ Tue, 14 Jul 2020 13:17:38: 7000000 INFO @ Tue, 14 Jul 2020 13:17:42: 3000000 INFO @ Tue, 14 Jul 2020 13:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.05_peaks.xls INFO @ Tue, 14 Jul 2020 13:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.05_summits.bed INFO @ Tue, 14 Jul 2020 13:17:42: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (1109 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:17:45: 8000000 INFO @ Tue, 14 Jul 2020 13:17:47: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 13:17:47: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 13:17:47: #1 total tags in treatment: 8361759 INFO @ Tue, 14 Jul 2020 13:17:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:17:47: #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 13:17:48: #1 tags after filtering in treatment: 8361614 INFO @ Tue, 14 Jul 2020 13:17:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:17:48: #1 finished! INFO @ Tue, 14 Jul 2020 13:17:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:17:48: 4000000 INFO @ Tue, 14 Jul 2020 13:17:48: #2 number of paired peaks: 458 WARNING @ Tue, 14 Jul 2020 13:17:48: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Tue, 14 Jul 2020 13:17:48: start model_add_line... INFO @ Tue, 14 Jul 2020 13:17:48: start X-correlation... INFO @ Tue, 14 Jul 2020 13:17:48: end of X-cor INFO @ Tue, 14 Jul 2020 13:17:48: #2 finished! INFO @ Tue, 14 Jul 2020 13:17:48: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 13:17:48: #2 alternative fragment length(s) may be 4,48,532,552,565 bps INFO @ Tue, 14 Jul 2020 13:17:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.10_model.r WARNING @ Tue, 14 Jul 2020 13:17:48: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:17:48: #2 You may need to consider one of the other alternative d(s): 4,48,532,552,565 WARNING @ Tue, 14 Jul 2020 13:17:48: #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 13:17:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:17:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:17:54: 5000000 INFO @ Tue, 14 Jul 2020 13:17:59: 6000000 INFO @ Tue, 14 Jul 2020 13:18:05: 7000000 INFO @ Tue, 14 Jul 2020 13:18:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 13:18:10: 8000000 INFO @ Tue, 14 Jul 2020 13:18:12: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 13:18:12: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 13:18:12: #1 total tags in treatment: 8361759 INFO @ Tue, 14 Jul 2020 13:18:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:18:12: #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 13:18:13: #1 tags after filtering in treatment: 8361614 INFO @ Tue, 14 Jul 2020 13:18:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:18:13: #1 finished! INFO @ Tue, 14 Jul 2020 13:18:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:18:13: #2 number of paired peaks: 458 WARNING @ Tue, 14 Jul 2020 13:18:13: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Tue, 14 Jul 2020 13:18:13: start model_add_line... INFO @ Tue, 14 Jul 2020 13:18:13: start X-correlation... INFO @ Tue, 14 Jul 2020 13:18:13: end of X-cor INFO @ Tue, 14 Jul 2020 13:18:13: #2 finished! INFO @ Tue, 14 Jul 2020 13:18:13: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 13:18:13: #2 alternative fragment length(s) may be 4,48,532,552,565 bps INFO @ Tue, 14 Jul 2020 13:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.20_model.r WARNING @ Tue, 14 Jul 2020 13:18:13: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:18:13: #2 You may need to consider one of the other alternative d(s): 4,48,532,552,565 WARNING @ Tue, 14 Jul 2020 13:18:13: #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 13:18:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:18:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.10_peaks.xls INFO @ Tue, 14 Jul 2020 13:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.10_summits.bed INFO @ Tue, 14 Jul 2020 13:18:14: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 13:18:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:18:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.20_peaks.xls INFO @ Tue, 14 Jul 2020 13:18:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:18:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521400/SRX8521400.20_summits.bed INFO @ Tue, 14 Jul 2020 13:18:39: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 11 millis CompletedMACS2peakCalling