Job ID = 6627434 SRX = SRX8521296 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: 00:08:12 56833069 reads; of these: 56833069 (100.00%) were unpaired; of these: 47346923 (83.31%) aligned 0 times 6955890 (12.24%) aligned exactly 1 time 2530256 (4.45%) aligned >1 times 16.69% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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] 1972301 / 9486146 = 0.2079 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 11:37:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.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 11:37:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:37:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:37:59: 1000000 INFO @ Tue, 14 Jul 2020 11:38:05: 2000000 INFO @ Tue, 14 Jul 2020 11:38:11: 3000000 INFO @ Tue, 14 Jul 2020 11:38:17: 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 11:38:23: 5000000 INFO @ Tue, 14 Jul 2020 11:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.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 11:38:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:38:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:38:29: 6000000 INFO @ Tue, 14 Jul 2020 11:38:30: 1000000 INFO @ Tue, 14 Jul 2020 11:38:36: 7000000 INFO @ Tue, 14 Jul 2020 11:38:36: 2000000 INFO @ Tue, 14 Jul 2020 11:38:39: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:38:39: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:38:39: #1 total tags in treatment: 7513845 INFO @ Tue, 14 Jul 2020 11:38:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:38:39: #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 11:38:40: #1 tags after filtering in treatment: 7513670 INFO @ Tue, 14 Jul 2020 11:38:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:38:40: #1 finished! INFO @ Tue, 14 Jul 2020 11:38:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:38:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:38:40: #2 number of paired peaks: 642 WARNING @ Tue, 14 Jul 2020 11:38:40: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Tue, 14 Jul 2020 11:38:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:38:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:38:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:38:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:38:40: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:38:40: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.05_model.r WARNING @ Tue, 14 Jul 2020 11:38:40: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:38:40: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:38:40: #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 11:38:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:38:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:38:43: 3000000 INFO @ Tue, 14 Jul 2020 11:38:49: 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 11:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.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 11:38:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:38:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:38:56: 5000000 INFO @ Tue, 14 Jul 2020 11:38:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:39:01: 1000000 INFO @ Tue, 14 Jul 2020 11:39:03: 6000000 INFO @ Tue, 14 Jul 2020 11:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.05_summits.bed INFO @ Tue, 14 Jul 2020 11:39:04: Done! pass1 - making usageList (295 chroms): 1 millis pass2 - checking and writing primary data (2296 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:39:08: 2000000 INFO @ Tue, 14 Jul 2020 11:39:10: 7000000 INFO @ Tue, 14 Jul 2020 11:39:14: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:39:14: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:39:14: #1 total tags in treatment: 7513845 INFO @ Tue, 14 Jul 2020 11:39:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:39:14: #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 11:39:14: 3000000 INFO @ Tue, 14 Jul 2020 11:39:14: #1 tags after filtering in treatment: 7513670 INFO @ Tue, 14 Jul 2020 11:39:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:39:14: #1 finished! INFO @ Tue, 14 Jul 2020 11:39:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:39:15: #2 number of paired peaks: 642 WARNING @ Tue, 14 Jul 2020 11:39:15: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Tue, 14 Jul 2020 11:39:15: start model_add_line... INFO @ Tue, 14 Jul 2020 11:39:15: start X-correlation... INFO @ Tue, 14 Jul 2020 11:39:15: end of X-cor INFO @ Tue, 14 Jul 2020 11:39:15: #2 finished! INFO @ Tue, 14 Jul 2020 11:39:15: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:39:15: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.10_model.r WARNING @ Tue, 14 Jul 2020 11:39:15: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:39:15: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:39:15: #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 11:39:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:39:21: 4000000 INFO @ Tue, 14 Jul 2020 11:39:28: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:39:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:39:35: 6000000 INFO @ Tue, 14 Jul 2020 11:39:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:39:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:39:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.10_summits.bed INFO @ Tue, 14 Jul 2020 11:39:39: Done! pass1 - making usageList (163 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:39:42: 7000000 INFO @ Tue, 14 Jul 2020 11:39:45: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:39:45: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:39:45: #1 total tags in treatment: 7513845 INFO @ Tue, 14 Jul 2020 11:39:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:39:45: #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 11:39:45: #1 tags after filtering in treatment: 7513670 INFO @ Tue, 14 Jul 2020 11:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:39:45: #1 finished! INFO @ Tue, 14 Jul 2020 11:39:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:39:46: #2 number of paired peaks: 642 WARNING @ Tue, 14 Jul 2020 11:39:46: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Tue, 14 Jul 2020 11:39:46: start model_add_line... INFO @ Tue, 14 Jul 2020 11:39:46: start X-correlation... INFO @ Tue, 14 Jul 2020 11:39:46: end of X-cor INFO @ Tue, 14 Jul 2020 11:39:46: #2 finished! INFO @ Tue, 14 Jul 2020 11:39:46: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:39:46: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.20_model.r WARNING @ Tue, 14 Jul 2020 11:39:46: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:39:46: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:39:46: #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 11:39:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:39:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:40:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521296/SRX8521296.20_summits.bed INFO @ Tue, 14 Jul 2020 11:40:10: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 4 millis CompletedMACS2peakCalling