Job ID = 6627433 SRX = SRX8521299 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: 00:08:51 52349346 reads; of these: 52349346 (100.00%) were unpaired; of these: 43656130 (83.39%) aligned 0 times 6311509 (12.06%) aligned exactly 1 time 2381707 (4.55%) aligned >1 times 16.61% overall alignment rate Time searching: 00:08:51 Overall time: 00:08:51 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] 1568143 / 8693216 = 0.1804 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 11:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.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 11:38:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:38:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:38:35: 1000000 INFO @ Tue, 14 Jul 2020 11:38:41: 2000000 INFO @ Tue, 14 Jul 2020 11:38:46: 3000000 INFO @ Tue, 14 Jul 2020 11:38:51: 4000000 INFO @ Tue, 14 Jul 2020 11:38:57: 5000000 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 11:39:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.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 11:39:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:39:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:39:02: 6000000 INFO @ Tue, 14 Jul 2020 11:39:06: 1000000 INFO @ Tue, 14 Jul 2020 11:39:08: 7000000 INFO @ Tue, 14 Jul 2020 11:39:09: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:39:09: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:39:09: #1 total tags in treatment: 7125073 INFO @ Tue, 14 Jul 2020 11:39:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:39:09: #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 11:39:09: #1 tags after filtering in treatment: 7124910 INFO @ Tue, 14 Jul 2020 11:39:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:39:09: #1 finished! INFO @ Tue, 14 Jul 2020 11:39:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:39:10: #2 number of paired peaks: 623 WARNING @ Tue, 14 Jul 2020 11:39:10: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Tue, 14 Jul 2020 11:39:10: start model_add_line... INFO @ Tue, 14 Jul 2020 11:39:10: start X-correlation... INFO @ Tue, 14 Jul 2020 11:39:10: end of X-cor INFO @ Tue, 14 Jul 2020 11:39:10: #2 finished! INFO @ Tue, 14 Jul 2020 11:39:10: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:39:10: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 11:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.05_model.r WARNING @ Tue, 14 Jul 2020 11:39:10: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:39:10: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 11:39:10: #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 11:39:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:39:13: 2000000 INFO @ Tue, 14 Jul 2020 11:39:19: 3000000 INFO @ Tue, 14 Jul 2020 11:39:25: 4000000 INFO @ Tue, 14 Jul 2020 11:39:25: #3 Call peaks for each chromosome... 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 11:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.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 11:39:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:39:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:39:31: 5000000 INFO @ Tue, 14 Jul 2020 11:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.05_summits.bed INFO @ Tue, 14 Jul 2020 11:39:33: Done! pass1 - making usageList (261 chroms): 1 millis pass2 - checking and writing primary data (1744 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:39:36: 1000000 INFO @ Tue, 14 Jul 2020 11:39:37: 6000000 INFO @ Tue, 14 Jul 2020 11:39:42: 2000000 INFO @ Tue, 14 Jul 2020 11:39:43: 7000000 INFO @ Tue, 14 Jul 2020 11:39:44: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:39:44: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:39:44: #1 total tags in treatment: 7125073 INFO @ Tue, 14 Jul 2020 11:39:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:39:44: #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 11:39:44: #1 tags after filtering in treatment: 7124910 INFO @ Tue, 14 Jul 2020 11:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:39:44: #1 finished! INFO @ Tue, 14 Jul 2020 11:39:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:39:45: #2 number of paired peaks: 623 WARNING @ Tue, 14 Jul 2020 11:39:45: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Tue, 14 Jul 2020 11:39:45: start model_add_line... INFO @ Tue, 14 Jul 2020 11:39:45: start X-correlation... INFO @ Tue, 14 Jul 2020 11:39:45: end of X-cor INFO @ Tue, 14 Jul 2020 11:39:45: #2 finished! INFO @ Tue, 14 Jul 2020 11:39:45: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:39:45: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 11:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.10_model.r WARNING @ Tue, 14 Jul 2020 11:39:45: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:39:45: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 11:39:45: #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 11:39:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:39:48: 3000000 INFO @ Tue, 14 Jul 2020 11:39:54: 4000000 INFO @ Tue, 14 Jul 2020 11:40:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:40:00: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:40:06: 6000000 INFO @ Tue, 14 Jul 2020 11:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:40:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:40:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.10_summits.bed INFO @ Tue, 14 Jul 2020 11:40:07: Done! pass1 - making usageList (156 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:40:12: 7000000 INFO @ Tue, 14 Jul 2020 11:40:13: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:40:13: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:40:13: #1 total tags in treatment: 7125073 INFO @ Tue, 14 Jul 2020 11:40:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:40:13: #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 11:40:14: #1 tags after filtering in treatment: 7124910 INFO @ Tue, 14 Jul 2020 11:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:40:14: #1 finished! INFO @ Tue, 14 Jul 2020 11:40:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:40:14: #2 number of paired peaks: 623 WARNING @ Tue, 14 Jul 2020 11:40:14: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Tue, 14 Jul 2020 11:40:14: start model_add_line... INFO @ Tue, 14 Jul 2020 11:40:14: start X-correlation... INFO @ Tue, 14 Jul 2020 11:40:14: end of X-cor INFO @ Tue, 14 Jul 2020 11:40:14: #2 finished! INFO @ Tue, 14 Jul 2020 11:40:14: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:40:14: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 11:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.20_model.r WARNING @ Tue, 14 Jul 2020 11:40:14: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:40:14: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 11:40:14: #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 11:40:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:40:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:40:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:40:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:40:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521299/SRX8521299.20_summits.bed INFO @ Tue, 14 Jul 2020 11:40:37: Done! pass1 - making usageList (98 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 4 millis CompletedMACS2peakCalling