Job ID = 6530005 SRX = SRX6386732 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: 00:04:36 16943864 reads; of these: 16943864 (100.00%) were unpaired; of these: 1425851 (8.42%) aligned 0 times 11142424 (65.76%) aligned exactly 1 time 4375589 (25.82%) aligned >1 times 91.58% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4232186 / 15518013 = 0.2727 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, 30 Jun 2020 03:22:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.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, 30 Jun 2020 03:22:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:29: 1000000 INFO @ Tue, 30 Jun 2020 03:22:36: 2000000 INFO @ Tue, 30 Jun 2020 03:22:42: 3000000 INFO @ Tue, 30 Jun 2020 03:22:49: 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, 30 Jun 2020 03:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.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, 30 Jun 2020 03:22:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:57: 5000000 INFO @ Tue, 30 Jun 2020 03:22:59: 1000000 INFO @ Tue, 30 Jun 2020 03:23:04: 6000000 INFO @ Tue, 30 Jun 2020 03:23:06: 2000000 INFO @ Tue, 30 Jun 2020 03:23:12: 7000000 INFO @ Tue, 30 Jun 2020 03:23:13: 3000000 INFO @ Tue, 30 Jun 2020 03:23:19: 8000000 INFO @ Tue, 30 Jun 2020 03:23:20: 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, 30 Jun 2020 03:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.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, 30 Jun 2020 03:23:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:27: 5000000 INFO @ Tue, 30 Jun 2020 03:23:27: 9000000 INFO @ Tue, 30 Jun 2020 03:23:29: 1000000 INFO @ Tue, 30 Jun 2020 03:23:34: 6000000 INFO @ Tue, 30 Jun 2020 03:23:35: 10000000 INFO @ Tue, 30 Jun 2020 03:23:36: 2000000 INFO @ Tue, 30 Jun 2020 03:23:41: 7000000 INFO @ Tue, 30 Jun 2020 03:23:43: 11000000 INFO @ Tue, 30 Jun 2020 03:23:43: 3000000 INFO @ Tue, 30 Jun 2020 03:23:45: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:23:45: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:23:45: #1 total tags in treatment: 11285827 INFO @ Tue, 30 Jun 2020 03:23:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:23:45: #1 tags after filtering in treatment: 11285816 INFO @ Tue, 30 Jun 2020 03:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:45: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:46: #2 number of paired peaks: 958 WARNING @ Tue, 30 Jun 2020 03:23:46: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:46: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:46: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:46: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:46: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:46: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 03:23:46: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 03:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.05_model.r WARNING @ Tue, 30 Jun 2020 03:23:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:23:46: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 03:23:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:23:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:23:48: 8000000 INFO @ Tue, 30 Jun 2020 03:23:50: 4000000 INFO @ Tue, 30 Jun 2020 03:23:55: 9000000 INFO @ Tue, 30 Jun 2020 03:23:57: 5000000 INFO @ Tue, 30 Jun 2020 03:24:02: 10000000 INFO @ Tue, 30 Jun 2020 03:24:04: 6000000 INFO @ Tue, 30 Jun 2020 03:24:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:09: 11000000 INFO @ Tue, 30 Jun 2020 03:24:10: 7000000 INFO @ Tue, 30 Jun 2020 03:24:10: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:24:10: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:24:10: #1 total tags in treatment: 11285827 INFO @ Tue, 30 Jun 2020 03:24:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:24:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:24:11: #1 tags after filtering in treatment: 11285816 INFO @ Tue, 30 Jun 2020 03:24:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:24:11: #1 finished! INFO @ Tue, 30 Jun 2020 03:24:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:24:12: #2 number of paired peaks: 958 WARNING @ Tue, 30 Jun 2020 03:24:12: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Tue, 30 Jun 2020 03:24:12: start model_add_line... INFO @ Tue, 30 Jun 2020 03:24:12: start X-correlation... INFO @ Tue, 30 Jun 2020 03:24:12: end of X-cor INFO @ Tue, 30 Jun 2020 03:24:12: #2 finished! INFO @ Tue, 30 Jun 2020 03:24:12: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 03:24:12: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 03:24:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.10_model.r WARNING @ Tue, 30 Jun 2020 03:24:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:24:12: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 03:24:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:24:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:24:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:24:16: 8000000 INFO @ Tue, 30 Jun 2020 03:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.05_summits.bed INFO @ Tue, 30 Jun 2020 03:24:19: Done! pass1 - making usageList (626 chroms): 2 millis pass2 - checking and writing primary data (2488 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:24:23: 9000000 INFO @ Tue, 30 Jun 2020 03:24:29: 10000000 INFO @ Tue, 30 Jun 2020 03:24:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:35: 11000000 INFO @ Tue, 30 Jun 2020 03:24:36: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:24:36: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:24:36: #1 total tags in treatment: 11285827 INFO @ Tue, 30 Jun 2020 03:24:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:24:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:24:37: #1 tags after filtering in treatment: 11285816 INFO @ Tue, 30 Jun 2020 03:24:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:24:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:24:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:24:37: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:24:38: #2 number of paired peaks: 958 WARNING @ Tue, 30 Jun 2020 03:24:38: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Tue, 30 Jun 2020 03:24:38: start model_add_line... INFO @ Tue, 30 Jun 2020 03:24:38: start X-correlation... INFO @ Tue, 30 Jun 2020 03:24:38: end of X-cor INFO @ Tue, 30 Jun 2020 03:24:38: #2 finished! INFO @ Tue, 30 Jun 2020 03:24:38: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 03:24:38: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 03:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.20_model.r WARNING @ Tue, 30 Jun 2020 03:24:38: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:24:38: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 03:24:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:24:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.10_summits.bed INFO @ Tue, 30 Jun 2020 03:24:43: Done! pass1 - making usageList (562 chroms): 2 millis pass2 - checking and writing primary data (2145 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:24:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:25:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:25:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:25:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386732/SRX6386732.20_summits.bed INFO @ Tue, 30 Jun 2020 03:25:10: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 12 millis CompletedMACS2peakCalling