Job ID = 16439409 SRX = SRX15206487 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: 00:08:09 16943550 reads; of these: 16943550 (100.00%) were unpaired; of these: 337368 (1.99%) aligned 0 times 12843933 (75.80%) aligned exactly 1 time 3762249 (22.20%) aligned >1 times 98.01% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 1457266 / 16606182 = 0.0878 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:19:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.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, 02 Aug 2022 15:19:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:19:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:19:33: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:19:46: 2000000 INFO @ Tue, 02 Aug 2022 15:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.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, 02 Aug 2022 15:19:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:19:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:19:59: 3000000 INFO @ Tue, 02 Aug 2022 15:20:00: 1000000 INFO @ Tue, 02 Aug 2022 15:20:11: 2000000 INFO @ Tue, 02 Aug 2022 15:20:12: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.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, 02 Aug 2022 15:20:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:20:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:20:22: 3000000 INFO @ Tue, 02 Aug 2022 15:20:26: 5000000 INFO @ Tue, 02 Aug 2022 15:20:33: 1000000 INFO @ Tue, 02 Aug 2022 15:20:33: 4000000 INFO @ Tue, 02 Aug 2022 15:20:40: 6000000 INFO @ Tue, 02 Aug 2022 15:20:45: 5000000 INFO @ Tue, 02 Aug 2022 15:20:48: 2000000 INFO @ Tue, 02 Aug 2022 15:20:55: 7000000 INFO @ Tue, 02 Aug 2022 15:20:56: 6000000 INFO @ Tue, 02 Aug 2022 15:21:02: 3000000 INFO @ Tue, 02 Aug 2022 15:21:08: 7000000 INFO @ Tue, 02 Aug 2022 15:21:10: 8000000 INFO @ Tue, 02 Aug 2022 15:21:17: 4000000 INFO @ Tue, 02 Aug 2022 15:21:20: 8000000 INFO @ Tue, 02 Aug 2022 15:21:25: 9000000 INFO @ Tue, 02 Aug 2022 15:21:31: 5000000 INFO @ Tue, 02 Aug 2022 15:21:32: 9000000 INFO @ Tue, 02 Aug 2022 15:21:40: 10000000 INFO @ Tue, 02 Aug 2022 15:21:42: 10000000 INFO @ Tue, 02 Aug 2022 15:21:46: 6000000 INFO @ Tue, 02 Aug 2022 15:21:53: 11000000 INFO @ Tue, 02 Aug 2022 15:21:55: 11000000 INFO @ Tue, 02 Aug 2022 15:22:02: 7000000 INFO @ Tue, 02 Aug 2022 15:22:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:22:11: 12000000 INFO @ Tue, 02 Aug 2022 15:22:14: 13000000 INFO @ Tue, 02 Aug 2022 15:22:17: 8000000 INFO @ Tue, 02 Aug 2022 15:22:24: 14000000 INFO @ Tue, 02 Aug 2022 15:22:26: 13000000 INFO @ Tue, 02 Aug 2022 15:22:33: 9000000 INFO @ Tue, 02 Aug 2022 15:22:34: 15000000 INFO @ Tue, 02 Aug 2022 15:22:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:22:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:22:36: #1 total tags in treatment: 15148916 INFO @ Tue, 02 Aug 2022 15:22:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:22:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:22:37: #1 tags after filtering in treatment: 15148813 INFO @ Tue, 02 Aug 2022 15:22:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:22:37: #1 finished! INFO @ Tue, 02 Aug 2022 15:22:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:22:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:22:38: #2 number of paired peaks: 624 WARNING @ Tue, 02 Aug 2022 15:22:38: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Tue, 02 Aug 2022 15:22:38: start model_add_line... INFO @ Tue, 02 Aug 2022 15:22:38: start X-correlation... INFO @ Tue, 02 Aug 2022 15:22:38: end of X-cor INFO @ Tue, 02 Aug 2022 15:22:38: #2 finished! INFO @ Tue, 02 Aug 2022 15:22:38: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 15:22:38: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 02 Aug 2022 15:22:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.10_model.r WARNING @ Tue, 02 Aug 2022 15:22:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:22:39: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 02 Aug 2022 15:22:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:22:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:22:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:22:42: 14000000 INFO @ Tue, 02 Aug 2022 15:22:48: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:22:58: 15000000 INFO @ Tue, 02 Aug 2022 15:23:00: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:23:00: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:23:00: #1 total tags in treatment: 15148916 INFO @ Tue, 02 Aug 2022 15:23:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:23:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:23:01: #1 tags after filtering in treatment: 15148813 INFO @ Tue, 02 Aug 2022 15:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:23:01: #1 finished! INFO @ Tue, 02 Aug 2022 15:23:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:23:02: #2 number of paired peaks: 624 WARNING @ Tue, 02 Aug 2022 15:23:02: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Tue, 02 Aug 2022 15:23:02: start model_add_line... INFO @ Tue, 02 Aug 2022 15:23:03: start X-correlation... INFO @ Tue, 02 Aug 2022 15:23:03: end of X-cor INFO @ Tue, 02 Aug 2022 15:23:03: #2 finished! INFO @ Tue, 02 Aug 2022 15:23:03: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 15:23:03: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 02 Aug 2022 15:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.05_model.r WARNING @ Tue, 02 Aug 2022 15:23:03: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:23:03: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 02 Aug 2022 15:23:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:23:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:23:04: 11000000 INFO @ Tue, 02 Aug 2022 15:23:18: 12000000 INFO @ Tue, 02 Aug 2022 15:23:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:23:32: 13000000 INFO @ Tue, 02 Aug 2022 15:23:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:23:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:23:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.10_summits.bed INFO @ Tue, 02 Aug 2022 15:23:39: Done! pass1 - making usageList (565 chroms): 2 millis pass2 - checking and writing primary data (1721 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:23:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:23:46: 14000000 INFO @ Tue, 02 Aug 2022 15:24:00: 15000000 INFO @ Tue, 02 Aug 2022 15:24:01: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:24:01: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:24:01: #1 total tags in treatment: 15148916 INFO @ Tue, 02 Aug 2022 15:24:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:24:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:24:02: #1 tags after filtering in treatment: 15148813 INFO @ Tue, 02 Aug 2022 15:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:24:02: #1 finished! INFO @ Tue, 02 Aug 2022 15:24:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.05_summits.bed INFO @ Tue, 02 Aug 2022 15:24:02: Done! pass1 - making usageList (623 chroms): 3 millis pass2 - checking and writing primary data (2280 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:24:03: #2 number of paired peaks: 624 WARNING @ Tue, 02 Aug 2022 15:24:03: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Tue, 02 Aug 2022 15:24:03: start model_add_line... INFO @ Tue, 02 Aug 2022 15:24:04: start X-correlation... INFO @ Tue, 02 Aug 2022 15:24:04: end of X-cor INFO @ Tue, 02 Aug 2022 15:24:04: #2 finished! INFO @ Tue, 02 Aug 2022 15:24:04: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 15:24:04: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 02 Aug 2022 15:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.20_model.r WARNING @ Tue, 02 Aug 2022 15:24:04: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:24:04: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 02 Aug 2022 15:24:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:24:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:24:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206487/SRX15206487.20_summits.bed INFO @ Tue, 02 Aug 2022 15:25:02: Done! pass1 - making usageList (449 chroms): 2 millis pass2 - checking and writing primary data (1084 records, 4 fields): 22 millis CompletedMACS2peakCalling