Job ID = 6529788 SRX = SRX4828016 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: 00:08:44 34196540 reads; of these: 34196540 (100.00%) were unpaired; of these: 1277261 (3.74%) aligned 0 times 26613415 (77.82%) aligned exactly 1 time 6305864 (18.44%) aligned >1 times 96.26% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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 16 files... [bam_rmdupse_core] 7489548 / 32919279 = 0.2275 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 03:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.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 03:08:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:32: 1000000 INFO @ Tue, 30 Jun 2020 03:08:39: 2000000 INFO @ Tue, 30 Jun 2020 03:08:46: 3000000 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 03:08:53: 4000000 INFO @ Tue, 30 Jun 2020 03:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.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 03:08:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:00: 5000000 INFO @ Tue, 30 Jun 2020 03:09:01: 1000000 INFO @ Tue, 30 Jun 2020 03:09:07: 6000000 INFO @ Tue, 30 Jun 2020 03:09:09: 2000000 INFO @ Tue, 30 Jun 2020 03:09:15: 7000000 INFO @ Tue, 30 Jun 2020 03:09:16: 3000000 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 03:09:23: 8000000 INFO @ Tue, 30 Jun 2020 03:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.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 03:09:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:24: 4000000 INFO @ Tue, 30 Jun 2020 03:09:31: 9000000 INFO @ Tue, 30 Jun 2020 03:09:32: 1000000 INFO @ Tue, 30 Jun 2020 03:09:32: 5000000 INFO @ Tue, 30 Jun 2020 03:09:38: 10000000 INFO @ Tue, 30 Jun 2020 03:09:40: 2000000 INFO @ Tue, 30 Jun 2020 03:09:40: 6000000 INFO @ Tue, 30 Jun 2020 03:09:46: 11000000 INFO @ Tue, 30 Jun 2020 03:09:48: 3000000 INFO @ Tue, 30 Jun 2020 03:09:48: 7000000 INFO @ Tue, 30 Jun 2020 03:09:54: 12000000 INFO @ Tue, 30 Jun 2020 03:09:56: 4000000 INFO @ Tue, 30 Jun 2020 03:09:56: 8000000 INFO @ Tue, 30 Jun 2020 03:10:02: 13000000 INFO @ Tue, 30 Jun 2020 03:10:04: 5000000 INFO @ Tue, 30 Jun 2020 03:10:04: 9000000 INFO @ Tue, 30 Jun 2020 03:10:10: 14000000 INFO @ Tue, 30 Jun 2020 03:10:12: 6000000 INFO @ Tue, 30 Jun 2020 03:10:12: 10000000 INFO @ Tue, 30 Jun 2020 03:10:18: 15000000 INFO @ Tue, 30 Jun 2020 03:10:20: 7000000 INFO @ Tue, 30 Jun 2020 03:10:20: 11000000 INFO @ Tue, 30 Jun 2020 03:10:26: 16000000 INFO @ Tue, 30 Jun 2020 03:10:28: 12000000 INFO @ Tue, 30 Jun 2020 03:10:28: 8000000 INFO @ Tue, 30 Jun 2020 03:10:34: 17000000 INFO @ Tue, 30 Jun 2020 03:10:36: 13000000 INFO @ Tue, 30 Jun 2020 03:10:36: 9000000 INFO @ Tue, 30 Jun 2020 03:10:42: 18000000 INFO @ Tue, 30 Jun 2020 03:10:44: 10000000 INFO @ Tue, 30 Jun 2020 03:10:44: 14000000 INFO @ Tue, 30 Jun 2020 03:10:50: 19000000 INFO @ Tue, 30 Jun 2020 03:10:52: 11000000 INFO @ Tue, 30 Jun 2020 03:10:52: 15000000 INFO @ Tue, 30 Jun 2020 03:10:59: 20000000 INFO @ Tue, 30 Jun 2020 03:11:00: 12000000 INFO @ Tue, 30 Jun 2020 03:11:00: 16000000 INFO @ Tue, 30 Jun 2020 03:11:07: 21000000 INFO @ Tue, 30 Jun 2020 03:11:08: 13000000 INFO @ Tue, 30 Jun 2020 03:11:08: 17000000 INFO @ Tue, 30 Jun 2020 03:11:15: 22000000 INFO @ Tue, 30 Jun 2020 03:11:16: 14000000 INFO @ Tue, 30 Jun 2020 03:11:16: 18000000 INFO @ Tue, 30 Jun 2020 03:11:22: 23000000 INFO @ Tue, 30 Jun 2020 03:11:23: 15000000 INFO @ Tue, 30 Jun 2020 03:11:24: 19000000 INFO @ Tue, 30 Jun 2020 03:11:30: 24000000 INFO @ Tue, 30 Jun 2020 03:11:31: 16000000 INFO @ Tue, 30 Jun 2020 03:11:32: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:11:38: 25000000 INFO @ Tue, 30 Jun 2020 03:11:39: 17000000 INFO @ Tue, 30 Jun 2020 03:11:40: 21000000 INFO @ Tue, 30 Jun 2020 03:11:42: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 03:11:42: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 03:11:42: #1 total tags in treatment: 25429731 INFO @ Tue, 30 Jun 2020 03:11:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:42: #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 03:11:43: #1 tags after filtering in treatment: 25429635 INFO @ Tue, 30 Jun 2020 03:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:43: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:45: #2 number of paired peaks: 374 WARNING @ Tue, 30 Jun 2020 03:11:45: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:45: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:45: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:45: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:45: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:45: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:11:45: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 30 Jun 2020 03:11:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:45: #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, 30 Jun 2020 03:11:45: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 30 Jun 2020 03:11:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:11:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:47: 18000000 INFO @ Tue, 30 Jun 2020 03:11:48: 22000000 INFO @ Tue, 30 Jun 2020 03:11:55: 19000000 INFO @ Tue, 30 Jun 2020 03:11:56: 23000000 INFO @ Tue, 30 Jun 2020 03:12:04: 20000000 INFO @ Tue, 30 Jun 2020 03:12:04: 24000000 INFO @ Tue, 30 Jun 2020 03:12:12: 21000000 INFO @ Tue, 30 Jun 2020 03:12:12: 25000000 INFO @ Tue, 30 Jun 2020 03:12:16: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 03:12:16: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 03:12:16: #1 total tags in treatment: 25429731 INFO @ Tue, 30 Jun 2020 03:12:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:16: #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 03:12:17: #1 tags after filtering in treatment: 25429635 INFO @ Tue, 30 Jun 2020 03:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:18: #2 number of paired peaks: 374 WARNING @ Tue, 30 Jun 2020 03:12:18: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:18: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:12:18: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 30 Jun 2020 03:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:18: #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, 30 Jun 2020 03:12:18: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 30 Jun 2020 03:12:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:12:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:19: 22000000 INFO @ Tue, 30 Jun 2020 03:12:27: 23000000 INFO @ Tue, 30 Jun 2020 03:12:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:34: 24000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:42: 25000000 INFO @ Tue, 30 Jun 2020 03:12:46: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 03:12:46: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 03:12:46: #1 total tags in treatment: 25429731 INFO @ Tue, 30 Jun 2020 03:12:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:46: #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 03:12:47: #1 tags after filtering in treatment: 25429635 INFO @ Tue, 30 Jun 2020 03:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:47: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:48: #2 number of paired peaks: 374 WARNING @ Tue, 30 Jun 2020 03:12:48: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:48: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:49: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:12:49: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 30 Jun 2020 03:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:49: #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, 30 Jun 2020 03:12:49: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 30 Jun 2020 03:12:49: #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 03:12:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.05_summits.bed INFO @ Tue, 30 Jun 2020 03:12:56: Done! pass1 - making usageList (669 chroms): 5 millis pass2 - checking and writing primary data (22299 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.10_summits.bed INFO @ Tue, 30 Jun 2020 03:13:29: Done! pass1 - making usageList (483 chroms): 2 millis pass2 - checking and writing primary data (5200 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828016/SRX4828016.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:58: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (847 records, 4 fields): 17 millis CompletedMACS2peakCalling