Job ID = 16438509 SRX = SRX10031703 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:17 36596780 reads; of these: 36596780 (100.00%) were unpaired; of these: 1518477 (4.15%) aligned 0 times 28731421 (78.51%) aligned exactly 1 time 6346882 (17.34%) aligned >1 times 95.85% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 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] 5970507 / 35078303 = 0.1702 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 14:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.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 14:14:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:14:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:14:07: 1000000 INFO @ Tue, 02 Aug 2022 14:14:14: 2000000 INFO @ Tue, 02 Aug 2022 14:14:20: 3000000 INFO @ Tue, 02 Aug 2022 14:14:26: 4000000 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 14:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.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 14:14:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:14:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:14:32: 5000000 INFO @ Tue, 02 Aug 2022 14:14:38: 1000000 INFO @ Tue, 02 Aug 2022 14:14:40: 6000000 INFO @ Tue, 02 Aug 2022 14:14:45: 2000000 INFO @ Tue, 02 Aug 2022 14:14:47: 7000000 INFO @ Tue, 02 Aug 2022 14:14:52: 3000000 INFO @ Tue, 02 Aug 2022 14:14:54: 8000000 INFO @ Tue, 02 Aug 2022 14:14:59: 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 14:15:01: 9000000 INFO @ Tue, 02 Aug 2022 14:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.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 14:15:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:15:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:15:06: 5000000 INFO @ Tue, 02 Aug 2022 14:15:09: 10000000 INFO @ Tue, 02 Aug 2022 14:15:10: 1000000 INFO @ Tue, 02 Aug 2022 14:15:14: 6000000 INFO @ Tue, 02 Aug 2022 14:15:17: 11000000 INFO @ Tue, 02 Aug 2022 14:15:18: 2000000 INFO @ Tue, 02 Aug 2022 14:15:21: 7000000 INFO @ Tue, 02 Aug 2022 14:15:25: 12000000 INFO @ Tue, 02 Aug 2022 14:15:26: 3000000 INFO @ Tue, 02 Aug 2022 14:15:29: 8000000 INFO @ Tue, 02 Aug 2022 14:15:32: 13000000 INFO @ Tue, 02 Aug 2022 14:15:34: 4000000 INFO @ Tue, 02 Aug 2022 14:15:36: 9000000 INFO @ Tue, 02 Aug 2022 14:15:40: 14000000 INFO @ Tue, 02 Aug 2022 14:15:42: 5000000 INFO @ Tue, 02 Aug 2022 14:15:44: 10000000 INFO @ Tue, 02 Aug 2022 14:15:48: 15000000 INFO @ Tue, 02 Aug 2022 14:15:51: 6000000 INFO @ Tue, 02 Aug 2022 14:15:52: 11000000 INFO @ Tue, 02 Aug 2022 14:15:56: 16000000 INFO @ Tue, 02 Aug 2022 14:15:59: 7000000 INFO @ Tue, 02 Aug 2022 14:16:00: 12000000 INFO @ Tue, 02 Aug 2022 14:16:04: 17000000 INFO @ Tue, 02 Aug 2022 14:16:07: 8000000 INFO @ Tue, 02 Aug 2022 14:16:08: 13000000 INFO @ Tue, 02 Aug 2022 14:16:11: 18000000 INFO @ Tue, 02 Aug 2022 14:16:15: 9000000 INFO @ Tue, 02 Aug 2022 14:16:15: 14000000 INFO @ Tue, 02 Aug 2022 14:16:19: 19000000 INFO @ Tue, 02 Aug 2022 14:16:23: 15000000 INFO @ Tue, 02 Aug 2022 14:16:23: 10000000 INFO @ Tue, 02 Aug 2022 14:16:27: 20000000 INFO @ Tue, 02 Aug 2022 14:16:31: 16000000 INFO @ Tue, 02 Aug 2022 14:16:31: 11000000 INFO @ Tue, 02 Aug 2022 14:16:34: 21000000 INFO @ Tue, 02 Aug 2022 14:16:39: 17000000 INFO @ Tue, 02 Aug 2022 14:16:39: 12000000 INFO @ Tue, 02 Aug 2022 14:16:42: 22000000 INFO @ Tue, 02 Aug 2022 14:16:46: 18000000 INFO @ Tue, 02 Aug 2022 14:16:47: 13000000 INFO @ Tue, 02 Aug 2022 14:16:50: 23000000 INFO @ Tue, 02 Aug 2022 14:16:54: 19000000 INFO @ Tue, 02 Aug 2022 14:16:55: 14000000 INFO @ Tue, 02 Aug 2022 14:16:58: 24000000 INFO @ Tue, 02 Aug 2022 14:17:02: 20000000 INFO @ Tue, 02 Aug 2022 14:17:03: 15000000 INFO @ Tue, 02 Aug 2022 14:17:06: 25000000 INFO @ Tue, 02 Aug 2022 14:17:10: 21000000 INFO @ Tue, 02 Aug 2022 14:17:11: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:17:14: 26000000 INFO @ Tue, 02 Aug 2022 14:17:18: 22000000 INFO @ Tue, 02 Aug 2022 14:17:20: 17000000 INFO @ Tue, 02 Aug 2022 14:17:22: 27000000 INFO @ Tue, 02 Aug 2022 14:17:26: 23000000 INFO @ Tue, 02 Aug 2022 14:17:28: 18000000 INFO @ Tue, 02 Aug 2022 14:17:30: 28000000 INFO @ Tue, 02 Aug 2022 14:17:34: 24000000 INFO @ Tue, 02 Aug 2022 14:17:37: 19000000 INFO @ Tue, 02 Aug 2022 14:17:38: 29000000 INFO @ Tue, 02 Aug 2022 14:17:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:17:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:17:39: #1 total tags in treatment: 29107796 INFO @ Tue, 02 Aug 2022 14:17:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:17:39: #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 14:17:40: #1 tags after filtering in treatment: 29107762 INFO @ Tue, 02 Aug 2022 14:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:17:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:17:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:17:41: #2 number of paired peaks: 224 WARNING @ Tue, 02 Aug 2022 14:17:41: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 02 Aug 2022 14:17:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:17:42: start X-correlation... INFO @ Tue, 02 Aug 2022 14:17:42: end of X-cor INFO @ Tue, 02 Aug 2022 14:17:42: #2 finished! INFO @ Tue, 02 Aug 2022 14:17:42: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 14:17:42: #2 alternative fragment length(s) may be 1,68,538 bps INFO @ Tue, 02 Aug 2022 14:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.05_model.r WARNING @ Tue, 02 Aug 2022 14:17:42: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:17:42: #2 You may need to consider one of the other alternative d(s): 1,68,538 WARNING @ Tue, 02 Aug 2022 14:17:42: #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 14:17:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:17:42: 25000000 INFO @ Tue, 02 Aug 2022 14:17:45: 20000000 INFO @ Tue, 02 Aug 2022 14:17:50: 26000000 INFO @ Tue, 02 Aug 2022 14:17:54: 21000000 INFO @ Tue, 02 Aug 2022 14:17:57: 27000000 INFO @ Tue, 02 Aug 2022 14:18:02: 22000000 INFO @ Tue, 02 Aug 2022 14:18:05: 28000000 INFO @ Tue, 02 Aug 2022 14:18:11: 23000000 INFO @ Tue, 02 Aug 2022 14:18:13: 29000000 INFO @ Tue, 02 Aug 2022 14:18:14: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:18:14: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:18:14: #1 total tags in treatment: 29107796 INFO @ Tue, 02 Aug 2022 14:18:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:14: #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 14:18:15: #1 tags after filtering in treatment: 29107762 INFO @ Tue, 02 Aug 2022 14:18:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:15: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:15: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:18:16: #2 number of paired peaks: 224 WARNING @ Tue, 02 Aug 2022 14:18:16: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:16: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:16: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:17: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 14:18:17: #2 alternative fragment length(s) may be 1,68,538 bps INFO @ Tue, 02 Aug 2022 14:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.10_model.r WARNING @ Tue, 02 Aug 2022 14:18:17: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:17: #2 You may need to consider one of the other alternative d(s): 1,68,538 WARNING @ Tue, 02 Aug 2022 14:18:17: #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 14:18:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:19: 24000000 INFO @ Tue, 02 Aug 2022 14:18:27: 25000000 INFO @ Tue, 02 Aug 2022 14:18:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:34: 26000000 INFO @ Tue, 02 Aug 2022 14:18:42: 27000000 INFO @ Tue, 02 Aug 2022 14:18:50: 28000000 INFO @ Tue, 02 Aug 2022 14:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.05_summits.bed INFO @ Tue, 02 Aug 2022 14:18:52: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (4896 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:18:57: 29000000 INFO @ Tue, 02 Aug 2022 14:18:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:18:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:18:58: #1 total tags in treatment: 29107796 INFO @ Tue, 02 Aug 2022 14:18:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:58: #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 14:18:59: #1 tags after filtering in treatment: 29107762 INFO @ Tue, 02 Aug 2022 14:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:59: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:01: #2 number of paired peaks: 224 WARNING @ Tue, 02 Aug 2022 14:19:01: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 02 Aug 2022 14:19:01: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:01: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:01: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:01: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:01: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 14:19:01: #2 alternative fragment length(s) may be 1,68,538 bps INFO @ Tue, 02 Aug 2022 14:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.20_model.r WARNING @ Tue, 02 Aug 2022 14:19:01: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:01: #2 You may need to consider one of the other alternative d(s): 1,68,538 WARNING @ Tue, 02 Aug 2022 14:19:01: #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 14:19:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:19:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.10_summits.bed INFO @ Tue, 02 Aug 2022 14:19:28: Done! pass1 - making usageList (436 chroms): 2 millis pass2 - checking and writing primary data (2382 records, 4 fields): 110 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:19:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031703/SRX10031703.20_summits.bed INFO @ Tue, 02 Aug 2022 14:20:10: Done! pass1 - making usageList (248 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 94 millis CompletedMACS2peakCalling