Job ID = 6529881 SRX = SRX5343153 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: 00:11:58 31676147 reads; of these: 31676147 (100.00%) were unpaired; of these: 1378882 (4.35%) aligned 0 times 21015651 (66.35%) aligned exactly 1 time 9281614 (29.30%) aligned >1 times 95.65% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 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] 4795826 / 30297265 = 0.1583 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 03:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.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 03:21:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:21:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:21:18: 1000000 INFO @ Tue, 30 Jun 2020 03:21:24: 2000000 INFO @ Tue, 30 Jun 2020 03:21:29: 3000000 INFO @ Tue, 30 Jun 2020 03:21:35: 4000000 INFO @ Tue, 30 Jun 2020 03:21:40: 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, 30 Jun 2020 03:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.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 03:21:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:21:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:21:46: 6000000 INFO @ Tue, 30 Jun 2020 03:21:49: 1000000 INFO @ Tue, 30 Jun 2020 03:21:53: 7000000 INFO @ Tue, 30 Jun 2020 03:21:56: 2000000 INFO @ Tue, 30 Jun 2020 03:21:59: 8000000 INFO @ Tue, 30 Jun 2020 03:22:02: 3000000 INFO @ Tue, 30 Jun 2020 03:22:05: 9000000 INFO @ Tue, 30 Jun 2020 03:22:09: 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 03:22:12: 10000000 INFO @ Tue, 30 Jun 2020 03:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.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 03:22:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:15: 5000000 INFO @ Tue, 30 Jun 2020 03:22:18: 11000000 INFO @ Tue, 30 Jun 2020 03:22:19: 1000000 INFO @ Tue, 30 Jun 2020 03:22:22: 6000000 INFO @ Tue, 30 Jun 2020 03:22:25: 12000000 INFO @ Tue, 30 Jun 2020 03:22:26: 2000000 INFO @ Tue, 30 Jun 2020 03:22:29: 7000000 INFO @ Tue, 30 Jun 2020 03:22:31: 13000000 INFO @ Tue, 30 Jun 2020 03:22:32: 3000000 INFO @ Tue, 30 Jun 2020 03:22:35: 8000000 INFO @ Tue, 30 Jun 2020 03:22:38: 14000000 INFO @ Tue, 30 Jun 2020 03:22:39: 4000000 INFO @ Tue, 30 Jun 2020 03:22:42: 9000000 INFO @ Tue, 30 Jun 2020 03:22:44: 15000000 INFO @ Tue, 30 Jun 2020 03:22:46: 5000000 INFO @ Tue, 30 Jun 2020 03:22:49: 10000000 INFO @ Tue, 30 Jun 2020 03:22:51: 16000000 INFO @ Tue, 30 Jun 2020 03:22:52: 6000000 INFO @ Tue, 30 Jun 2020 03:22:55: 11000000 INFO @ Tue, 30 Jun 2020 03:22:57: 17000000 INFO @ Tue, 30 Jun 2020 03:22:59: 7000000 INFO @ Tue, 30 Jun 2020 03:23:02: 12000000 INFO @ Tue, 30 Jun 2020 03:23:04: 18000000 INFO @ Tue, 30 Jun 2020 03:23:05: 8000000 INFO @ Tue, 30 Jun 2020 03:23:09: 13000000 INFO @ Tue, 30 Jun 2020 03:23:10: 19000000 INFO @ Tue, 30 Jun 2020 03:23:12: 9000000 INFO @ Tue, 30 Jun 2020 03:23:15: 14000000 INFO @ Tue, 30 Jun 2020 03:23:17: 20000000 INFO @ Tue, 30 Jun 2020 03:23:18: 10000000 INFO @ Tue, 30 Jun 2020 03:23:22: 15000000 INFO @ Tue, 30 Jun 2020 03:23:23: 21000000 INFO @ Tue, 30 Jun 2020 03:23:25: 11000000 INFO @ Tue, 30 Jun 2020 03:23:29: 16000000 INFO @ Tue, 30 Jun 2020 03:23:30: 22000000 INFO @ Tue, 30 Jun 2020 03:23:31: 12000000 INFO @ Tue, 30 Jun 2020 03:23:35: 17000000 INFO @ Tue, 30 Jun 2020 03:23:37: 23000000 INFO @ Tue, 30 Jun 2020 03:23:38: 13000000 INFO @ Tue, 30 Jun 2020 03:23:42: 18000000 INFO @ Tue, 30 Jun 2020 03:23:43: 24000000 INFO @ Tue, 30 Jun 2020 03:23:45: 14000000 INFO @ Tue, 30 Jun 2020 03:23:49: 19000000 INFO @ Tue, 30 Jun 2020 03:23:50: 25000000 INFO @ Tue, 30 Jun 2020 03:23:51: 15000000 INFO @ Tue, 30 Jun 2020 03:23:54: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:23:54: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:23:54: #1 total tags in treatment: 25501439 INFO @ Tue, 30 Jun 2020 03:23:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:54: #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 03:23:54: #1 tags after filtering in treatment: 25501438 INFO @ Tue, 30 Jun 2020 03:23:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:54: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:55: 20000000 INFO @ Tue, 30 Jun 2020 03:23:56: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 03:23:56: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:56: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:56: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:56: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:56: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:56: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:23:56: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 03:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.05_model.r WARNING @ Tue, 30 Jun 2020 03:23:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:23:56: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 03:23:56: #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 03:23:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:23:58: 16000000 INFO @ Tue, 30 Jun 2020 03:24:02: 21000000 INFO @ Tue, 30 Jun 2020 03:24:04: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:24:09: 22000000 INFO @ Tue, 30 Jun 2020 03:24:11: 18000000 INFO @ Tue, 30 Jun 2020 03:24:15: 23000000 INFO @ Tue, 30 Jun 2020 03:24:17: 19000000 INFO @ Tue, 30 Jun 2020 03:24:22: 24000000 INFO @ Tue, 30 Jun 2020 03:24:24: 20000000 INFO @ Tue, 30 Jun 2020 03:24:28: 25000000 INFO @ Tue, 30 Jun 2020 03:24:30: 21000000 INFO @ Tue, 30 Jun 2020 03:24:32: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:24:32: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:24:32: #1 total tags in treatment: 25501439 INFO @ Tue, 30 Jun 2020 03:24:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:24:32: #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 03:24:33: #1 tags after filtering in treatment: 25501438 INFO @ Tue, 30 Jun 2020 03:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:24:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:24:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:24:34: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 03:24:34: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 03:24:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:24:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:24:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:24:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:24:34: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:24:34: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 03:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.10_model.r WARNING @ Tue, 30 Jun 2020 03:24:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:24:34: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 03:24:34: #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 03:24:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:24:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:37: 22000000 INFO @ Tue, 30 Jun 2020 03:24:43: 23000000 INFO @ Tue, 30 Jun 2020 03:24:49: 24000000 INFO @ Tue, 30 Jun 2020 03:24:56: 25000000 INFO @ Tue, 30 Jun 2020 03:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.05_summits.bed INFO @ Tue, 30 Jun 2020 03:24:56: Done! pass1 - making usageList (781 chroms): 1 millis pass2 - checking and writing primary data (2757 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:24:59: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:24:59: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:24:59: #1 total tags in treatment: 25501439 INFO @ Tue, 30 Jun 2020 03:24:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:24:59: #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 03:25:00: #1 tags after filtering in treatment: 25501438 INFO @ Tue, 30 Jun 2020 03:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:25:00: #1 finished! INFO @ Tue, 30 Jun 2020 03:25:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:25:01: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 03:25:01: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 03:25:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:25:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:25:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:25:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:25:01: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:25:01: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 03:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.20_model.r WARNING @ Tue, 30 Jun 2020 03:25:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:25:01: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 03:25:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:25:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:25:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:25:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.10_summits.bed INFO @ Tue, 30 Jun 2020 03:25:37: Done! pass1 - making usageList (587 chroms): 1 millis pass2 - checking and writing primary data (1898 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:25:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343153/SRX5343153.20_summits.bed INFO @ Tue, 30 Jun 2020 03:26:03: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 10 millis CompletedMACS2peakCalling