Job ID = 6529576 SRX = SRX3279756 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: 00:12:22 33978547 reads; of these: 33978547 (100.00%) were unpaired; of these: 1220416 (3.59%) aligned 0 times 27750911 (81.67%) aligned exactly 1 time 5007220 (14.74%) aligned >1 times 96.41% overall alignment rate Time searching: 00:12:22 Overall time: 00:12:22 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] 2984601 / 32758131 = 0.0911 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 02:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.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 02:45:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:31: 1000000 INFO @ Tue, 30 Jun 2020 02:45:39: 2000000 INFO @ Tue, 30 Jun 2020 02:45:47: 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 02:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.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 02:45:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:56: 4000000 INFO @ Tue, 30 Jun 2020 02:46:02: 1000000 INFO @ Tue, 30 Jun 2020 02:46:04: 5000000 INFO @ Tue, 30 Jun 2020 02:46:10: 2000000 INFO @ Tue, 30 Jun 2020 02:46:12: 6000000 INFO @ Tue, 30 Jun 2020 02:46:18: 3000000 INFO @ Tue, 30 Jun 2020 02:46:20: 7000000 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 02:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.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 02:46:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:27: 4000000 INFO @ Tue, 30 Jun 2020 02:46:28: 8000000 INFO @ Tue, 30 Jun 2020 02:46:31: 1000000 INFO @ Tue, 30 Jun 2020 02:46:35: 5000000 INFO @ Tue, 30 Jun 2020 02:46:36: 9000000 INFO @ Tue, 30 Jun 2020 02:46:38: 2000000 INFO @ Tue, 30 Jun 2020 02:46:43: 6000000 INFO @ Tue, 30 Jun 2020 02:46:44: 10000000 INFO @ Tue, 30 Jun 2020 02:46:46: 3000000 INFO @ Tue, 30 Jun 2020 02:46:51: 7000000 INFO @ Tue, 30 Jun 2020 02:46:53: 11000000 INFO @ Tue, 30 Jun 2020 02:46:53: 4000000 INFO @ Tue, 30 Jun 2020 02:46:59: 8000000 INFO @ Tue, 30 Jun 2020 02:47:00: 5000000 INFO @ Tue, 30 Jun 2020 02:47:01: 12000000 INFO @ Tue, 30 Jun 2020 02:47:07: 9000000 INFO @ Tue, 30 Jun 2020 02:47:07: 6000000 INFO @ Tue, 30 Jun 2020 02:47:08: 13000000 INFO @ Tue, 30 Jun 2020 02:47:15: 7000000 INFO @ Tue, 30 Jun 2020 02:47:15: 10000000 INFO @ Tue, 30 Jun 2020 02:47:16: 14000000 INFO @ Tue, 30 Jun 2020 02:47:22: 8000000 INFO @ Tue, 30 Jun 2020 02:47:23: 11000000 INFO @ Tue, 30 Jun 2020 02:47:24: 15000000 INFO @ Tue, 30 Jun 2020 02:47:29: 9000000 INFO @ Tue, 30 Jun 2020 02:47:31: 12000000 INFO @ Tue, 30 Jun 2020 02:47:31: 16000000 INFO @ Tue, 30 Jun 2020 02:47:37: 10000000 INFO @ Tue, 30 Jun 2020 02:47:39: 13000000 INFO @ Tue, 30 Jun 2020 02:47:39: 17000000 INFO @ Tue, 30 Jun 2020 02:47:44: 11000000 INFO @ Tue, 30 Jun 2020 02:47:46: 18000000 INFO @ Tue, 30 Jun 2020 02:47:47: 14000000 INFO @ Tue, 30 Jun 2020 02:47:52: 12000000 INFO @ Tue, 30 Jun 2020 02:47:54: 19000000 INFO @ Tue, 30 Jun 2020 02:47:54: 15000000 INFO @ Tue, 30 Jun 2020 02:47:59: 13000000 INFO @ Tue, 30 Jun 2020 02:48:02: 20000000 INFO @ Tue, 30 Jun 2020 02:48:02: 16000000 INFO @ Tue, 30 Jun 2020 02:48:06: 14000000 INFO @ Tue, 30 Jun 2020 02:48:09: 21000000 INFO @ Tue, 30 Jun 2020 02:48:10: 17000000 INFO @ Tue, 30 Jun 2020 02:48:13: 15000000 INFO @ Tue, 30 Jun 2020 02:48:16: 22000000 INFO @ Tue, 30 Jun 2020 02:48:18: 18000000 INFO @ Tue, 30 Jun 2020 02:48:20: 16000000 INFO @ Tue, 30 Jun 2020 02:48:24: 23000000 INFO @ Tue, 30 Jun 2020 02:48:26: 19000000 INFO @ Tue, 30 Jun 2020 02:48:28: 17000000 INFO @ Tue, 30 Jun 2020 02:48:32: 24000000 INFO @ Tue, 30 Jun 2020 02:48:34: 20000000 INFO @ Tue, 30 Jun 2020 02:48:35: 18000000 INFO @ Tue, 30 Jun 2020 02:48:39: 25000000 INFO @ Tue, 30 Jun 2020 02:48:41: 21000000 INFO @ Tue, 30 Jun 2020 02:48:42: 19000000 INFO @ Tue, 30 Jun 2020 02:48:47: 26000000 INFO @ Tue, 30 Jun 2020 02:48:49: 20000000 INFO @ Tue, 30 Jun 2020 02:48:49: 22000000 INFO @ Tue, 30 Jun 2020 02:48:54: 27000000 INFO @ Tue, 30 Jun 2020 02:48:56: 21000000 INFO @ Tue, 30 Jun 2020 02:48:56: 23000000 INFO @ Tue, 30 Jun 2020 02:49:01: 28000000 INFO @ Tue, 30 Jun 2020 02:49:02: 22000000 INFO @ Tue, 30 Jun 2020 02:49:04: 24000000 INFO @ Tue, 30 Jun 2020 02:49:08: 29000000 INFO @ Tue, 30 Jun 2020 02:49:10: 23000000 INFO @ Tue, 30 Jun 2020 02:49:12: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:49:15: #1 tag size is determined as 79 bps INFO @ Tue, 30 Jun 2020 02:49:15: #1 tag size = 79 INFO @ Tue, 30 Jun 2020 02:49:15: #1 total tags in treatment: 29773530 INFO @ Tue, 30 Jun 2020 02:49:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:15: #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 02:49:16: #1 tags after filtering in treatment: 29773432 INFO @ Tue, 30 Jun 2020 02:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:17: 24000000 INFO @ Tue, 30 Jun 2020 02:49:17: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 02:49:17: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:18: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:49:18: #2 alternative fragment length(s) may be 2,81 bps INFO @ Tue, 30 Jun 2020 02:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:18: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:18: #2 You may need to consider one of the other alternative d(s): 2,81 WARNING @ Tue, 30 Jun 2020 02:49:18: #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 02:49:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:19: 26000000 INFO @ Tue, 30 Jun 2020 02:49:24: 25000000 INFO @ Tue, 30 Jun 2020 02:49:26: 27000000 INFO @ Tue, 30 Jun 2020 02:49:31: 26000000 INFO @ Tue, 30 Jun 2020 02:49:32: 28000000 INFO @ Tue, 30 Jun 2020 02:49:38: 27000000 INFO @ Tue, 30 Jun 2020 02:49:39: 29000000 INFO @ Tue, 30 Jun 2020 02:49:45: 28000000 INFO @ Tue, 30 Jun 2020 02:49:45: #1 tag size is determined as 79 bps INFO @ Tue, 30 Jun 2020 02:49:45: #1 tag size = 79 INFO @ Tue, 30 Jun 2020 02:49:45: #1 total tags in treatment: 29773530 INFO @ Tue, 30 Jun 2020 02:49:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:45: #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 02:49:46: #1 tags after filtering in treatment: 29773432 INFO @ Tue, 30 Jun 2020 02:49:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:46: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:48: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 02:49:48: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:48: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:48: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:48: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:48: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:49:48: #2 alternative fragment length(s) may be 2,81 bps INFO @ Tue, 30 Jun 2020 02:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.10_model.r WARNING @ Tue, 30 Jun 2020 02:49:49: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:49: #2 You may need to consider one of the other alternative d(s): 2,81 WARNING @ Tue, 30 Jun 2020 02:49:49: #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 02:49:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:52: 29000000 INFO @ Tue, 30 Jun 2020 02:49:59: #1 tag size is determined as 79 bps INFO @ Tue, 30 Jun 2020 02:49:59: #1 tag size = 79 INFO @ Tue, 30 Jun 2020 02:49:59: #1 total tags in treatment: 29773530 INFO @ Tue, 30 Jun 2020 02:49:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:59: #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 02:50:00: #1 tags after filtering in treatment: 29773432 INFO @ Tue, 30 Jun 2020 02:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:02: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 02:50:02: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:02: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:50:02: #2 alternative fragment length(s) may be 2,81 bps INFO @ Tue, 30 Jun 2020 02:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:02: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:02: #2 You may need to consider one of the other alternative d(s): 2,81 WARNING @ Tue, 30 Jun 2020 02:50:02: #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 02:50:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:32: Done! pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (1502 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:50:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.10_summits.bed INFO @ Tue, 30 Jun 2020 02:51:05: Done! pass1 - making usageList (381 chroms): 3 millis pass2 - checking and writing primary data (1060 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3279756/SRX3279756.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:17: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 14 millis CompletedMACS2peakCalling