Job ID = 6529198 SRX = SRX041384 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: 00:10:18 49586813 reads; of these: 49586813 (100.00%) were unpaired; of these: 1322291 (2.67%) aligned 0 times 39130304 (78.91%) aligned exactly 1 time 9134218 (18.42%) aligned >1 times 97.33% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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 12 files... [bam_rmdupse_core] 15196607 / 48264522 = 0.3149 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 01:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.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 01:45:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:16: 1000000 INFO @ Tue, 30 Jun 2020 01:45:21: 2000000 INFO @ Tue, 30 Jun 2020 01:45:25: 3000000 INFO @ Tue, 30 Jun 2020 01:45:29: 4000000 INFO @ Tue, 30 Jun 2020 01:45:34: 5000000 INFO @ Tue, 30 Jun 2020 01:45:38: 6000000 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 01:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.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 01:45:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:43: 7000000 INFO @ Tue, 30 Jun 2020 01:45:46: 1000000 INFO @ Tue, 30 Jun 2020 01:45:48: 8000000 INFO @ Tue, 30 Jun 2020 01:45:51: 2000000 INFO @ Tue, 30 Jun 2020 01:45:53: 9000000 INFO @ Tue, 30 Jun 2020 01:45:56: 3000000 INFO @ Tue, 30 Jun 2020 01:45:59: 10000000 INFO @ Tue, 30 Jun 2020 01:46:01: 4000000 INFO @ Tue, 30 Jun 2020 01:46:04: 11000000 INFO @ Tue, 30 Jun 2020 01:46:06: 5000000 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 01:46:10: 12000000 INFO @ Tue, 30 Jun 2020 01:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.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 01:46:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:12: 6000000 INFO @ Tue, 30 Jun 2020 01:46:15: 13000000 INFO @ Tue, 30 Jun 2020 01:46:16: 1000000 INFO @ Tue, 30 Jun 2020 01:46:17: 7000000 INFO @ Tue, 30 Jun 2020 01:46:20: 14000000 INFO @ Tue, 30 Jun 2020 01:46:20: 2000000 INFO @ Tue, 30 Jun 2020 01:46:23: 8000000 INFO @ Tue, 30 Jun 2020 01:46:25: 3000000 INFO @ Tue, 30 Jun 2020 01:46:25: 15000000 INFO @ Tue, 30 Jun 2020 01:46:29: 9000000 INFO @ Tue, 30 Jun 2020 01:46:29: 4000000 INFO @ Tue, 30 Jun 2020 01:46:31: 16000000 INFO @ Tue, 30 Jun 2020 01:46:34: 5000000 INFO @ Tue, 30 Jun 2020 01:46:34: 10000000 INFO @ Tue, 30 Jun 2020 01:46:37: 17000000 INFO @ Tue, 30 Jun 2020 01:46:38: 6000000 INFO @ Tue, 30 Jun 2020 01:46:40: 11000000 INFO @ Tue, 30 Jun 2020 01:46:42: 18000000 INFO @ Tue, 30 Jun 2020 01:46:43: 7000000 INFO @ Tue, 30 Jun 2020 01:46:46: 12000000 INFO @ Tue, 30 Jun 2020 01:46:48: 8000000 INFO @ Tue, 30 Jun 2020 01:46:48: 19000000 INFO @ Tue, 30 Jun 2020 01:46:51: 13000000 INFO @ Tue, 30 Jun 2020 01:46:52: 9000000 INFO @ Tue, 30 Jun 2020 01:46:54: 20000000 INFO @ Tue, 30 Jun 2020 01:46:57: 10000000 INFO @ Tue, 30 Jun 2020 01:46:57: 14000000 INFO @ Tue, 30 Jun 2020 01:47:00: 21000000 INFO @ Tue, 30 Jun 2020 01:47:02: 11000000 INFO @ Tue, 30 Jun 2020 01:47:02: 15000000 INFO @ Tue, 30 Jun 2020 01:47:06: 22000000 INFO @ Tue, 30 Jun 2020 01:47:07: 12000000 INFO @ Tue, 30 Jun 2020 01:47:08: 16000000 INFO @ Tue, 30 Jun 2020 01:47:11: 23000000 INFO @ Tue, 30 Jun 2020 01:47:12: 13000000 INFO @ Tue, 30 Jun 2020 01:47:14: 17000000 INFO @ Tue, 30 Jun 2020 01:47:17: 24000000 INFO @ Tue, 30 Jun 2020 01:47:17: 14000000 INFO @ Tue, 30 Jun 2020 01:47:19: 18000000 INFO @ Tue, 30 Jun 2020 01:47:23: 25000000 INFO @ Tue, 30 Jun 2020 01:47:23: 15000000 INFO @ Tue, 30 Jun 2020 01:47:25: 19000000 INFO @ Tue, 30 Jun 2020 01:47:28: 16000000 INFO @ Tue, 30 Jun 2020 01:47:28: 26000000 INFO @ Tue, 30 Jun 2020 01:47:31: 20000000 INFO @ Tue, 30 Jun 2020 01:47:33: 17000000 INFO @ Tue, 30 Jun 2020 01:47:35: 27000000 INFO @ Tue, 30 Jun 2020 01:47:37: 21000000 INFO @ Tue, 30 Jun 2020 01:47:38: 18000000 INFO @ Tue, 30 Jun 2020 01:47:41: 28000000 INFO @ Tue, 30 Jun 2020 01:47:42: 22000000 INFO @ Tue, 30 Jun 2020 01:47:43: 19000000 INFO @ Tue, 30 Jun 2020 01:47:47: 29000000 INFO @ Tue, 30 Jun 2020 01:47:48: 23000000 INFO @ Tue, 30 Jun 2020 01:47:48: 20000000 INFO @ Tue, 30 Jun 2020 01:47:53: 30000000 INFO @ Tue, 30 Jun 2020 01:47:53: 21000000 INFO @ Tue, 30 Jun 2020 01:47:54: 24000000 INFO @ Tue, 30 Jun 2020 01:47:58: 22000000 INFO @ Tue, 30 Jun 2020 01:47:58: 31000000 INFO @ Tue, 30 Jun 2020 01:47:59: 25000000 INFO @ Tue, 30 Jun 2020 01:48:03: 23000000 INFO @ Tue, 30 Jun 2020 01:48:04: 32000000 INFO @ Tue, 30 Jun 2020 01:48:05: 26000000 INFO @ Tue, 30 Jun 2020 01:48:08: 24000000 INFO @ Tue, 30 Jun 2020 01:48:11: 33000000 INFO @ Tue, 30 Jun 2020 01:48:12: 27000000 INFO @ Tue, 30 Jun 2020 01:48:12: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:48:12: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:48:12: #1 total tags in treatment: 33067915 INFO @ Tue, 30 Jun 2020 01:48:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:12: #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 01:48:13: #1 tags after filtering in treatment: 33067915 INFO @ Tue, 30 Jun 2020 01:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:13: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:13: 25000000 INFO @ Tue, 30 Jun 2020 01:48:15: #2 number of paired peaks: 133 WARNING @ Tue, 30 Jun 2020 01:48:15: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:15: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:15: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:15: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:15: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:15: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:48:15: #2 alternative fragment length(s) may be 2,46,120 bps INFO @ Tue, 30 Jun 2020 01:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.05_model.r WARNING @ Tue, 30 Jun 2020 01:48:15: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:15: #2 You may need to consider one of the other alternative d(s): 2,46,120 WARNING @ Tue, 30 Jun 2020 01:48:15: #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 01:48:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:17: 28000000 INFO @ Tue, 30 Jun 2020 01:48:18: 26000000 INFO @ Tue, 30 Jun 2020 01:48:23: 29000000 INFO @ Tue, 30 Jun 2020 01:48:24: 27000000 INFO @ Tue, 30 Jun 2020 01:48:29: 30000000 INFO @ Tue, 30 Jun 2020 01:48:29: 28000000 INFO @ Tue, 30 Jun 2020 01:48:34: 29000000 INFO @ Tue, 30 Jun 2020 01:48:34: 31000000 INFO @ Tue, 30 Jun 2020 01:48:40: 30000000 INFO @ Tue, 30 Jun 2020 01:48:40: 32000000 INFO @ Tue, 30 Jun 2020 01:48:45: 31000000 INFO @ Tue, 30 Jun 2020 01:48:46: 33000000 INFO @ Tue, 30 Jun 2020 01:48:47: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:48:47: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:48:47: #1 total tags in treatment: 33067915 INFO @ Tue, 30 Jun 2020 01:48:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:47: #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 01:48:48: #1 tags after filtering in treatment: 33067915 INFO @ Tue, 30 Jun 2020 01:48:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:48: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:48: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:48:50: 32000000 INFO @ Tue, 30 Jun 2020 01:48:50: #2 number of paired peaks: 133 WARNING @ Tue, 30 Jun 2020 01:48:50: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:50: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:50: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:50: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:50: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:50: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:48:50: #2 alternative fragment length(s) may be 2,46,120 bps INFO @ Tue, 30 Jun 2020 01:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.10_model.r WARNING @ Tue, 30 Jun 2020 01:48:50: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:50: #2 You may need to consider one of the other alternative d(s): 2,46,120 WARNING @ Tue, 30 Jun 2020 01:48:50: #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 01:48:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:55: 33000000 INFO @ Tue, 30 Jun 2020 01:48:56: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:48:56: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:48:56: #1 total tags in treatment: 33067915 INFO @ Tue, 30 Jun 2020 01:48:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:56: #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 01:48:57: #1 tags after filtering in treatment: 33067915 INFO @ Tue, 30 Jun 2020 01:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:57: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:59: #2 number of paired peaks: 133 WARNING @ Tue, 30 Jun 2020 01:48:59: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:59: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:59: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:59: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:59: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:59: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:48:59: #2 alternative fragment length(s) may be 2,46,120 bps INFO @ Tue, 30 Jun 2020 01:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.20_model.r WARNING @ Tue, 30 Jun 2020 01:48:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:59: #2 You may need to consider one of the other alternative d(s): 2,46,120 WARNING @ Tue, 30 Jun 2020 01:48:59: #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 01:48:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:49:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.05_summits.bed INFO @ Tue, 30 Jun 2020 01:49:31: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (3004 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:49:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:50:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:50:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.10_summits.bed INFO @ Tue, 30 Jun 2020 01:50:05: Done! pass1 - making usageList (427 chroms): 2 millis pass2 - checking and writing primary data (2006 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041384/SRX041384.20_summits.bed INFO @ Tue, 30 Jun 2020 01:50:15: Done! pass1 - making usageList (309 chroms): 1 millis pass2 - checking and writing primary data (777 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。