Job ID = 6529933 SRX = SRX5379461 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: 00:07:49 31375850 reads; of these: 31375850 (100.00%) were unpaired; of these: 1212003 (3.86%) aligned 0 times 26180520 (83.44%) aligned exactly 1 time 3983327 (12.70%) aligned >1 times 96.14% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 3949267 / 30163847 = 0.1309 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 03:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.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 03:11:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:00: 1000000 INFO @ Tue, 30 Jun 2020 03:12:07: 2000000 INFO @ Tue, 30 Jun 2020 03:12:13: 3000000 INFO @ Tue, 30 Jun 2020 03:12:20: 4000000 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 03:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.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 03:12:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:27: 5000000 INFO @ Tue, 30 Jun 2020 03:12:31: 1000000 INFO @ Tue, 30 Jun 2020 03:12:34: 6000000 INFO @ Tue, 30 Jun 2020 03:12:38: 2000000 INFO @ Tue, 30 Jun 2020 03:12:41: 7000000 INFO @ Tue, 30 Jun 2020 03:12:45: 3000000 INFO @ Tue, 30 Jun 2020 03:12:48: 8000000 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 03:12:52: 4000000 INFO @ Tue, 30 Jun 2020 03:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.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 03:12:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:55: 9000000 INFO @ Tue, 30 Jun 2020 03:13:00: 5000000 INFO @ Tue, 30 Jun 2020 03:13:01: 1000000 INFO @ Tue, 30 Jun 2020 03:13:02: 10000000 INFO @ Tue, 30 Jun 2020 03:13:07: 6000000 INFO @ Tue, 30 Jun 2020 03:13:08: 2000000 INFO @ Tue, 30 Jun 2020 03:13:09: 11000000 INFO @ Tue, 30 Jun 2020 03:13:15: 7000000 INFO @ Tue, 30 Jun 2020 03:13:16: 3000000 INFO @ Tue, 30 Jun 2020 03:13:16: 12000000 INFO @ Tue, 30 Jun 2020 03:13:22: 8000000 INFO @ Tue, 30 Jun 2020 03:13:23: 13000000 INFO @ Tue, 30 Jun 2020 03:13:23: 4000000 INFO @ Tue, 30 Jun 2020 03:13:30: 9000000 INFO @ Tue, 30 Jun 2020 03:13:30: 14000000 INFO @ Tue, 30 Jun 2020 03:13:31: 5000000 INFO @ Tue, 30 Jun 2020 03:13:37: 10000000 INFO @ Tue, 30 Jun 2020 03:13:37: 15000000 INFO @ Tue, 30 Jun 2020 03:13:38: 6000000 INFO @ Tue, 30 Jun 2020 03:13:44: 16000000 INFO @ Tue, 30 Jun 2020 03:13:44: 11000000 INFO @ Tue, 30 Jun 2020 03:13:46: 7000000 INFO @ Tue, 30 Jun 2020 03:13:51: 17000000 INFO @ Tue, 30 Jun 2020 03:13:52: 12000000 INFO @ Tue, 30 Jun 2020 03:13:53: 8000000 INFO @ Tue, 30 Jun 2020 03:13:58: 18000000 INFO @ Tue, 30 Jun 2020 03:13:59: 13000000 INFO @ Tue, 30 Jun 2020 03:14:00: 9000000 INFO @ Tue, 30 Jun 2020 03:14:05: 19000000 INFO @ Tue, 30 Jun 2020 03:14:06: 14000000 INFO @ Tue, 30 Jun 2020 03:14:07: 10000000 INFO @ Tue, 30 Jun 2020 03:14:11: 20000000 INFO @ Tue, 30 Jun 2020 03:14:12: 15000000 INFO @ Tue, 30 Jun 2020 03:14:13: 11000000 INFO @ Tue, 30 Jun 2020 03:14:19: 21000000 INFO @ Tue, 30 Jun 2020 03:14:19: 16000000 INFO @ Tue, 30 Jun 2020 03:14:20: 12000000 INFO @ Tue, 30 Jun 2020 03:14:25: 22000000 INFO @ Tue, 30 Jun 2020 03:14:26: 17000000 INFO @ Tue, 30 Jun 2020 03:14:27: 13000000 INFO @ Tue, 30 Jun 2020 03:14:32: 23000000 INFO @ Tue, 30 Jun 2020 03:14:33: 18000000 INFO @ Tue, 30 Jun 2020 03:14:34: 14000000 INFO @ Tue, 30 Jun 2020 03:14:39: 24000000 INFO @ Tue, 30 Jun 2020 03:14:39: 19000000 INFO @ Tue, 30 Jun 2020 03:14:40: 15000000 INFO @ Tue, 30 Jun 2020 03:14:45: 25000000 INFO @ Tue, 30 Jun 2020 03:14:46: 20000000 INFO @ Tue, 30 Jun 2020 03:14:47: 16000000 INFO @ Tue, 30 Jun 2020 03:14:52: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:14:53: 21000000 INFO @ Tue, 30 Jun 2020 03:14:54: 17000000 INFO @ Tue, 30 Jun 2020 03:14:54: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:14:54: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:14:54: #1 total tags in treatment: 26214580 INFO @ Tue, 30 Jun 2020 03:14:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:54: #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 03:14:55: #1 tags after filtering in treatment: 26214499 INFO @ Tue, 30 Jun 2020 03:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:56: #2 number of paired peaks: 134 WARNING @ Tue, 30 Jun 2020 03:14:56: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:56: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:57: #2 predicted fragment length is 70 bps INFO @ Tue, 30 Jun 2020 03:14:57: #2 alternative fragment length(s) may be 2,53,70,108,120,139 bps INFO @ Tue, 30 Jun 2020 03:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.05_model.r WARNING @ Tue, 30 Jun 2020 03:14:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:14:57: #2 You may need to consider one of the other alternative d(s): 2,53,70,108,120,139 WARNING @ Tue, 30 Jun 2020 03:14:57: #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 03:14:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:59: 22000000 INFO @ Tue, 30 Jun 2020 03:15:00: 18000000 INFO @ Tue, 30 Jun 2020 03:15:05: 23000000 INFO @ Tue, 30 Jun 2020 03:15:06: 19000000 INFO @ Tue, 30 Jun 2020 03:15:11: 24000000 INFO @ Tue, 30 Jun 2020 03:15:12: 20000000 INFO @ Tue, 30 Jun 2020 03:15:18: 25000000 INFO @ Tue, 30 Jun 2020 03:15:18: 21000000 INFO @ Tue, 30 Jun 2020 03:15:24: 26000000 INFO @ Tue, 30 Jun 2020 03:15:24: 22000000 INFO @ Tue, 30 Jun 2020 03:15:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:15:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:15:25: #1 total tags in treatment: 26214580 INFO @ Tue, 30 Jun 2020 03:15:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:25: #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 03:15:26: #1 tags after filtering in treatment: 26214499 INFO @ Tue, 30 Jun 2020 03:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:26: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:28: #2 number of paired peaks: 134 WARNING @ Tue, 30 Jun 2020 03:15:28: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:28: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:28: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:28: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:28: #2 predicted fragment length is 70 bps INFO @ Tue, 30 Jun 2020 03:15:28: #2 alternative fragment length(s) may be 2,53,70,108,120,139 bps INFO @ Tue, 30 Jun 2020 03:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.10_model.r WARNING @ Tue, 30 Jun 2020 03:15:28: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:28: #2 You may need to consider one of the other alternative d(s): 2,53,70,108,120,139 WARNING @ Tue, 30 Jun 2020 03:15:28: #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 03:15:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:30: 23000000 INFO @ Tue, 30 Jun 2020 03:15:36: 24000000 INFO @ Tue, 30 Jun 2020 03:15:42: 25000000 INFO @ Tue, 30 Jun 2020 03:15:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:48: 26000000 INFO @ Tue, 30 Jun 2020 03:15:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:15:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:15:50: #1 total tags in treatment: 26214580 INFO @ Tue, 30 Jun 2020 03:15:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:50: #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 03:15:50: #1 tags after filtering in treatment: 26214499 INFO @ Tue, 30 Jun 2020 03:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:52: #2 number of paired peaks: 134 WARNING @ Tue, 30 Jun 2020 03:15:52: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:52: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:52: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:52: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:52: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:52: #2 predicted fragment length is 70 bps INFO @ Tue, 30 Jun 2020 03:15:52: #2 alternative fragment length(s) may be 2,53,70,108,120,139 bps INFO @ Tue, 30 Jun 2020 03:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.20_model.r WARNING @ Tue, 30 Jun 2020 03:15:52: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:52: #2 You may need to consider one of the other alternative d(s): 2,53,70,108,120,139 WARNING @ Tue, 30 Jun 2020 03:15:52: #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 03:15:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.05_summits.bed INFO @ Tue, 30 Jun 2020 03:16:14: Done! pass1 - making usageList (340 chroms): 1 millis pass2 - checking and writing primary data (1022 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:16:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:16:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.10_summits.bed INFO @ Tue, 30 Jun 2020 03:16:45: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379461/SRX5379461.20_summits.bed INFO @ Tue, 30 Jun 2020 03:17:07: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 5 millis CompletedMACS2peakCalling