Job ID = 6529678 SRX = SRX3981652 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: 00:10:39 42463232 reads; of these: 42463232 (100.00%) were unpaired; of these: 1359487 (3.20%) aligned 0 times 30145738 (70.99%) aligned exactly 1 time 10958007 (25.81%) aligned >1 times 96.80% overall alignment rate Time searching: 00:10:39 Overall time: 00:10:39 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 20 files... [bam_rmdupse_core] 5856028 / 41103745 = 0.1425 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 03:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.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 03:09:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:39: 1000000 INFO @ Tue, 30 Jun 2020 03:09:44: 2000000 INFO @ Tue, 30 Jun 2020 03:09:49: 3000000 INFO @ Tue, 30 Jun 2020 03:09:53: 4000000 INFO @ Tue, 30 Jun 2020 03:09:58: 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 03:10:03: 6000000 INFO @ Tue, 30 Jun 2020 03:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.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 03:10:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:07: 7000000 INFO @ Tue, 30 Jun 2020 03:10:09: 1000000 INFO @ Tue, 30 Jun 2020 03:10:12: 8000000 INFO @ Tue, 30 Jun 2020 03:10:13: 2000000 INFO @ Tue, 30 Jun 2020 03:10:17: 9000000 INFO @ Tue, 30 Jun 2020 03:10:18: 3000000 INFO @ Tue, 30 Jun 2020 03:10:22: 10000000 INFO @ Tue, 30 Jun 2020 03:10:23: 4000000 INFO @ Tue, 30 Jun 2020 03:10:28: 11000000 INFO @ Tue, 30 Jun 2020 03:10:28: 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 03:10:32: 12000000 INFO @ Tue, 30 Jun 2020 03:10:33: 6000000 INFO @ Tue, 30 Jun 2020 03:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.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 03:10:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:37: 13000000 INFO @ Tue, 30 Jun 2020 03:10:38: 7000000 INFO @ Tue, 30 Jun 2020 03:10:39: 1000000 INFO @ Tue, 30 Jun 2020 03:10:42: 14000000 INFO @ Tue, 30 Jun 2020 03:10:42: 8000000 INFO @ Tue, 30 Jun 2020 03:10:44: 2000000 INFO @ Tue, 30 Jun 2020 03:10:47: 15000000 INFO @ Tue, 30 Jun 2020 03:10:47: 9000000 INFO @ Tue, 30 Jun 2020 03:10:48: 3000000 INFO @ Tue, 30 Jun 2020 03:10:52: 16000000 INFO @ Tue, 30 Jun 2020 03:10:52: 10000000 INFO @ Tue, 30 Jun 2020 03:10:53: 4000000 INFO @ Tue, 30 Jun 2020 03:10:56: 17000000 INFO @ Tue, 30 Jun 2020 03:10:57: 11000000 INFO @ Tue, 30 Jun 2020 03:10:58: 5000000 INFO @ Tue, 30 Jun 2020 03:11:01: 18000000 INFO @ Tue, 30 Jun 2020 03:11:02: 12000000 INFO @ Tue, 30 Jun 2020 03:11:03: 6000000 INFO @ Tue, 30 Jun 2020 03:11:06: 19000000 INFO @ Tue, 30 Jun 2020 03:11:07: 13000000 INFO @ Tue, 30 Jun 2020 03:11:08: 7000000 INFO @ Tue, 30 Jun 2020 03:11:11: 20000000 INFO @ Tue, 30 Jun 2020 03:11:11: 14000000 INFO @ Tue, 30 Jun 2020 03:11:13: 8000000 INFO @ Tue, 30 Jun 2020 03:11:16: 21000000 INFO @ Tue, 30 Jun 2020 03:11:16: 15000000 INFO @ Tue, 30 Jun 2020 03:11:18: 9000000 INFO @ Tue, 30 Jun 2020 03:11:20: 22000000 INFO @ Tue, 30 Jun 2020 03:11:21: 16000000 INFO @ Tue, 30 Jun 2020 03:11:23: 10000000 INFO @ Tue, 30 Jun 2020 03:11:25: 23000000 INFO @ Tue, 30 Jun 2020 03:11:26: 17000000 INFO @ Tue, 30 Jun 2020 03:11:27: 11000000 INFO @ Tue, 30 Jun 2020 03:11:30: 24000000 INFO @ Tue, 30 Jun 2020 03:11:31: 18000000 INFO @ Tue, 30 Jun 2020 03:11:32: 12000000 INFO @ Tue, 30 Jun 2020 03:11:35: 25000000 INFO @ Tue, 30 Jun 2020 03:11:35: 19000000 INFO @ Tue, 30 Jun 2020 03:11:37: 13000000 INFO @ Tue, 30 Jun 2020 03:11:40: 26000000 INFO @ Tue, 30 Jun 2020 03:11:40: 20000000 INFO @ Tue, 30 Jun 2020 03:11:42: 14000000 INFO @ Tue, 30 Jun 2020 03:11:45: 27000000 INFO @ Tue, 30 Jun 2020 03:11:45: 21000000 INFO @ Tue, 30 Jun 2020 03:11:47: 15000000 INFO @ Tue, 30 Jun 2020 03:11:50: 28000000 INFO @ Tue, 30 Jun 2020 03:11:50: 22000000 INFO @ Tue, 30 Jun 2020 03:11:52: 16000000 INFO @ Tue, 30 Jun 2020 03:11:55: 29000000 INFO @ Tue, 30 Jun 2020 03:11:55: 23000000 INFO @ Tue, 30 Jun 2020 03:11:57: 17000000 INFO @ Tue, 30 Jun 2020 03:12:00: 24000000 INFO @ Tue, 30 Jun 2020 03:12:00: 30000000 INFO @ Tue, 30 Jun 2020 03:12:01: 18000000 INFO @ Tue, 30 Jun 2020 03:12:05: 25000000 INFO @ Tue, 30 Jun 2020 03:12:05: 31000000 INFO @ Tue, 30 Jun 2020 03:12:06: 19000000 INFO @ Tue, 30 Jun 2020 03:12:10: 26000000 INFO @ Tue, 30 Jun 2020 03:12:10: 32000000 INFO @ Tue, 30 Jun 2020 03:12:11: 20000000 INFO @ Tue, 30 Jun 2020 03:12:15: 27000000 INFO @ Tue, 30 Jun 2020 03:12:15: 33000000 INFO @ Tue, 30 Jun 2020 03:12:16: 21000000 INFO @ Tue, 30 Jun 2020 03:12:20: 28000000 INFO @ Tue, 30 Jun 2020 03:12:20: 34000000 INFO @ Tue, 30 Jun 2020 03:12:21: 22000000 INFO @ Tue, 30 Jun 2020 03:12:25: 29000000 INFO @ Tue, 30 Jun 2020 03:12:25: 35000000 INFO @ Tue, 30 Jun 2020 03:12:26: 23000000 INFO @ Tue, 30 Jun 2020 03:12:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:12:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:12:27: #1 total tags in treatment: 35247717 INFO @ Tue, 30 Jun 2020 03:12:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:27: #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 03:12:28: #1 tags after filtering in treatment: 35247669 INFO @ Tue, 30 Jun 2020 03:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:28: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:30: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 03:12:30: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:30: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:12:30: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 30 Jun 2020 03:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.05_model.r WARNING @ Tue, 30 Jun 2020 03:12:30: #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 03:12:30: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 30 Jun 2020 03:12:30: #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 03:12:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:30: 30000000 INFO @ Tue, 30 Jun 2020 03:12:32: 24000000 INFO @ Tue, 30 Jun 2020 03:12:35: 31000000 INFO @ Tue, 30 Jun 2020 03:12:37: 25000000 INFO @ Tue, 30 Jun 2020 03:12:40: 32000000 INFO @ Tue, 30 Jun 2020 03:12:41: 26000000 INFO @ Tue, 30 Jun 2020 03:12:45: 33000000 INFO @ Tue, 30 Jun 2020 03:12:46: 27000000 INFO @ Tue, 30 Jun 2020 03:12:50: 34000000 INFO @ Tue, 30 Jun 2020 03:12:51: 28000000 INFO @ Tue, 30 Jun 2020 03:12:55: 35000000 INFO @ Tue, 30 Jun 2020 03:12:56: 29000000 INFO @ Tue, 30 Jun 2020 03:12:57: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:12:57: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:12:57: #1 total tags in treatment: 35247717 INFO @ Tue, 30 Jun 2020 03:12:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:58: #1 tags after filtering in treatment: 35247669 INFO @ Tue, 30 Jun 2020 03:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:58: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:00: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 03:13:00: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:00: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:00: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:00: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:00: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:00: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:13:00: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 30 Jun 2020 03:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.10_model.r WARNING @ Tue, 30 Jun 2020 03:13:00: #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 03:13:00: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 30 Jun 2020 03:13:00: #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 03:13:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:01: 30000000 INFO @ Tue, 30 Jun 2020 03:13:06: 31000000 INFO @ Tue, 30 Jun 2020 03:13:11: 32000000 INFO @ Tue, 30 Jun 2020 03:13:15: 33000000 INFO @ Tue, 30 Jun 2020 03:13:20: 34000000 INFO @ Tue, 30 Jun 2020 03:13:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:25: 35000000 INFO @ Tue, 30 Jun 2020 03:13:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:13:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:13:27: #1 total tags in treatment: 35247717 INFO @ Tue, 30 Jun 2020 03:13:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:27: #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 03:13:27: #1 tags after filtering in treatment: 35247669 INFO @ Tue, 30 Jun 2020 03:13:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:30: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 03:13:30: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:30: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:13:30: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 30 Jun 2020 03:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:30: #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 03:13:30: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 30 Jun 2020 03:13:30: #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 03:13:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.05_summits.bed INFO @ Tue, 30 Jun 2020 03:13:51: Done! pass1 - making usageList (661 chroms): 2 millis pass2 - checking and writing primary data (3147 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:14:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.10_summits.bed INFO @ Tue, 30 Jun 2020 03:14:21: Done! pass1 - making usageList (518 chroms): 2 millis pass2 - checking and writing primary data (2124 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981652/SRX3981652.20_summits.bed INFO @ Tue, 30 Jun 2020 03:14:51: Done! pass1 - making usageList (294 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 9 millis CompletedMACS2peakCalling