Job ID = 6529302 SRX = SRX1433363 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: 00:11:35 40210964 reads; of these: 40210964 (100.00%) were unpaired; of these: 1106887 (2.75%) aligned 0 times 30468529 (75.77%) aligned exactly 1 time 8635548 (21.48%) aligned >1 times 97.25% overall alignment rate Time searching: 00:11:35 Overall time: 00:11:35 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] 9354359 / 39104077 = 0.2392 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 02:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.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 02:09:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:50: 1000000 INFO @ Tue, 30 Jun 2020 02:09:55: 2000000 INFO @ Tue, 30 Jun 2020 02:10:01: 3000000 INFO @ Tue, 30 Jun 2020 02:10:07: 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 02:10:13: 5000000 INFO @ Tue, 30 Jun 2020 02:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.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 02:10:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:20: 6000000 INFO @ Tue, 30 Jun 2020 02:10:20: 1000000 INFO @ Tue, 30 Jun 2020 02:10:26: 2000000 INFO @ Tue, 30 Jun 2020 02:10:26: 7000000 INFO @ Tue, 30 Jun 2020 02:10:33: 3000000 INFO @ Tue, 30 Jun 2020 02:10:33: 8000000 INFO @ Tue, 30 Jun 2020 02:10:39: 4000000 INFO @ Tue, 30 Jun 2020 02:10:39: 9000000 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 02:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.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 02:10:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:45: 5000000 INFO @ Tue, 30 Jun 2020 02:10:46: 10000000 INFO @ Tue, 30 Jun 2020 02:10:50: 1000000 INFO @ Tue, 30 Jun 2020 02:10:52: 6000000 INFO @ Tue, 30 Jun 2020 02:10:52: 11000000 INFO @ Tue, 30 Jun 2020 02:10:58: 2000000 INFO @ Tue, 30 Jun 2020 02:10:59: 12000000 INFO @ Tue, 30 Jun 2020 02:10:59: 7000000 INFO @ Tue, 30 Jun 2020 02:11:05: 3000000 INFO @ Tue, 30 Jun 2020 02:11:06: 13000000 INFO @ Tue, 30 Jun 2020 02:11:06: 8000000 INFO @ Tue, 30 Jun 2020 02:11:12: 4000000 INFO @ Tue, 30 Jun 2020 02:11:12: 14000000 INFO @ Tue, 30 Jun 2020 02:11:13: 9000000 INFO @ Tue, 30 Jun 2020 02:11:19: 5000000 INFO @ Tue, 30 Jun 2020 02:11:19: 15000000 INFO @ Tue, 30 Jun 2020 02:11:20: 10000000 INFO @ Tue, 30 Jun 2020 02:11:26: 6000000 INFO @ Tue, 30 Jun 2020 02:11:26: 16000000 INFO @ Tue, 30 Jun 2020 02:11:26: 11000000 INFO @ Tue, 30 Jun 2020 02:11:33: 17000000 INFO @ Tue, 30 Jun 2020 02:11:33: 12000000 INFO @ Tue, 30 Jun 2020 02:11:33: 7000000 INFO @ Tue, 30 Jun 2020 02:11:39: 18000000 INFO @ Tue, 30 Jun 2020 02:11:40: 13000000 INFO @ Tue, 30 Jun 2020 02:11:40: 8000000 INFO @ Tue, 30 Jun 2020 02:11:46: 19000000 INFO @ Tue, 30 Jun 2020 02:11:46: 14000000 INFO @ Tue, 30 Jun 2020 02:11:48: 9000000 INFO @ Tue, 30 Jun 2020 02:11:52: 20000000 INFO @ Tue, 30 Jun 2020 02:11:53: 15000000 INFO @ Tue, 30 Jun 2020 02:11:54: 10000000 INFO @ Tue, 30 Jun 2020 02:11:59: 21000000 INFO @ Tue, 30 Jun 2020 02:11:59: 16000000 INFO @ Tue, 30 Jun 2020 02:12:01: 11000000 INFO @ Tue, 30 Jun 2020 02:12:05: 22000000 INFO @ Tue, 30 Jun 2020 02:12:06: 17000000 INFO @ Tue, 30 Jun 2020 02:12:08: 12000000 INFO @ Tue, 30 Jun 2020 02:12:12: 23000000 INFO @ Tue, 30 Jun 2020 02:12:13: 18000000 INFO @ Tue, 30 Jun 2020 02:12:15: 13000000 INFO @ Tue, 30 Jun 2020 02:12:19: 19000000 INFO @ Tue, 30 Jun 2020 02:12:19: 24000000 INFO @ Tue, 30 Jun 2020 02:12:21: 14000000 INFO @ Tue, 30 Jun 2020 02:12:25: 20000000 INFO @ Tue, 30 Jun 2020 02:12:26: 25000000 INFO @ Tue, 30 Jun 2020 02:12:28: 15000000 INFO @ Tue, 30 Jun 2020 02:12:32: 21000000 INFO @ Tue, 30 Jun 2020 02:12:33: 26000000 INFO @ Tue, 30 Jun 2020 02:12:35: 16000000 INFO @ Tue, 30 Jun 2020 02:12:38: 22000000 INFO @ Tue, 30 Jun 2020 02:12:40: 27000000 INFO @ Tue, 30 Jun 2020 02:12:42: 17000000 INFO @ Tue, 30 Jun 2020 02:12:45: 23000000 INFO @ Tue, 30 Jun 2020 02:12:47: 28000000 INFO @ Tue, 30 Jun 2020 02:12:49: 18000000 INFO @ Tue, 30 Jun 2020 02:12:52: 24000000 INFO @ Tue, 30 Jun 2020 02:12:54: 29000000 INFO @ Tue, 30 Jun 2020 02:12:56: 19000000 INFO @ Tue, 30 Jun 2020 02:12:59: 25000000 INFO @ Tue, 30 Jun 2020 02:12:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:12:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:12:59: #1 total tags in treatment: 29749718 INFO @ Tue, 30 Jun 2020 02:12:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:59: #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 02:13:01: #1 tags after filtering in treatment: 29749681 INFO @ Tue, 30 Jun 2020 02:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:02: 20000000 INFO @ Tue, 30 Jun 2020 02:13:03: #2 number of paired peaks: 107 WARNING @ Tue, 30 Jun 2020 02:13:03: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:03: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:13:03: #2 alternative fragment length(s) may be 2,50,531,578 bps INFO @ Tue, 30 Jun 2020 02:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.05_model.r WARNING @ Tue, 30 Jun 2020 02:13:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:13:03: #2 You may need to consider one of the other alternative d(s): 2,50,531,578 WARNING @ Tue, 30 Jun 2020 02:13:03: #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 02:13:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:05: 26000000 INFO @ Tue, 30 Jun 2020 02:13:08: 21000000 INFO @ Tue, 30 Jun 2020 02:13:12: 27000000 INFO @ Tue, 30 Jun 2020 02:13:15: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:13:18: 28000000 INFO @ Tue, 30 Jun 2020 02:13:21: 23000000 INFO @ Tue, 30 Jun 2020 02:13:25: 29000000 INFO @ Tue, 30 Jun 2020 02:13:28: 24000000 INFO @ Tue, 30 Jun 2020 02:13:30: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:30: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:30: #1 total tags in treatment: 29749718 INFO @ Tue, 30 Jun 2020 02:13:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:30: #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 02:13:31: #1 tags after filtering in treatment: 29749681 INFO @ Tue, 30 Jun 2020 02:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:33: #2 number of paired peaks: 107 WARNING @ Tue, 30 Jun 2020 02:13:33: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:33: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:13:33: #2 alternative fragment length(s) may be 2,50,531,578 bps INFO @ Tue, 30 Jun 2020 02:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.10_model.r WARNING @ Tue, 30 Jun 2020 02:13:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:13:33: #2 You may need to consider one of the other alternative d(s): 2,50,531,578 WARNING @ Tue, 30 Jun 2020 02:13:33: #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 02:13:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:34: 25000000 INFO @ Tue, 30 Jun 2020 02:13:40: 26000000 INFO @ Tue, 30 Jun 2020 02:13:46: 27000000 INFO @ Tue, 30 Jun 2020 02:13:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:53: 28000000 INFO @ Tue, 30 Jun 2020 02:13:59: 29000000 INFO @ Tue, 30 Jun 2020 02:14:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:14:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:14:04: #1 total tags in treatment: 29749718 INFO @ Tue, 30 Jun 2020 02:14:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:14:04: #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 02:14:05: #1 tags after filtering in treatment: 29749681 INFO @ Tue, 30 Jun 2020 02:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:14:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:14:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:14:07: #2 number of paired peaks: 107 WARNING @ Tue, 30 Jun 2020 02:14:07: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Tue, 30 Jun 2020 02:14:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:14:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:14:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:14:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:14:07: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:14:07: #2 alternative fragment length(s) may be 2,50,531,578 bps INFO @ Tue, 30 Jun 2020 02:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.20_model.r WARNING @ Tue, 30 Jun 2020 02:14:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:14:07: #2 You may need to consider one of the other alternative d(s): 2,50,531,578 WARNING @ Tue, 30 Jun 2020 02:14:07: #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 02:14:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:14:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.05_summits.bed INFO @ Tue, 30 Jun 2020 02:14:15: Done! pass1 - making usageList (481 chroms): 2 millis pass2 - checking and writing primary data (2135 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:14:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.10_summits.bed INFO @ Tue, 30 Jun 2020 02:14:44: Done! pass1 - making usageList (256 chroms): 2 millis pass2 - checking and writing primary data (735 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:14:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433363/SRX1433363.20_summits.bed INFO @ Tue, 30 Jun 2020 02:15:19: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 7 millis CompletedMACS2peakCalling