Job ID = 6529880 SRX = SRX5343148 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: 00:14:08 34725896 reads; of these: 34725896 (100.00%) were unpaired; of these: 1558811 (4.49%) aligned 0 times 23117107 (66.57%) aligned exactly 1 time 10049978 (28.94%) aligned >1 times 95.51% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 5368385 / 33167085 = 0.1619 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 03:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.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 03:22:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:21: 1000000 INFO @ Tue, 30 Jun 2020 03:22:27: 2000000 INFO @ Tue, 30 Jun 2020 03:22:33: 3000000 INFO @ Tue, 30 Jun 2020 03:22:39: 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 03:22:45: 5000000 INFO @ Tue, 30 Jun 2020 03:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.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 03:22:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:51: 6000000 INFO @ Tue, 30 Jun 2020 03:22:53: 1000000 INFO @ Tue, 30 Jun 2020 03:22:58: 7000000 INFO @ Tue, 30 Jun 2020 03:23:01: 2000000 INFO @ Tue, 30 Jun 2020 03:23:05: 8000000 INFO @ Tue, 30 Jun 2020 03:23:09: 3000000 INFO @ Tue, 30 Jun 2020 03:23:12: 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 03:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.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 03:23:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:17: 4000000 INFO @ Tue, 30 Jun 2020 03:23:19: 10000000 INFO @ Tue, 30 Jun 2020 03:23:22: 1000000 INFO @ Tue, 30 Jun 2020 03:23:25: 5000000 INFO @ Tue, 30 Jun 2020 03:23:26: 11000000 INFO @ Tue, 30 Jun 2020 03:23:30: 2000000 INFO @ Tue, 30 Jun 2020 03:23:34: 6000000 INFO @ Tue, 30 Jun 2020 03:23:34: 12000000 INFO @ Tue, 30 Jun 2020 03:23:37: 3000000 INFO @ Tue, 30 Jun 2020 03:23:41: 13000000 INFO @ Tue, 30 Jun 2020 03:23:43: 7000000 INFO @ Tue, 30 Jun 2020 03:23:44: 4000000 INFO @ Tue, 30 Jun 2020 03:23:48: 14000000 INFO @ Tue, 30 Jun 2020 03:23:51: 5000000 INFO @ Tue, 30 Jun 2020 03:23:53: 8000000 INFO @ Tue, 30 Jun 2020 03:23:55: 15000000 INFO @ Tue, 30 Jun 2020 03:23:58: 6000000 INFO @ Tue, 30 Jun 2020 03:24:02: 9000000 INFO @ Tue, 30 Jun 2020 03:24:03: 16000000 INFO @ Tue, 30 Jun 2020 03:24:06: 7000000 INFO @ Tue, 30 Jun 2020 03:24:10: 17000000 INFO @ Tue, 30 Jun 2020 03:24:12: 10000000 INFO @ Tue, 30 Jun 2020 03:24:13: 8000000 INFO @ Tue, 30 Jun 2020 03:24:17: 18000000 INFO @ Tue, 30 Jun 2020 03:24:20: 9000000 INFO @ Tue, 30 Jun 2020 03:24:22: 11000000 INFO @ Tue, 30 Jun 2020 03:24:25: 19000000 INFO @ Tue, 30 Jun 2020 03:24:28: 10000000 INFO @ Tue, 30 Jun 2020 03:24:32: 12000000 INFO @ Tue, 30 Jun 2020 03:24:32: 20000000 INFO @ Tue, 30 Jun 2020 03:24:35: 11000000 INFO @ Tue, 30 Jun 2020 03:24:39: 21000000 INFO @ Tue, 30 Jun 2020 03:24:42: 13000000 INFO @ Tue, 30 Jun 2020 03:24:42: 12000000 INFO @ Tue, 30 Jun 2020 03:24:47: 22000000 INFO @ Tue, 30 Jun 2020 03:24:50: 13000000 INFO @ Tue, 30 Jun 2020 03:24:52: 14000000 INFO @ Tue, 30 Jun 2020 03:24:54: 23000000 INFO @ Tue, 30 Jun 2020 03:24:58: 14000000 INFO @ Tue, 30 Jun 2020 03:25:02: 15000000 INFO @ Tue, 30 Jun 2020 03:25:02: 24000000 INFO @ Tue, 30 Jun 2020 03:25:05: 15000000 INFO @ Tue, 30 Jun 2020 03:25:10: 25000000 INFO @ Tue, 30 Jun 2020 03:25:12: 16000000 INFO @ Tue, 30 Jun 2020 03:25:13: 16000000 INFO @ Tue, 30 Jun 2020 03:25:17: 26000000 INFO @ Tue, 30 Jun 2020 03:25:21: 17000000 INFO @ Tue, 30 Jun 2020 03:25:23: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:25:25: 27000000 INFO @ Tue, 30 Jun 2020 03:25:29: 18000000 INFO @ Tue, 30 Jun 2020 03:25:31: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:25:31: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:25:31: #1 total tags in treatment: 27798700 INFO @ Tue, 30 Jun 2020 03:25:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:25:31: #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 03:25:32: 18000000 INFO @ Tue, 30 Jun 2020 03:25:32: #1 tags after filtering in treatment: 27798699 INFO @ Tue, 30 Jun 2020 03:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:25:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:25:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:25:34: #2 number of paired peaks: 186 WARNING @ Tue, 30 Jun 2020 03:25:34: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 30 Jun 2020 03:25:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:25:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:25:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:25:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:25:34: #2 predicted fragment length is 33 bps INFO @ Tue, 30 Jun 2020 03:25:34: #2 alternative fragment length(s) may be 2,33 bps INFO @ Tue, 30 Jun 2020 03:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.05_model.r WARNING @ Tue, 30 Jun 2020 03:25:34: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:25:34: #2 You may need to consider one of the other alternative d(s): 2,33 WARNING @ Tue, 30 Jun 2020 03:25:34: #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 03:25:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:25:36: 19000000 INFO @ Tue, 30 Jun 2020 03:25:41: 19000000 INFO @ Tue, 30 Jun 2020 03:25:44: 20000000 INFO @ Tue, 30 Jun 2020 03:25:51: 20000000 INFO @ Tue, 30 Jun 2020 03:25:51: 21000000 INFO @ Tue, 30 Jun 2020 03:25:59: 22000000 INFO @ Tue, 30 Jun 2020 03:26:00: 21000000 INFO @ Tue, 30 Jun 2020 03:26:06: 23000000 INFO @ Tue, 30 Jun 2020 03:26:10: 22000000 INFO @ Tue, 30 Jun 2020 03:26:14: 24000000 INFO @ Tue, 30 Jun 2020 03:26:20: 23000000 INFO @ Tue, 30 Jun 2020 03:26:22: 25000000 INFO @ Tue, 30 Jun 2020 03:26:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:26:29: 26000000 INFO @ Tue, 30 Jun 2020 03:26:31: 24000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:26:37: 27000000 INFO @ Tue, 30 Jun 2020 03:26:41: 25000000 INFO @ Tue, 30 Jun 2020 03:26:43: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:26:43: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:26:43: #1 total tags in treatment: 27798700 INFO @ Tue, 30 Jun 2020 03:26:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:43: #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 03:26:44: #1 tags after filtering in treatment: 27798699 INFO @ Tue, 30 Jun 2020 03:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:44: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.05_summits.bed INFO @ Tue, 30 Jun 2020 03:26:45: Done! pass1 - making usageList (735 chroms): 1 millis pass2 - checking and writing primary data (2683 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:26:46: #2 number of paired peaks: 186 WARNING @ Tue, 30 Jun 2020 03:26:46: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 30 Jun 2020 03:26:46: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:46: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:46: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:46: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:46: #2 predicted fragment length is 33 bps INFO @ Tue, 30 Jun 2020 03:26:46: #2 alternative fragment length(s) may be 2,33 bps INFO @ Tue, 30 Jun 2020 03:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.20_model.r WARNING @ Tue, 30 Jun 2020 03:26:46: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:46: #2 You may need to consider one of the other alternative d(s): 2,33 WARNING @ Tue, 30 Jun 2020 03:26:46: #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 03:26:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:50: 26000000 INFO @ Tue, 30 Jun 2020 03:26:59: 27000000 INFO @ Tue, 30 Jun 2020 03:27:07: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:27:07: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:27:07: #1 total tags in treatment: 27798700 INFO @ Tue, 30 Jun 2020 03:27:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:07: #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 03:27:08: #1 tags after filtering in treatment: 27798699 INFO @ Tue, 30 Jun 2020 03:27:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:08: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:10: #2 number of paired peaks: 186 WARNING @ Tue, 30 Jun 2020 03:27:10: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:10: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:10: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:10: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:10: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:10: #2 predicted fragment length is 33 bps INFO @ Tue, 30 Jun 2020 03:27:10: #2 alternative fragment length(s) may be 2,33 bps INFO @ Tue, 30 Jun 2020 03:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.10_model.r WARNING @ Tue, 30 Jun 2020 03:27:10: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:10: #2 You may need to consider one of the other alternative d(s): 2,33 WARNING @ Tue, 30 Jun 2020 03:27:10: #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 03:27:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:27:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.20_summits.bed INFO @ Tue, 30 Jun 2020 03:27:56: Done! pass1 - making usageList (227 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:27:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343148/SRX5343148.10_summits.bed INFO @ Tue, 30 Jun 2020 03:28:19: Done! pass1 - making usageList (537 chroms): 1 millis pass2 - checking and writing primary data (1630 records, 4 fields): 19 millis CompletedMACS2peakCalling