Job ID = 6529696 SRX = SRX3981677 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: 00:09:51 35601525 reads; of these: 35601525 (100.00%) were unpaired; of these: 1026814 (2.88%) aligned 0 times 25325397 (71.14%) aligned exactly 1 time 9249314 (25.98%) aligned >1 times 97.12% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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] 4530951 / 34574711 = 0.1310 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 02:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.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 02:46:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:07: 1000000 INFO @ Tue, 30 Jun 2020 02:46:14: 2000000 INFO @ Tue, 30 Jun 2020 02:46:20: 3000000 INFO @ Tue, 30 Jun 2020 02:46:27: 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 02:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.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 02:46:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:33: 5000000 INFO @ Tue, 30 Jun 2020 02:46:38: 1000000 INFO @ Tue, 30 Jun 2020 02:46:40: 6000000 INFO @ Tue, 30 Jun 2020 02:46:44: 2000000 INFO @ Tue, 30 Jun 2020 02:46:47: 7000000 INFO @ Tue, 30 Jun 2020 02:46:51: 3000000 INFO @ Tue, 30 Jun 2020 02:46:54: 8000000 INFO @ Tue, 30 Jun 2020 02:46:57: 4000000 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 02:47:01: 9000000 INFO @ Tue, 30 Jun 2020 02:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.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 02:47:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:04: 5000000 INFO @ Tue, 30 Jun 2020 02:47:07: 10000000 INFO @ Tue, 30 Jun 2020 02:47:08: 1000000 INFO @ Tue, 30 Jun 2020 02:47:11: 6000000 INFO @ Tue, 30 Jun 2020 02:47:14: 11000000 INFO @ Tue, 30 Jun 2020 02:47:14: 2000000 INFO @ Tue, 30 Jun 2020 02:47:17: 7000000 INFO @ Tue, 30 Jun 2020 02:47:21: 3000000 INFO @ Tue, 30 Jun 2020 02:47:21: 12000000 INFO @ Tue, 30 Jun 2020 02:47:24: 8000000 INFO @ Tue, 30 Jun 2020 02:47:28: 4000000 INFO @ Tue, 30 Jun 2020 02:47:28: 13000000 INFO @ Tue, 30 Jun 2020 02:47:31: 9000000 INFO @ Tue, 30 Jun 2020 02:47:34: 5000000 INFO @ Tue, 30 Jun 2020 02:47:35: 14000000 INFO @ Tue, 30 Jun 2020 02:47:38: 10000000 INFO @ Tue, 30 Jun 2020 02:47:41: 6000000 INFO @ Tue, 30 Jun 2020 02:47:42: 15000000 INFO @ Tue, 30 Jun 2020 02:47:44: 11000000 INFO @ Tue, 30 Jun 2020 02:47:48: 7000000 INFO @ Tue, 30 Jun 2020 02:47:49: 16000000 INFO @ Tue, 30 Jun 2020 02:47:51: 12000000 INFO @ Tue, 30 Jun 2020 02:47:54: 8000000 INFO @ Tue, 30 Jun 2020 02:47:56: 17000000 INFO @ Tue, 30 Jun 2020 02:47:58: 13000000 INFO @ Tue, 30 Jun 2020 02:48:01: 9000000 INFO @ Tue, 30 Jun 2020 02:48:03: 18000000 INFO @ Tue, 30 Jun 2020 02:48:05: 14000000 INFO @ Tue, 30 Jun 2020 02:48:08: 10000000 INFO @ Tue, 30 Jun 2020 02:48:09: 19000000 INFO @ Tue, 30 Jun 2020 02:48:12: 15000000 INFO @ Tue, 30 Jun 2020 02:48:15: 11000000 INFO @ Tue, 30 Jun 2020 02:48:16: 20000000 INFO @ Tue, 30 Jun 2020 02:48:19: 16000000 INFO @ Tue, 30 Jun 2020 02:48:21: 12000000 INFO @ Tue, 30 Jun 2020 02:48:23: 21000000 INFO @ Tue, 30 Jun 2020 02:48:26: 17000000 INFO @ Tue, 30 Jun 2020 02:48:28: 13000000 INFO @ Tue, 30 Jun 2020 02:48:30: 22000000 INFO @ Tue, 30 Jun 2020 02:48:33: 18000000 INFO @ Tue, 30 Jun 2020 02:48:35: 14000000 INFO @ Tue, 30 Jun 2020 02:48:37: 23000000 INFO @ Tue, 30 Jun 2020 02:48:40: 19000000 INFO @ Tue, 30 Jun 2020 02:48:42: 15000000 INFO @ Tue, 30 Jun 2020 02:48:44: 24000000 INFO @ Tue, 30 Jun 2020 02:48:47: 20000000 INFO @ Tue, 30 Jun 2020 02:48:49: 16000000 INFO @ Tue, 30 Jun 2020 02:48:51: 25000000 INFO @ Tue, 30 Jun 2020 02:48:54: 21000000 INFO @ Tue, 30 Jun 2020 02:48:55: 17000000 INFO @ Tue, 30 Jun 2020 02:48:58: 26000000 INFO @ Tue, 30 Jun 2020 02:49:01: 22000000 INFO @ Tue, 30 Jun 2020 02:49:02: 18000000 INFO @ Tue, 30 Jun 2020 02:49:05: 27000000 INFO @ Tue, 30 Jun 2020 02:49:08: 23000000 INFO @ Tue, 30 Jun 2020 02:49:09: 19000000 INFO @ Tue, 30 Jun 2020 02:49:12: 28000000 INFO @ Tue, 30 Jun 2020 02:49:15: 24000000 INFO @ Tue, 30 Jun 2020 02:49:16: 20000000 INFO @ Tue, 30 Jun 2020 02:49:19: 29000000 INFO @ Tue, 30 Jun 2020 02:49:22: 25000000 INFO @ Tue, 30 Jun 2020 02:49:23: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:49:26: 30000000 INFO @ Tue, 30 Jun 2020 02:49:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:49:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:49:27: #1 total tags in treatment: 30043760 INFO @ Tue, 30 Jun 2020 02:49:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:27: #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 02:49:28: #1 tags after filtering in treatment: 30043712 INFO @ Tue, 30 Jun 2020 02:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:30: 26000000 INFO @ Tue, 30 Jun 2020 02:49:30: #2 number of paired peaks: 219 WARNING @ Tue, 30 Jun 2020 02:49:30: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:30: 22000000 INFO @ Tue, 30 Jun 2020 02:49:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:30: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:49:30: #2 alternative fragment length(s) may be 1,41,54,593 bps INFO @ Tue, 30 Jun 2020 02:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:30: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:30: #2 You may need to consider one of the other alternative d(s): 1,41,54,593 WARNING @ Tue, 30 Jun 2020 02:49:30: #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 02:49:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:37: 23000000 INFO @ Tue, 30 Jun 2020 02:49:37: 27000000 INFO @ Tue, 30 Jun 2020 02:49:44: 24000000 INFO @ Tue, 30 Jun 2020 02:49:44: 28000000 INFO @ Tue, 30 Jun 2020 02:49:50: 25000000 INFO @ Tue, 30 Jun 2020 02:49:51: 29000000 INFO @ Tue, 30 Jun 2020 02:49:58: 26000000 INFO @ Tue, 30 Jun 2020 02:49:58: 30000000 INFO @ Tue, 30 Jun 2020 02:49:59: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:49:59: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:49:59: #1 total tags in treatment: 30043760 INFO @ Tue, 30 Jun 2020 02:49:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:59: #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 02:50:00: #1 tags after filtering in treatment: 30043712 INFO @ Tue, 30 Jun 2020 02:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:02: #2 number of paired peaks: 219 WARNING @ Tue, 30 Jun 2020 02:50:02: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:02: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:50:02: #2 alternative fragment length(s) may be 1,41,54,593 bps INFO @ Tue, 30 Jun 2020 02:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:02: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:02: #2 You may need to consider one of the other alternative d(s): 1,41,54,593 WARNING @ Tue, 30 Jun 2020 02:50:02: #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 02:50:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:04: 27000000 INFO @ Tue, 30 Jun 2020 02:50:11: 28000000 INFO @ Tue, 30 Jun 2020 02:50:18: 29000000 INFO @ Tue, 30 Jun 2020 02:50:24: 30000000 INFO @ Tue, 30 Jun 2020 02:50:25: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:50:25: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:50:25: #1 total tags in treatment: 30043760 INFO @ Tue, 30 Jun 2020 02:50:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:25: #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 02:50:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:26: #1 tags after filtering in treatment: 30043712 INFO @ Tue, 30 Jun 2020 02:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:28: #2 number of paired peaks: 219 WARNING @ Tue, 30 Jun 2020 02:50:28: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:28: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:50:28: #2 alternative fragment length(s) may be 1,41,54,593 bps INFO @ Tue, 30 Jun 2020 02:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:28: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:28: #2 You may need to consider one of the other alternative d(s): 1,41,54,593 WARNING @ Tue, 30 Jun 2020 02:50:28: #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 02:50:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:54: Done! pass1 - making usageList (643 chroms): 2 millis pass2 - checking and writing primary data (3002 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.10_summits.bed INFO @ Tue, 30 Jun 2020 02:51:30: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1957 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981677/SRX3981677.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:52: Done! pass1 - making usageList (306 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 10 millis CompletedMACS2peakCalling