Job ID = 6456802 SRX = SRX3981693 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:51:03 prefetch.2.10.7: 1) Downloading 'SRR7050467'... 2020-06-21T11:51:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:30 prefetch.2.10.7: 'SRR7050467' is valid 2020-06-21T11:52:30 prefetch.2.10.7: 1) 'SRR7050467' was downloaded successfully 2020-06-21T11:52:30 prefetch.2.10.7: 'SRR7050467' has 0 unresolved dependencies Read 8702669 spots for SRR7050467/SRR7050467.sra Written 8702669 spots for SRR7050467/SRR7050467.sra 2020-06-21T11:53:07 prefetch.2.10.7: 1) Downloading 'SRR7050468'... 2020-06-21T11:53:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:54:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:54:41 prefetch.2.10.7: 'SRR7050468' is valid 2020-06-21T11:54:41 prefetch.2.10.7: 1) 'SRR7050468' was downloaded successfully 2020-06-21T11:54:41 prefetch.2.10.7: 'SRR7050468' has 0 unresolved dependencies Read 8688608 spots for SRR7050468/SRR7050468.sra Written 8688608 spots for SRR7050468/SRR7050468.sra 2020-06-21T11:55:17 prefetch.2.10.7: 1) Downloading 'SRR7050469'... 2020-06-21T11:55:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:56:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:56:47 prefetch.2.10.7: 'SRR7050469' is valid 2020-06-21T11:56:47 prefetch.2.10.7: 1) 'SRR7050469' was downloaded successfully 2020-06-21T11:56:47 prefetch.2.10.7: 'SRR7050469' has 0 unresolved dependencies Read 8726350 spots for SRR7050469/SRR7050469.sra Written 8726350 spots for SRR7050469/SRR7050469.sra 2020-06-21T11:57:27 prefetch.2.10.7: 1) Downloading 'SRR7050470'... 2020-06-21T11:57:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:58:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:58:33 prefetch.2.10.7: 'SRR7050470' is valid 2020-06-21T11:58:33 prefetch.2.10.7: 1) 'SRR7050470' was downloaded successfully 2020-06-21T11:58:33 prefetch.2.10.7: 'SRR7050470' has 0 unresolved dependencies Read 8771846 spots for SRR7050470/SRR7050470.sra Written 8771846 spots for SRR7050470/SRR7050470.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:19 34889473 reads; of these: 34889473 (100.00%) were unpaired; of these: 1102684 (3.16%) aligned 0 times 26369160 (75.58%) aligned exactly 1 time 7417629 (21.26%) aligned >1 times 96.84% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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] 4858031 / 33786789 = 0.1438 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 @ Sun, 21 Jun 2020 21:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.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 @ Sun, 21 Jun 2020 21:13:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:55: 1000000 INFO @ Sun, 21 Jun 2020 21:14:00: 2000000 INFO @ Sun, 21 Jun 2020 21:14:05: 3000000 INFO @ Sun, 21 Jun 2020 21:14:11: 4000000 INFO @ Sun, 21 Jun 2020 21:14:16: 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 @ Sun, 21 Jun 2020 21:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.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 @ Sun, 21 Jun 2020 21:14:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:21: 6000000 INFO @ Sun, 21 Jun 2020 21:14:26: 1000000 INFO @ Sun, 21 Jun 2020 21:14:26: 7000000 INFO @ Sun, 21 Jun 2020 21:14:31: 2000000 INFO @ Sun, 21 Jun 2020 21:14:32: 8000000 INFO @ Sun, 21 Jun 2020 21:14:37: 3000000 INFO @ Sun, 21 Jun 2020 21:14:37: 9000000 INFO @ Sun, 21 Jun 2020 21:14:42: 4000000 INFO @ Sun, 21 Jun 2020 21:14:43: 10000000 INFO @ Sun, 21 Jun 2020 21:14:48: 5000000 INFO @ Sun, 21 Jun 2020 21:14:48: 11000000 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 @ Sun, 21 Jun 2020 21:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.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 @ Sun, 21 Jun 2020 21:14:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:53: 6000000 INFO @ Sun, 21 Jun 2020 21:14:54: 12000000 INFO @ Sun, 21 Jun 2020 21:14:56: 1000000 INFO @ Sun, 21 Jun 2020 21:14:59: 7000000 INFO @ Sun, 21 Jun 2020 21:14:59: 13000000 INFO @ Sun, 21 Jun 2020 21:15:02: 2000000 INFO @ Sun, 21 Jun 2020 21:15:04: 8000000 INFO @ Sun, 21 Jun 2020 21:15:05: 14000000 INFO @ Sun, 21 Jun 2020 21:15:07: 3000000 INFO @ Sun, 21 Jun 2020 21:15:10: 9000000 INFO @ Sun, 21 Jun 2020 21:15:10: 15000000 INFO @ Sun, 21 Jun 2020 21:15:13: 4000000 INFO @ Sun, 21 Jun 2020 21:15:16: 10000000 INFO @ Sun, 21 Jun 2020 21:15:16: 16000000 INFO @ Sun, 21 Jun 2020 21:15:18: 5000000 INFO @ Sun, 21 Jun 2020 21:15:21: 11000000 INFO @ Sun, 21 Jun 2020 21:15:21: 17000000 INFO @ Sun, 21 Jun 2020 21:15:24: 6000000 INFO @ Sun, 21 Jun 2020 21:15:27: 12000000 INFO @ Sun, 21 Jun 2020 21:15:27: 18000000 INFO @ Sun, 21 Jun 2020 21:15:29: 7000000 INFO @ Sun, 21 Jun 2020 21:15:32: 13000000 INFO @ Sun, 21 Jun 2020 21:15:33: 19000000 INFO @ Sun, 21 Jun 2020 21:15:35: 8000000 INFO @ Sun, 21 Jun 2020 21:15:38: 14000000 INFO @ Sun, 21 Jun 2020 21:15:38: 20000000 INFO @ Sun, 21 Jun 2020 21:15:40: 9000000 INFO @ Sun, 21 Jun 2020 21:15:43: 15000000 INFO @ Sun, 21 Jun 2020 21:15:44: 21000000 INFO @ Sun, 21 Jun 2020 21:15:46: 10000000 INFO @ Sun, 21 Jun 2020 21:15:49: 16000000 INFO @ Sun, 21 Jun 2020 21:15:49: 22000000 INFO @ Sun, 21 Jun 2020 21:15:51: 11000000 INFO @ Sun, 21 Jun 2020 21:15:54: 17000000 INFO @ Sun, 21 Jun 2020 21:15:55: 23000000 INFO @ Sun, 21 Jun 2020 21:15:57: 12000000 INFO @ Sun, 21 Jun 2020 21:16:00: 18000000 INFO @ Sun, 21 Jun 2020 21:16:00: 24000000 INFO @ Sun, 21 Jun 2020 21:16:02: 13000000 INFO @ Sun, 21 Jun 2020 21:16:06: 19000000 INFO @ Sun, 21 Jun 2020 21:16:06: 25000000 INFO @ Sun, 21 Jun 2020 21:16:08: 14000000 INFO @ Sun, 21 Jun 2020 21:16:11: 20000000 INFO @ Sun, 21 Jun 2020 21:16:11: 26000000 INFO @ Sun, 21 Jun 2020 21:16:13: 15000000 INFO @ Sun, 21 Jun 2020 21:16:16: 21000000 INFO @ Sun, 21 Jun 2020 21:16:17: 27000000 INFO @ Sun, 21 Jun 2020 21:16:18: 16000000 INFO @ Sun, 21 Jun 2020 21:16:22: 22000000 INFO @ Sun, 21 Jun 2020 21:16:22: 28000000 INFO @ Sun, 21 Jun 2020 21:16:24: 17000000 INFO @ Sun, 21 Jun 2020 21:16:27: 23000000 INFO @ Sun, 21 Jun 2020 21:16:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:16:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:16:28: #1 total tags in treatment: 28928758 INFO @ Sun, 21 Jun 2020 21:16:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:16:28: #1 tags after filtering in treatment: 28928707 INFO @ Sun, 21 Jun 2020 21:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:29: 18000000 INFO @ Sun, 21 Jun 2020 21:16:30: #2 number of paired peaks: 232 WARNING @ Sun, 21 Jun 2020 21:16:30: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 21 Jun 2020 21:16:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:30: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:16:30: #2 alternative fragment length(s) may be 2,52,578,598 bps INFO @ Sun, 21 Jun 2020 21:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.05_model.r WARNING @ Sun, 21 Jun 2020 21:16:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:16:30: #2 You may need to consider one of the other alternative d(s): 2,52,578,598 WARNING @ Sun, 21 Jun 2020 21:16:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:16:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:33: 24000000 INFO @ Sun, 21 Jun 2020 21:16:35: 19000000 INFO @ Sun, 21 Jun 2020 21:16:38: 25000000 INFO @ Sun, 21 Jun 2020 21:16:40: 20000000 INFO @ Sun, 21 Jun 2020 21:16:44: 26000000 INFO @ Sun, 21 Jun 2020 21:16:45: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:49: 27000000 INFO @ Sun, 21 Jun 2020 21:16:51: 22000000 INFO @ Sun, 21 Jun 2020 21:16:55: 28000000 INFO @ Sun, 21 Jun 2020 21:16:56: 23000000 INFO @ Sun, 21 Jun 2020 21:17:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:17:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:17:00: #1 total tags in treatment: 28928758 INFO @ Sun, 21 Jun 2020 21:17:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:17:01: #1 tags after filtering in treatment: 28928707 INFO @ Sun, 21 Jun 2020 21:17:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:01: 24000000 INFO @ Sun, 21 Jun 2020 21:17:02: #2 number of paired peaks: 232 WARNING @ Sun, 21 Jun 2020 21:17:02: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 21 Jun 2020 21:17:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:03: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:17:03: #2 alternative fragment length(s) may be 2,52,578,598 bps INFO @ Sun, 21 Jun 2020 21:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.10_model.r WARNING @ Sun, 21 Jun 2020 21:17:03: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:03: #2 You may need to consider one of the other alternative d(s): 2,52,578,598 WARNING @ Sun, 21 Jun 2020 21:17:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:17:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:07: 25000000 INFO @ Sun, 21 Jun 2020 21:17:12: 26000000 INFO @ Sun, 21 Jun 2020 21:17:17: 27000000 INFO @ Sun, 21 Jun 2020 21:17:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:22: 28000000 INFO @ Sun, 21 Jun 2020 21:17:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:17:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:17:27: #1 total tags in treatment: 28928758 INFO @ Sun, 21 Jun 2020 21:17:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:17:28: #1 tags after filtering in treatment: 28928707 INFO @ Sun, 21 Jun 2020 21:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:29: #2 number of paired peaks: 232 WARNING @ Sun, 21 Jun 2020 21:17:29: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 21 Jun 2020 21:17:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:30: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:17:30: #2 alternative fragment length(s) may be 2,52,578,598 bps INFO @ Sun, 21 Jun 2020 21:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.20_model.r WARNING @ Sun, 21 Jun 2020 21:17:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:30: #2 You may need to consider one of the other alternative d(s): 2,52,578,598 WARNING @ Sun, 21 Jun 2020 21:17:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:17:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.05_summits.bed INFO @ Sun, 21 Jun 2020 21:17:42: Done! pass1 - making usageList (567 chroms): 1 millis pass2 - checking and writing primary data (3267 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:17:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.10_summits.bed INFO @ Sun, 21 Jun 2020 21:18:16: Done! pass1 - making usageList (321 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981693/SRX3981693.20_summits.bed INFO @ Sun, 21 Jun 2020 21:18:41: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 6 millis CompletedMACS2peakCalling