Job ID = 6458893 SRX = SRX5736593 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:07:16 prefetch.2.10.7: 1) Downloading 'SRR8957003'... 2020-06-21T13:07:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:10:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:10:04 prefetch.2.10.7: 1) 'SRR8957003' was downloaded successfully Read 27764747 spots for SRR8957003/SRR8957003.sra Written 27764747 spots for SRR8957003/SRR8957003.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:35 27764747 reads; of these: 27764747 (100.00%) were unpaired; of these: 577220 (2.08%) aligned 0 times 21535112 (77.56%) aligned exactly 1 time 5652415 (20.36%) aligned >1 times 97.92% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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 12 files... [bam_rmdupse_core] 11052033 / 27187527 = 0.4065 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 22:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.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 22:24:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:28: 1000000 INFO @ Sun, 21 Jun 2020 22:24:35: 2000000 INFO @ Sun, 21 Jun 2020 22:24:42: 3000000 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 22:24:49: 4000000 INFO @ Sun, 21 Jun 2020 22:24:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.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 22:24:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:56: 5000000 INFO @ Sun, 21 Jun 2020 22:24:58: 1000000 INFO @ Sun, 21 Jun 2020 22:25:03: 6000000 INFO @ Sun, 21 Jun 2020 22:25:05: 2000000 INFO @ Sun, 21 Jun 2020 22:25:10: 7000000 INFO @ Sun, 21 Jun 2020 22:25:12: 3000000 INFO @ Sun, 21 Jun 2020 22:25:17: 8000000 INFO @ Sun, 21 Jun 2020 22:25:18: 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 @ Sun, 21 Jun 2020 22:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.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 22:25:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:24: 9000000 INFO @ Sun, 21 Jun 2020 22:25:25: 5000000 INFO @ Sun, 21 Jun 2020 22:25:28: 1000000 INFO @ Sun, 21 Jun 2020 22:25:31: 10000000 INFO @ Sun, 21 Jun 2020 22:25:32: 6000000 INFO @ Sun, 21 Jun 2020 22:25:35: 2000000 INFO @ Sun, 21 Jun 2020 22:25:38: 11000000 INFO @ Sun, 21 Jun 2020 22:25:39: 7000000 INFO @ Sun, 21 Jun 2020 22:25:42: 3000000 INFO @ Sun, 21 Jun 2020 22:25:46: 12000000 INFO @ Sun, 21 Jun 2020 22:25:46: 8000000 INFO @ Sun, 21 Jun 2020 22:25:50: 4000000 INFO @ Sun, 21 Jun 2020 22:25:53: 9000000 INFO @ Sun, 21 Jun 2020 22:25:54: 13000000 INFO @ Sun, 21 Jun 2020 22:25:57: 5000000 INFO @ Sun, 21 Jun 2020 22:25:59: 10000000 INFO @ Sun, 21 Jun 2020 22:26:01: 14000000 INFO @ Sun, 21 Jun 2020 22:26:04: 6000000 INFO @ Sun, 21 Jun 2020 22:26:06: 11000000 INFO @ Sun, 21 Jun 2020 22:26:08: 15000000 INFO @ Sun, 21 Jun 2020 22:26:11: 7000000 INFO @ Sun, 21 Jun 2020 22:26:13: 12000000 INFO @ Sun, 21 Jun 2020 22:26:16: 16000000 INFO @ Sun, 21 Jun 2020 22:26:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:26:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:26:17: #1 total tags in treatment: 16135494 INFO @ Sun, 21 Jun 2020 22:26:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:17: #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 22:26:18: #1 tags after filtering in treatment: 16135402 INFO @ Sun, 21 Jun 2020 22:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:18: 8000000 INFO @ Sun, 21 Jun 2020 22:26:19: #2 number of paired peaks: 507 WARNING @ Sun, 21 Jun 2020 22:26:19: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Sun, 21 Jun 2020 22:26:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:19: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 22:26:19: #2 alternative fragment length(s) may be 32,35,47,82,100,120,148,198,262,313,440,505,559,591 bps INFO @ Sun, 21 Jun 2020 22:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.05_model.r WARNING @ Sun, 21 Jun 2020 22:26:19: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:26:19: #2 You may need to consider one of the other alternative d(s): 32,35,47,82,100,120,148,198,262,313,440,505,559,591 WARNING @ Sun, 21 Jun 2020 22:26:19: #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 22:26:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:26:21: 13000000 INFO @ Sun, 21 Jun 2020 22:26:25: 9000000 INFO @ Sun, 21 Jun 2020 22:26:28: 14000000 INFO @ Sun, 21 Jun 2020 22:26:32: 10000000 INFO @ Sun, 21 Jun 2020 22:26:35: 15000000 INFO @ Sun, 21 Jun 2020 22:26:40: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:26:43: 16000000 INFO @ Sun, 21 Jun 2020 22:26:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:26:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:26:44: #1 total tags in treatment: 16135494 INFO @ Sun, 21 Jun 2020 22:26:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:44: #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 22:26:44: #1 tags after filtering in treatment: 16135402 INFO @ Sun, 21 Jun 2020 22:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:45: #2 number of paired peaks: 507 WARNING @ Sun, 21 Jun 2020 22:26:45: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Sun, 21 Jun 2020 22:26:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:46: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 22:26:46: #2 alternative fragment length(s) may be 32,35,47,82,100,120,148,198,262,313,440,505,559,591 bps INFO @ Sun, 21 Jun 2020 22:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.10_model.r WARNING @ Sun, 21 Jun 2020 22:26:46: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:26:46: #2 You may need to consider one of the other alternative d(s): 32,35,47,82,100,120,148,198,262,313,440,505,559,591 WARNING @ Sun, 21 Jun 2020 22:26:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:26:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:26:47: 12000000 INFO @ Sun, 21 Jun 2020 22:26:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:55: 13000000 INFO @ Sun, 21 Jun 2020 22:27:02: 14000000 INFO @ Sun, 21 Jun 2020 22:27:09: 15000000 INFO @ Sun, 21 Jun 2020 22:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.05_summits.bed INFO @ Sun, 21 Jun 2020 22:27:11: Done! pass1 - making usageList (451 chroms): 2 millis pass2 - checking and writing primary data (3853 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:27:17: 16000000 INFO @ Sun, 21 Jun 2020 22:27:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:27:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:27:18: #1 total tags in treatment: 16135494 INFO @ Sun, 21 Jun 2020 22:27:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:18: #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 22:27:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:27:19: #1 tags after filtering in treatment: 16135402 INFO @ Sun, 21 Jun 2020 22:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:27:20: #2 number of paired peaks: 507 WARNING @ Sun, 21 Jun 2020 22:27:20: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Sun, 21 Jun 2020 22:27:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:27:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:27:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:27:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:27:20: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 22:27:20: #2 alternative fragment length(s) may be 32,35,47,82,100,120,148,198,262,313,440,505,559,591 bps INFO @ Sun, 21 Jun 2020 22:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.20_model.r WARNING @ Sun, 21 Jun 2020 22:27:20: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:27:20: #2 You may need to consider one of the other alternative d(s): 32,35,47,82,100,120,148,198,262,313,440,505,559,591 WARNING @ Sun, 21 Jun 2020 22:27:20: #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 22:27:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:27:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.10_summits.bed INFO @ Sun, 21 Jun 2020 22:27:36: Done! pass1 - making usageList (315 chroms): 1 millis pass2 - checking and writing primary data (937 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:27:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736593/SRX5736593.20_summits.bed INFO @ Sun, 21 Jun 2020 22:28:10: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 6 millis CompletedMACS2peakCalling