Job ID = 6458835 SRX = SRX5661481 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:43:25 prefetch.2.10.7: 1) Downloading 'SRR8874488'... 2020-06-21T12:43:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:08 prefetch.2.10.7: 1) 'SRR8874488' was downloaded successfully 2020-06-21T12:47:08 prefetch.2.10.7: 'SRR8874488' has 0 unresolved dependencies Read 36582891 spots for SRR8874488/SRR8874488.sra Written 36582891 spots for SRR8874488/SRR8874488.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: 00:00:01 Multiseed full-index search: 00:11:16 36582891 reads; of these: 36582891 (100.00%) were unpaired; of these: 4528110 (12.38%) aligned 0 times 23549930 (64.37%) aligned exactly 1 time 8504851 (23.25%) aligned >1 times 87.62% overall alignment rate Time searching: 00:11:17 Overall time: 00:11:17 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] 15052240 / 32054781 = 0.4696 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 22:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.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 22:07:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:46: 1000000 INFO @ Sun, 21 Jun 2020 22:07:52: 2000000 INFO @ Sun, 21 Jun 2020 22:07:58: 3000000 INFO @ Sun, 21 Jun 2020 22:08:03: 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 @ Sun, 21 Jun 2020 22:08:09: 5000000 INFO @ Sun, 21 Jun 2020 22:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.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 22:08:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:16: 6000000 INFO @ Sun, 21 Jun 2020 22:08:17: 1000000 INFO @ Sun, 21 Jun 2020 22:08:22: 7000000 INFO @ Sun, 21 Jun 2020 22:08:23: 2000000 INFO @ Sun, 21 Jun 2020 22:08:28: 8000000 INFO @ Sun, 21 Jun 2020 22:08:29: 3000000 INFO @ Sun, 21 Jun 2020 22:08:35: 9000000 INFO @ Sun, 21 Jun 2020 22:08:36: 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 22:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.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 22:08:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:41: 10000000 INFO @ Sun, 21 Jun 2020 22:08:42: 5000000 INFO @ Sun, 21 Jun 2020 22:08:47: 1000000 INFO @ Sun, 21 Jun 2020 22:08:49: 11000000 INFO @ Sun, 21 Jun 2020 22:08:49: 6000000 INFO @ Sun, 21 Jun 2020 22:08:54: 2000000 INFO @ Sun, 21 Jun 2020 22:08:56: 12000000 INFO @ Sun, 21 Jun 2020 22:08:57: 7000000 INFO @ Sun, 21 Jun 2020 22:09:02: 3000000 INFO @ Sun, 21 Jun 2020 22:09:03: 13000000 INFO @ Sun, 21 Jun 2020 22:09:04: 8000000 INFO @ Sun, 21 Jun 2020 22:09:08: 4000000 INFO @ Sun, 21 Jun 2020 22:09:11: 9000000 INFO @ Sun, 21 Jun 2020 22:09:11: 14000000 INFO @ Sun, 21 Jun 2020 22:09:15: 5000000 INFO @ Sun, 21 Jun 2020 22:09:17: 10000000 INFO @ Sun, 21 Jun 2020 22:09:19: 15000000 INFO @ Sun, 21 Jun 2020 22:09:22: 6000000 INFO @ Sun, 21 Jun 2020 22:09:24: 11000000 INFO @ Sun, 21 Jun 2020 22:09:26: 16000000 INFO @ Sun, 21 Jun 2020 22:09:30: 7000000 INFO @ Sun, 21 Jun 2020 22:09:31: 12000000 INFO @ Sun, 21 Jun 2020 22:09:34: 17000000 INFO @ Sun, 21 Jun 2020 22:09:34: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:09:34: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:09:34: #1 total tags in treatment: 17002541 INFO @ Sun, 21 Jun 2020 22:09:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:34: #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 22:09:35: #1 tags after filtering in treatment: 17002540 INFO @ Sun, 21 Jun 2020 22:09:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:35: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:36: 8000000 INFO @ Sun, 21 Jun 2020 22:09:36: #2 number of paired peaks: 525 WARNING @ Sun, 21 Jun 2020 22:09:36: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Sun, 21 Jun 2020 22:09:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:37: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 22:09:37: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 22:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.05_model.r WARNING @ Sun, 21 Jun 2020 22:09:37: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:09:37: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 22:09:37: #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 22:09:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:38: 13000000 INFO @ Sun, 21 Jun 2020 22:09:42: 9000000 INFO @ Sun, 21 Jun 2020 22:09:45: 14000000 INFO @ Sun, 21 Jun 2020 22:09:49: 10000000 INFO @ Sun, 21 Jun 2020 22:09:51: 15000000 INFO @ Sun, 21 Jun 2020 22:09:55: 11000000 INFO @ Sun, 21 Jun 2020 22:09:58: 16000000 INFO @ Sun, 21 Jun 2020 22:10:01: 12000000 INFO @ Sun, 21 Jun 2020 22:10:05: 17000000 INFO @ Sun, 21 Jun 2020 22:10:05: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:10:05: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:10:05: #1 total tags in treatment: 17002541 INFO @ Sun, 21 Jun 2020 22:10:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:05: #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 22:10:06: #1 tags after filtering in treatment: 17002540 INFO @ Sun, 21 Jun 2020 22:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:06: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:07: #2 number of paired peaks: 525 WARNING @ Sun, 21 Jun 2020 22:10:07: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:07: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 22:10:07: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 22:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.10_model.r WARNING @ Sun, 21 Jun 2020 22:10:07: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:07: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 22:10:07: #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 22:10:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:07: 13000000 INFO @ Sun, 21 Jun 2020 22:10:13: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:10:19: 15000000 INFO @ Sun, 21 Jun 2020 22:10:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.05_summits.bed INFO @ Sun, 21 Jun 2020 22:10:21: Done! pass1 - making usageList (839 chroms): 2 millis pass2 - checking and writing primary data (3711 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:10:25: 16000000 INFO @ Sun, 21 Jun 2020 22:10:31: 17000000 INFO @ Sun, 21 Jun 2020 22:10:31: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:10:31: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:10:31: #1 total tags in treatment: 17002541 INFO @ Sun, 21 Jun 2020 22:10:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:31: #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 22:10:32: #1 tags after filtering in treatment: 17002540 INFO @ Sun, 21 Jun 2020 22:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:33: #2 number of paired peaks: 525 WARNING @ Sun, 21 Jun 2020 22:10:33: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:33: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 22:10:33: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 22:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.20_model.r WARNING @ Sun, 21 Jun 2020 22:10:33: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:33: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 22:10:33: #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 22:10:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.10_summits.bed INFO @ Sun, 21 Jun 2020 22:10:51: Done! pass1 - making usageList (646 chroms): 2 millis pass2 - checking and writing primary data (2341 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:11:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661481/SRX5661481.20_summits.bed INFO @ Sun, 21 Jun 2020 22:11:17: Done! pass1 - making usageList (489 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 28 millis CompletedMACS2peakCalling