Job ID = 6458613 SRX = SRX5343144 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:04 prefetch.2.10.7: 1) Downloading 'SRR8540844'... 2020-06-21T12:31:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:34:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:34:37 prefetch.2.10.7: 1) 'SRR8540844' was downloaded successfully 2020-06-21T12:34:37 prefetch.2.10.7: 'SRR8540844' has 0 unresolved dependencies Read 31093103 spots for SRR8540844/SRR8540844.sra Written 31093103 spots for SRR8540844/SRR8540844.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: 00:09:56 31093103 reads; of these: 31093103 (100.00%) were unpaired; of these: 3016518 (9.70%) aligned 0 times 20098411 (64.64%) aligned exactly 1 time 7978174 (25.66%) aligned >1 times 90.30% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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] 10108604 / 28076585 = 0.3600 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 21:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.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 21:52:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:17: 1000000 INFO @ Sun, 21 Jun 2020 21:52:23: 2000000 INFO @ Sun, 21 Jun 2020 21:52:29: 3000000 INFO @ Sun, 21 Jun 2020 21:52:35: 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 21:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.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 21:52:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:41: 5000000 INFO @ Sun, 21 Jun 2020 21:52:47: 1000000 INFO @ Sun, 21 Jun 2020 21:52:48: 6000000 INFO @ Sun, 21 Jun 2020 21:52:53: 2000000 INFO @ Sun, 21 Jun 2020 21:52:54: 7000000 INFO @ Sun, 21 Jun 2020 21:52:59: 3000000 INFO @ Sun, 21 Jun 2020 21:53:00: 8000000 INFO @ Sun, 21 Jun 2020 21:53:06: 4000000 INFO @ Sun, 21 Jun 2020 21:53:06: 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 @ Sun, 21 Jun 2020 21:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.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 21:53:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:12: 5000000 INFO @ Sun, 21 Jun 2020 21:53:13: 10000000 INFO @ Sun, 21 Jun 2020 21:53:17: 1000000 INFO @ Sun, 21 Jun 2020 21:53:18: 6000000 INFO @ Sun, 21 Jun 2020 21:53:19: 11000000 INFO @ Sun, 21 Jun 2020 21:53:23: 2000000 INFO @ Sun, 21 Jun 2020 21:53:25: 7000000 INFO @ Sun, 21 Jun 2020 21:53:25: 12000000 INFO @ Sun, 21 Jun 2020 21:53:29: 3000000 INFO @ Sun, 21 Jun 2020 21:53:31: 8000000 INFO @ Sun, 21 Jun 2020 21:53:31: 13000000 INFO @ Sun, 21 Jun 2020 21:53:36: 4000000 INFO @ Sun, 21 Jun 2020 21:53:37: 9000000 INFO @ Sun, 21 Jun 2020 21:53:38: 14000000 INFO @ Sun, 21 Jun 2020 21:53:42: 5000000 INFO @ Sun, 21 Jun 2020 21:53:43: 10000000 INFO @ Sun, 21 Jun 2020 21:53:44: 15000000 INFO @ Sun, 21 Jun 2020 21:53:48: 6000000 INFO @ Sun, 21 Jun 2020 21:53:50: 11000000 INFO @ Sun, 21 Jun 2020 21:53:50: 16000000 INFO @ Sun, 21 Jun 2020 21:53:55: 7000000 INFO @ Sun, 21 Jun 2020 21:53:56: 12000000 INFO @ Sun, 21 Jun 2020 21:53:57: 17000000 INFO @ Sun, 21 Jun 2020 21:54:02: 8000000 INFO @ Sun, 21 Jun 2020 21:54:02: 13000000 INFO @ Sun, 21 Jun 2020 21:54:03: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:03: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:03: #1 total tags in treatment: 17967981 INFO @ Sun, 21 Jun 2020 21:54:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:03: #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 21:54:04: #1 tags after filtering in treatment: 17967981 INFO @ Sun, 21 Jun 2020 21:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:05: #2 number of paired peaks: 444 WARNING @ Sun, 21 Jun 2020 21:54:05: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:05: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:54:05: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 21 Jun 2020 21:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:05: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:05: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 21 Jun 2020 21:54:05: #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 21:54:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:08: 14000000 INFO @ Sun, 21 Jun 2020 21:54:08: 9000000 INFO @ Sun, 21 Jun 2020 21:54:14: 10000000 INFO @ Sun, 21 Jun 2020 21:54:15: 15000000 INFO @ Sun, 21 Jun 2020 21:54:21: 11000000 INFO @ Sun, 21 Jun 2020 21:54:21: 16000000 INFO @ Sun, 21 Jun 2020 21:54:27: 12000000 INFO @ Sun, 21 Jun 2020 21:54:27: 17000000 INFO @ Sun, 21 Jun 2020 21:54:33: 13000000 INFO @ Sun, 21 Jun 2020 21:54:34: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:34: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:34: #1 total tags in treatment: 17967981 INFO @ Sun, 21 Jun 2020 21:54:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:34: #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 21:54:34: #1 tags after filtering in treatment: 17967981 INFO @ Sun, 21 Jun 2020 21:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:34: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:35: #2 number of paired peaks: 444 WARNING @ Sun, 21 Jun 2020 21:54:35: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:35: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:54:35: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 21 Jun 2020 21:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:35: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:35: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 21 Jun 2020 21:54:35: #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 21:54:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:54:39: 14000000 INFO @ Sun, 21 Jun 2020 21:54:46: 15000000 INFO @ Sun, 21 Jun 2020 21:54:52: 16000000 INFO @ Sun, 21 Jun 2020 21:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:54: Done! pass1 - making usageList (841 chroms): 2 millis pass2 - checking and writing primary data (3258 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:58: 17000000 INFO @ Sun, 21 Jun 2020 21:55:04: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:04: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:04: #1 total tags in treatment: 17967981 INFO @ Sun, 21 Jun 2020 21:55:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:04: #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 21:55:05: #1 tags after filtering in treatment: 17967981 INFO @ Sun, 21 Jun 2020 21:55:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:06: #2 number of paired peaks: 444 WARNING @ Sun, 21 Jun 2020 21:55:06: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:06: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:55:06: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 21 Jun 2020 21:55:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:06: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:06: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 21 Jun 2020 21:55:06: #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 21:55:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:24: Done! pass1 - making usageList (526 chroms): 1 millis pass2 - checking and writing primary data (1321 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343144/SRX5343144.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:55: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 9 millis CompletedMACS2peakCalling