Job ID = 6529510 SRX = SRX287874 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: 00:05:43 21014950 reads; of these: 21014950 (100.00%) were unpaired; of these: 1319265 (6.28%) aligned 0 times 15033955 (71.54%) aligned exactly 1 time 4661730 (22.18%) aligned >1 times 93.72% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 3193914 / 19695685 = 0.1622 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 02:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.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 02:52:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:31: 1000000 INFO @ Tue, 30 Jun 2020 02:52:38: 2000000 INFO @ Tue, 30 Jun 2020 02:52:46: 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 @ Tue, 30 Jun 2020 02:52:53: 4000000 INFO @ Tue, 30 Jun 2020 02:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.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 02:52:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:01: 5000000 INFO @ Tue, 30 Jun 2020 02:53:01: 1000000 INFO @ Tue, 30 Jun 2020 02:53:09: 6000000 INFO @ Tue, 30 Jun 2020 02:53:09: 2000000 INFO @ Tue, 30 Jun 2020 02:53:16: 3000000 INFO @ Tue, 30 Jun 2020 02:53:17: 7000000 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 02:53:24: 4000000 INFO @ Tue, 30 Jun 2020 02:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.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 02:53:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:25: 8000000 INFO @ Tue, 30 Jun 2020 02:53:31: 5000000 INFO @ Tue, 30 Jun 2020 02:53:32: 1000000 INFO @ Tue, 30 Jun 2020 02:53:33: 9000000 INFO @ Tue, 30 Jun 2020 02:53:39: 6000000 INFO @ Tue, 30 Jun 2020 02:53:39: 2000000 INFO @ Tue, 30 Jun 2020 02:53:41: 10000000 INFO @ Tue, 30 Jun 2020 02:53:46: 7000000 INFO @ Tue, 30 Jun 2020 02:53:47: 3000000 INFO @ Tue, 30 Jun 2020 02:53:50: 11000000 INFO @ Tue, 30 Jun 2020 02:53:54: 8000000 INFO @ Tue, 30 Jun 2020 02:53:54: 4000000 INFO @ Tue, 30 Jun 2020 02:53:58: 12000000 INFO @ Tue, 30 Jun 2020 02:54:01: 9000000 INFO @ Tue, 30 Jun 2020 02:54:02: 5000000 INFO @ Tue, 30 Jun 2020 02:54:06: 13000000 INFO @ Tue, 30 Jun 2020 02:54:09: 10000000 INFO @ Tue, 30 Jun 2020 02:54:09: 6000000 INFO @ Tue, 30 Jun 2020 02:54:15: 14000000 INFO @ Tue, 30 Jun 2020 02:54:16: 11000000 INFO @ Tue, 30 Jun 2020 02:54:17: 7000000 INFO @ Tue, 30 Jun 2020 02:54:23: 15000000 INFO @ Tue, 30 Jun 2020 02:54:24: 12000000 INFO @ Tue, 30 Jun 2020 02:54:24: 8000000 INFO @ Tue, 30 Jun 2020 02:54:31: 13000000 INFO @ Tue, 30 Jun 2020 02:54:31: 16000000 INFO @ Tue, 30 Jun 2020 02:54:32: 9000000 INFO @ Tue, 30 Jun 2020 02:54:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:36: #1 total tags in treatment: 16501771 INFO @ Tue, 30 Jun 2020 02:54:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:36: #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 02:54:36: #1 tags after filtering in treatment: 16501771 INFO @ Tue, 30 Jun 2020 02:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:38: #2 number of paired peaks: 460 WARNING @ Tue, 30 Jun 2020 02:54:38: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:38: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:38: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:38: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:38: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:38: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:54:38: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.05_model.r WARNING @ Tue, 30 Jun 2020 02:54:38: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:38: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:54:38: #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 02:54:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:54:39: 14000000 INFO @ Tue, 30 Jun 2020 02:54:39: 10000000 INFO @ Tue, 30 Jun 2020 02:54:45: 15000000 INFO @ Tue, 30 Jun 2020 02:54:45: 11000000 INFO @ Tue, 30 Jun 2020 02:54:52: 12000000 INFO @ Tue, 30 Jun 2020 02:54:52: 16000000 INFO @ Tue, 30 Jun 2020 02:54:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:55: #1 total tags in treatment: 16501771 INFO @ Tue, 30 Jun 2020 02:54:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:55: #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 02:54:56: #1 tags after filtering in treatment: 16501771 INFO @ Tue, 30 Jun 2020 02:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:57: #2 number of paired peaks: 460 WARNING @ Tue, 30 Jun 2020 02:54:57: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:57: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:54:57: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.10_model.r WARNING @ Tue, 30 Jun 2020 02:54:57: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:57: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:54:57: #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 02:54:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:58: 13000000 INFO @ Tue, 30 Jun 2020 02:55:04: 14000000 INFO @ Tue, 30 Jun 2020 02:55:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:10: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:55:15: 16000000 INFO @ Tue, 30 Jun 2020 02:55:19: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:55:19: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:55:19: #1 total tags in treatment: 16501771 INFO @ Tue, 30 Jun 2020 02:55:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:19: #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 02:55:19: #1 tags after filtering in treatment: 16501771 INFO @ Tue, 30 Jun 2020 02:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:20: #2 number of paired peaks: 460 WARNING @ Tue, 30 Jun 2020 02:55:20: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:20: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:55:20: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:55:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.20_model.r WARNING @ Tue, 30 Jun 2020 02:55:20: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:20: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:55:20: #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 02:55:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.05_summits.bed INFO @ Tue, 30 Jun 2020 02:55:24: Done! pass1 - making usageList (522 chroms): 2 millis pass2 - checking and writing primary data (2069 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.10_summits.bed INFO @ Tue, 30 Jun 2020 02:55:41: Done! pass1 - making usageList (465 chroms): 1 millis pass2 - checking and writing primary data (1830 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287874/SRX287874.20_summits.bed INFO @ Tue, 30 Jun 2020 02:56:05: Done! pass1 - making usageList (329 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 9 millis CompletedMACS2peakCalling