Job ID = 6529763 SRX = SRX467105 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:50 11329840 reads; of these: 11329840 (100.00%) were unpaired; of these: 1989459 (17.56%) aligned 0 times 7512960 (66.31%) aligned exactly 1 time 1827421 (16.13%) aligned >1 times 82.44% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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_rmdupse_core] 729791 / 9340381 = 0.0781 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 02:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.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 02:43:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:43:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:43:08: 1000000 INFO @ Tue, 30 Jun 2020 02:43:14: 2000000 INFO @ Tue, 30 Jun 2020 02:43:20: 3000000 INFO @ Tue, 30 Jun 2020 02:43:26: 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 @ Tue, 30 Jun 2020 02:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.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 02:43:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:43:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:43:32: 5000000 INFO @ Tue, 30 Jun 2020 02:43:38: 1000000 INFO @ Tue, 30 Jun 2020 02:43:38: 6000000 INFO @ Tue, 30 Jun 2020 02:43:45: 2000000 INFO @ Tue, 30 Jun 2020 02:43:45: 7000000 INFO @ Tue, 30 Jun 2020 02:43:52: 3000000 INFO @ Tue, 30 Jun 2020 02:43:53: 8000000 INFO @ Tue, 30 Jun 2020 02:43:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:43:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:43:57: #1 total tags in treatment: 8610590 INFO @ Tue, 30 Jun 2020 02:43:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:57: #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 02:43:57: #1 tags after filtering in treatment: 8610568 INFO @ Tue, 30 Jun 2020 02:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:58: #2 number of paired peaks: 241 WARNING @ Tue, 30 Jun 2020 02:43:58: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:58: #2 predicted fragment length is 79 bps INFO @ Tue, 30 Jun 2020 02:43:58: #2 alternative fragment length(s) may be 79 bps INFO @ Tue, 30 Jun 2020 02:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.05_model.r WARNING @ Tue, 30 Jun 2020 02:43:58: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:58: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Tue, 30 Jun 2020 02:43:58: #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 02:43:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:59: 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 @ Tue, 30 Jun 2020 02:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.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 02:44:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:05: 5000000 INFO @ Tue, 30 Jun 2020 02:44:08: 1000000 INFO @ Tue, 30 Jun 2020 02:44:12: 6000000 INFO @ Tue, 30 Jun 2020 02:44:15: 2000000 INFO @ Tue, 30 Jun 2020 02:44:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:44:18: 7000000 INFO @ Tue, 30 Jun 2020 02:44:21: 3000000 INFO @ Tue, 30 Jun 2020 02:44:25: 8000000 INFO @ Tue, 30 Jun 2020 02:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.05_summits.bed INFO @ Tue, 30 Jun 2020 02:44:26: Done! pass1 - making usageList (374 chroms): 1 millis pass2 - checking and writing primary data (1028 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:44:28: 4000000 INFO @ Tue, 30 Jun 2020 02:44:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:44:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:44:29: #1 total tags in treatment: 8610590 INFO @ Tue, 30 Jun 2020 02:44:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:44:29: #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 02:44:30: #1 tags after filtering in treatment: 8610568 INFO @ Tue, 30 Jun 2020 02:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:44:30: #1 finished! INFO @ Tue, 30 Jun 2020 02:44:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:44:30: #2 number of paired peaks: 241 WARNING @ Tue, 30 Jun 2020 02:44:30: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 30 Jun 2020 02:44:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:44:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:44:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:44:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:44:30: #2 predicted fragment length is 79 bps INFO @ Tue, 30 Jun 2020 02:44:30: #2 alternative fragment length(s) may be 79 bps INFO @ Tue, 30 Jun 2020 02:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.10_model.r WARNING @ Tue, 30 Jun 2020 02:44:30: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:44:30: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Tue, 30 Jun 2020 02:44:30: #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 02:44:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:44:34: 5000000 INFO @ Tue, 30 Jun 2020 02:44:40: 6000000 INFO @ Tue, 30 Jun 2020 02:44:46: 7000000 INFO @ Tue, 30 Jun 2020 02:44:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:44:53: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:44:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:44:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:44:57: #1 total tags in treatment: 8610590 INFO @ Tue, 30 Jun 2020 02:44:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:44:57: #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 02:44:57: #1 tags after filtering in treatment: 8610568 INFO @ Tue, 30 Jun 2020 02:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:44:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:44:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:44:58: #2 number of paired peaks: 241 WARNING @ Tue, 30 Jun 2020 02:44:58: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 30 Jun 2020 02:44:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:44:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:44:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:44:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:44:58: #2 predicted fragment length is 79 bps INFO @ Tue, 30 Jun 2020 02:44:58: #2 alternative fragment length(s) may be 79 bps INFO @ Tue, 30 Jun 2020 02:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.20_model.r WARNING @ Tue, 30 Jun 2020 02:44:58: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:44:58: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Tue, 30 Jun 2020 02:44:58: #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 02:44:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.10_summits.bed INFO @ Tue, 30 Jun 2020 02:44:59: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:45:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467105/SRX467105.20_summits.bed INFO @ Tue, 30 Jun 2020 02:45:27: Done! pass1 - making usageList (113 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 5 millis CompletedMACS2peakCalling