Job ID = 6529724 SRX = SRX450793 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: 00:05:34 38801502 reads; of these: 38801502 (100.00%) were unpaired; of these: 17364006 (44.75%) aligned 0 times 19035230 (49.06%) aligned exactly 1 time 2402266 (6.19%) aligned >1 times 55.25% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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 8 files... [bam_rmdupse_core] 10416651 / 21437496 = 0.4859 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 02:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.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 02:41:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:42:05: 1000000 INFO @ Tue, 30 Jun 2020 02:42:12: 2000000 INFO @ Tue, 30 Jun 2020 02:42:19: 3000000 INFO @ Tue, 30 Jun 2020 02:42:25: 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 02:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.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 02:42:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:42:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:42:32: 5000000 INFO @ Tue, 30 Jun 2020 02:42:36: 1000000 INFO @ Tue, 30 Jun 2020 02:42:39: 6000000 INFO @ Tue, 30 Jun 2020 02:42:42: 2000000 INFO @ Tue, 30 Jun 2020 02:42:45: 7000000 INFO @ Tue, 30 Jun 2020 02:42:49: 3000000 INFO @ Tue, 30 Jun 2020 02:42:52: 8000000 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 02:42:56: 4000000 INFO @ Tue, 30 Jun 2020 02:42:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.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 02:42:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:42:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:42:59: 9000000 INFO @ Tue, 30 Jun 2020 02:43:03: 5000000 INFO @ Tue, 30 Jun 2020 02:43:05: 1000000 INFO @ Tue, 30 Jun 2020 02:43:06: 10000000 INFO @ Tue, 30 Jun 2020 02:43:10: 6000000 INFO @ Tue, 30 Jun 2020 02:43:11: 2000000 INFO @ Tue, 30 Jun 2020 02:43:13: 11000000 INFO @ Tue, 30 Jun 2020 02:43:13: #1 tag size is determined as 41 bps INFO @ Tue, 30 Jun 2020 02:43:13: #1 tag size = 41 INFO @ Tue, 30 Jun 2020 02:43:13: #1 total tags in treatment: 11020845 INFO @ Tue, 30 Jun 2020 02:43:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:13: #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 02:43:14: #1 tags after filtering in treatment: 11020781 INFO @ Tue, 30 Jun 2020 02:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:14: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:43:14: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:14: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:14: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:15: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:15: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:15: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:43:15: #2 alternative fragment length(s) may be 45,581 bps INFO @ Tue, 30 Jun 2020 02:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.05_model.r WARNING @ Tue, 30 Jun 2020 02:43:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:15: #2 You may need to consider one of the other alternative d(s): 45,581 WARNING @ Tue, 30 Jun 2020 02:43:15: #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 02:43:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:17: 7000000 INFO @ Tue, 30 Jun 2020 02:43:17: 3000000 INFO @ Tue, 30 Jun 2020 02:43:23: 4000000 INFO @ Tue, 30 Jun 2020 02:43:24: 8000000 INFO @ Tue, 30 Jun 2020 02:43:28: 5000000 INFO @ Tue, 30 Jun 2020 02:43:31: 9000000 INFO @ Tue, 30 Jun 2020 02:43:34: 6000000 INFO @ Tue, 30 Jun 2020 02:43:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:43:38: 10000000 INFO @ Tue, 30 Jun 2020 02:43:40: 7000000 INFO @ Tue, 30 Jun 2020 02:43:44: 11000000 INFO @ Tue, 30 Jun 2020 02:43:45: #1 tag size is determined as 41 bps INFO @ Tue, 30 Jun 2020 02:43:45: #1 tag size = 41 INFO @ Tue, 30 Jun 2020 02:43:45: #1 total tags in treatment: 11020845 INFO @ Tue, 30 Jun 2020 02:43:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:45: #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 02:43:45: #1 tags after filtering in treatment: 11020781 INFO @ Tue, 30 Jun 2020 02:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:45: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:46: 8000000 INFO @ Tue, 30 Jun 2020 02:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.05_summits.bed INFO @ Tue, 30 Jun 2020 02:43:46: Done! INFO @ Tue, 30 Jun 2020 02:43:46: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:43:46: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:46: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:43:46: #2 alternative fragment length(s) may be 45,581 bps INFO @ Tue, 30 Jun 2020 02:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.10_model.r WARNING @ Tue, 30 Jun 2020 02:43:46: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:46: #2 You may need to consider one of the other alternative d(s): 45,581 WARNING @ Tue, 30 Jun 2020 02:43:46: #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 02:43:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:46: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:43:52: 9000000 INFO @ Tue, 30 Jun 2020 02:43:57: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:44:03: 11000000 INFO @ Tue, 30 Jun 2020 02:44:04: #1 tag size is determined as 41 bps INFO @ Tue, 30 Jun 2020 02:44:04: #1 tag size = 41 INFO @ Tue, 30 Jun 2020 02:44:04: #1 total tags in treatment: 11020845 INFO @ Tue, 30 Jun 2020 02:44:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:44:04: #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 02:44:04: #1 tags after filtering in treatment: 11020781 INFO @ Tue, 30 Jun 2020 02:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:44:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:44:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:44:05: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:44:05: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:44:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:44:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:44:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:44:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:44:05: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:44:05: #2 alternative fragment length(s) may be 45,581 bps INFO @ Tue, 30 Jun 2020 02:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.20_model.r WARNING @ Tue, 30 Jun 2020 02:44:05: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:44:05: #2 You may need to consider one of the other alternative d(s): 45,581 WARNING @ Tue, 30 Jun 2020 02:44:05: #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 02:44:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:44:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:44:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.10_summits.bed INFO @ Tue, 30 Jun 2020 02:44:18: Done! pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:44:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:44:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450793/SRX450793.20_summits.bed INFO @ Tue, 30 Jun 2020 02:44:36: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 5 millis CompletedMACS2peakCalling