Job ID = 6529229 SRX = SRX104981 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: 00:08:18 39143586 reads; of these: 39143586 (100.00%) were unpaired; of these: 5184440 (13.24%) aligned 0 times 24928814 (63.69%) aligned exactly 1 time 9030332 (23.07%) aligned >1 times 86.76% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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] 6946612 / 33959146 = 0.2046 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 02:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.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 02:20:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:20:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:20:49: 1000000 INFO @ Tue, 30 Jun 2020 02:20:55: 2000000 INFO @ Tue, 30 Jun 2020 02:21:01: 3000000 INFO @ Tue, 30 Jun 2020 02:21:07: 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 02:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.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 02:21:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:14: 5000000 INFO @ Tue, 30 Jun 2020 02:21:18: 1000000 INFO @ Tue, 30 Jun 2020 02:21:20: 6000000 INFO @ Tue, 30 Jun 2020 02:21:24: 2000000 INFO @ Tue, 30 Jun 2020 02:21:27: 7000000 INFO @ Tue, 30 Jun 2020 02:21:30: 3000000 INFO @ Tue, 30 Jun 2020 02:21:34: 8000000 INFO @ Tue, 30 Jun 2020 02:21:36: 4000000 INFO @ Tue, 30 Jun 2020 02:21:40: 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 @ Tue, 30 Jun 2020 02:21:42: 5000000 INFO @ Tue, 30 Jun 2020 02:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.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 02:21:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:47: 10000000 INFO @ Tue, 30 Jun 2020 02:21:48: 6000000 INFO @ Tue, 30 Jun 2020 02:21:48: 1000000 INFO @ Tue, 30 Jun 2020 02:21:54: 11000000 INFO @ Tue, 30 Jun 2020 02:21:54: 7000000 INFO @ Tue, 30 Jun 2020 02:21:54: 2000000 INFO @ Tue, 30 Jun 2020 02:22:00: 8000000 INFO @ Tue, 30 Jun 2020 02:22:00: 12000000 INFO @ Tue, 30 Jun 2020 02:22:00: 3000000 INFO @ Tue, 30 Jun 2020 02:22:05: 9000000 INFO @ Tue, 30 Jun 2020 02:22:06: 4000000 INFO @ Tue, 30 Jun 2020 02:22:07: 13000000 INFO @ Tue, 30 Jun 2020 02:22:11: 10000000 INFO @ Tue, 30 Jun 2020 02:22:12: 5000000 INFO @ Tue, 30 Jun 2020 02:22:14: 14000000 INFO @ Tue, 30 Jun 2020 02:22:17: 11000000 INFO @ Tue, 30 Jun 2020 02:22:18: 6000000 INFO @ Tue, 30 Jun 2020 02:22:20: 15000000 INFO @ Tue, 30 Jun 2020 02:22:23: 12000000 INFO @ Tue, 30 Jun 2020 02:22:24: 7000000 INFO @ Tue, 30 Jun 2020 02:22:27: 16000000 INFO @ Tue, 30 Jun 2020 02:22:29: 13000000 INFO @ Tue, 30 Jun 2020 02:22:30: 8000000 INFO @ Tue, 30 Jun 2020 02:22:34: 17000000 INFO @ Tue, 30 Jun 2020 02:22:35: 14000000 INFO @ Tue, 30 Jun 2020 02:22:36: 9000000 INFO @ Tue, 30 Jun 2020 02:22:40: 18000000 INFO @ Tue, 30 Jun 2020 02:22:41: 15000000 INFO @ Tue, 30 Jun 2020 02:22:42: 10000000 INFO @ Tue, 30 Jun 2020 02:22:47: 19000000 INFO @ Tue, 30 Jun 2020 02:22:47: 16000000 INFO @ Tue, 30 Jun 2020 02:22:48: 11000000 INFO @ Tue, 30 Jun 2020 02:22:53: 17000000 INFO @ Tue, 30 Jun 2020 02:22:54: 20000000 INFO @ Tue, 30 Jun 2020 02:22:54: 12000000 INFO @ Tue, 30 Jun 2020 02:22:59: 18000000 INFO @ Tue, 30 Jun 2020 02:23:00: 13000000 INFO @ Tue, 30 Jun 2020 02:23:00: 21000000 INFO @ Tue, 30 Jun 2020 02:23:05: 19000000 INFO @ Tue, 30 Jun 2020 02:23:06: 14000000 INFO @ Tue, 30 Jun 2020 02:23:07: 22000000 INFO @ Tue, 30 Jun 2020 02:23:11: 20000000 INFO @ Tue, 30 Jun 2020 02:23:12: 15000000 INFO @ Tue, 30 Jun 2020 02:23:14: 23000000 INFO @ Tue, 30 Jun 2020 02:23:17: 21000000 INFO @ Tue, 30 Jun 2020 02:23:18: 16000000 INFO @ Tue, 30 Jun 2020 02:23:21: 24000000 INFO @ Tue, 30 Jun 2020 02:23:23: 22000000 INFO @ Tue, 30 Jun 2020 02:23:24: 17000000 INFO @ Tue, 30 Jun 2020 02:23:28: 25000000 INFO @ Tue, 30 Jun 2020 02:23:29: 23000000 INFO @ Tue, 30 Jun 2020 02:23:30: 18000000 INFO @ Tue, 30 Jun 2020 02:23:34: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:23:35: 24000000 INFO @ Tue, 30 Jun 2020 02:23:36: 19000000 INFO @ Tue, 30 Jun 2020 02:23:41: 25000000 INFO @ Tue, 30 Jun 2020 02:23:41: 27000000 INFO @ Tue, 30 Jun 2020 02:23:41: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:23:41: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:23:41: #1 total tags in treatment: 27012534 INFO @ Tue, 30 Jun 2020 02:23:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:41: #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 02:23:42: 20000000 INFO @ Tue, 30 Jun 2020 02:23:42: #1 tags after filtering in treatment: 27012534 INFO @ Tue, 30 Jun 2020 02:23:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:44: #2 number of paired peaks: 148 WARNING @ Tue, 30 Jun 2020 02:23:44: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:44: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:23:44: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.05_model.r WARNING @ Tue, 30 Jun 2020 02:23:44: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:44: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:23:44: #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 02:23:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:47: 26000000 INFO @ Tue, 30 Jun 2020 02:23:48: 21000000 INFO @ Tue, 30 Jun 2020 02:23:53: 27000000 INFO @ Tue, 30 Jun 2020 02:23:53: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:23:53: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:23:53: #1 total tags in treatment: 27012534 INFO @ Tue, 30 Jun 2020 02:23:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:53: #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 02:23:54: #1 tags after filtering in treatment: 27012534 INFO @ Tue, 30 Jun 2020 02:23:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:54: 22000000 INFO @ Tue, 30 Jun 2020 02:23:55: #2 number of paired peaks: 148 WARNING @ Tue, 30 Jun 2020 02:23:55: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:55: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:23:55: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:23:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.10_model.r WARNING @ Tue, 30 Jun 2020 02:23:55: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:55: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:23:55: #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 02:23:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:00: 23000000 INFO @ Tue, 30 Jun 2020 02:24:05: 24000000 INFO @ Tue, 30 Jun 2020 02:24:11: 25000000 INFO @ Tue, 30 Jun 2020 02:24:16: 26000000 INFO @ Tue, 30 Jun 2020 02:24:22: 27000000 INFO @ Tue, 30 Jun 2020 02:24:22: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:24:22: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:24:22: #1 total tags in treatment: 27012534 INFO @ Tue, 30 Jun 2020 02:24:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:22: #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 02:24:23: #1 tags after filtering in treatment: 27012534 INFO @ Tue, 30 Jun 2020 02:24:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:25: #2 number of paired peaks: 148 WARNING @ Tue, 30 Jun 2020 02:24:25: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:25: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:24:25: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:24:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.20_model.r WARNING @ Tue, 30 Jun 2020 02:24:25: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:25: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:24:25: #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 02:24:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:24:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.05_summits.bed INFO @ Tue, 30 Jun 2020 02:24:49: Done! pass1 - making usageList (700 chroms): 2 millis pass2 - checking and writing primary data (3880 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.10_summits.bed INFO @ Tue, 30 Jun 2020 02:25:01: Done! pass1 - making usageList (539 chroms): 1 millis pass2 - checking and writing primary data (2636 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104981/SRX104981.20_summits.bed INFO @ Tue, 30 Jun 2020 02:25:28: Done! pass1 - making usageList (312 chroms): 1 millis pass2 - checking and writing primary data (730 records, 4 fields): 9 millis CompletedMACS2peakCalling