Job ID = 6529837 SRX = SRX495306 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: 00:05:33 29099060 reads; of these: 29099060 (100.00%) were unpaired; of these: 15090275 (51.86%) aligned 0 times 11251138 (38.66%) aligned exactly 1 time 2757647 (9.48%) aligned >1 times 48.14% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 3633809 / 14008785 = 0.2594 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 02:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.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 02:48:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:05: 1000000 INFO @ Tue, 30 Jun 2020 02:49:12: 2000000 INFO @ Tue, 30 Jun 2020 02:49:20: 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 02:49:27: 4000000 INFO @ Tue, 30 Jun 2020 02:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.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 02:49:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:34: 5000000 INFO @ Tue, 30 Jun 2020 02:49:36: 1000000 INFO @ Tue, 30 Jun 2020 02:49:42: 6000000 INFO @ Tue, 30 Jun 2020 02:49:44: 2000000 INFO @ Tue, 30 Jun 2020 02:49:50: 7000000 INFO @ Tue, 30 Jun 2020 02:49:52: 3000000 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 02:49:57: 8000000 INFO @ Tue, 30 Jun 2020 02:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.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 02:49:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:00: 4000000 INFO @ Tue, 30 Jun 2020 02:50:05: 1000000 INFO @ Tue, 30 Jun 2020 02:50:06: 9000000 INFO @ Tue, 30 Jun 2020 02:50:08: 5000000 INFO @ Tue, 30 Jun 2020 02:50:12: 2000000 INFO @ Tue, 30 Jun 2020 02:50:14: 10000000 INFO @ Tue, 30 Jun 2020 02:50:17: 6000000 INFO @ Tue, 30 Jun 2020 02:50:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:18: #1 total tags in treatment: 10374976 INFO @ Tue, 30 Jun 2020 02:50:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:18: #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 02:50:18: #1 tags after filtering in treatment: 10374945 INFO @ Tue, 30 Jun 2020 02:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:19: #2 number of paired peaks: 344 WARNING @ Tue, 30 Jun 2020 02:50:19: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:19: #2 predicted fragment length is 4 bps INFO @ Tue, 30 Jun 2020 02:50:19: #2 alternative fragment length(s) may be 4,9,31,550 bps INFO @ Tue, 30 Jun 2020 02:50:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.05_model.r WARNING @ Tue, 30 Jun 2020 02:50:19: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:19: #2 You may need to consider one of the other alternative d(s): 4,9,31,550 WARNING @ Tue, 30 Jun 2020 02:50:19: #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 02:50:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:19: 3000000 INFO @ Tue, 30 Jun 2020 02:50:25: 7000000 INFO @ Tue, 30 Jun 2020 02:50:26: 4000000 INFO @ Tue, 30 Jun 2020 02:50:33: 8000000 INFO @ Tue, 30 Jun 2020 02:50:33: 5000000 INFO @ Tue, 30 Jun 2020 02:50:40: 6000000 INFO @ Tue, 30 Jun 2020 02:50:41: 9000000 INFO @ Tue, 30 Jun 2020 02:50:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:47: 7000000 INFO @ Tue, 30 Jun 2020 02:50:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:50:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:53: #1 total tags in treatment: 10374976 INFO @ Tue, 30 Jun 2020 02:50:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:53: #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 02:50:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:54: #1 tags after filtering in treatment: 10374945 INFO @ Tue, 30 Jun 2020 02:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:54: 8000000 INFO @ Tue, 30 Jun 2020 02:50:55: #2 number of paired peaks: 344 WARNING @ Tue, 30 Jun 2020 02:50:55: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:55: #2 predicted fragment length is 4 bps INFO @ Tue, 30 Jun 2020 02:50:55: #2 alternative fragment length(s) may be 4,9,31,550 bps INFO @ Tue, 30 Jun 2020 02:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:55: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:55: #2 You may need to consider one of the other alternative d(s): 4,9,31,550 WARNING @ Tue, 30 Jun 2020 02:50:55: #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 02:50:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:01: 9000000 INFO @ Tue, 30 Jun 2020 02:51:07: 10000000 INFO @ Tue, 30 Jun 2020 02:51:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:51:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:51:09: #1 total tags in treatment: 10374976 INFO @ Tue, 30 Jun 2020 02:51:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:09: #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 02:51:10: #1 tags after filtering in treatment: 10374945 INFO @ Tue, 30 Jun 2020 02:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:10: #2 number of paired peaks: 344 WARNING @ Tue, 30 Jun 2020 02:51:10: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:11: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:11: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:11: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:11: #2 predicted fragment length is 4 bps INFO @ Tue, 30 Jun 2020 02:51:11: #2 alternative fragment length(s) may be 4,9,31,550 bps INFO @ Tue, 30 Jun 2020 02:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.20_model.r WARNING @ Tue, 30 Jun 2020 02:51:11: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:11: #2 You may need to consider one of the other alternative d(s): 4,9,31,550 WARNING @ Tue, 30 Jun 2020 02:51:11: #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 02:51:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:51:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.10_summits.bed INFO @ Tue, 30 Jun 2020 02:51:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495306/SRX495306.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling