Job ID = 6529700 SRX = SRX3981696 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: 00:09:46 35978264 reads; of these: 35978264 (100.00%) were unpaired; of these: 1051612 (2.92%) aligned 0 times 27336179 (75.98%) aligned exactly 1 time 7590473 (21.10%) aligned >1 times 97.08% overall alignment rate Time searching: 00:09:46 Overall time: 00:09:46 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 16 files... [bam_rmdupse_core] 4747282 / 34926652 = 0.1359 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 02:40:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.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 02:40:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:32: 1000000 INFO @ Tue, 30 Jun 2020 02:40:38: 2000000 INFO @ Tue, 30 Jun 2020 02:40:44: 3000000 INFO @ Tue, 30 Jun 2020 02:40:50: 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 02:40:56: 5000000 INFO @ Tue, 30 Jun 2020 02:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.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 02:40:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:02: 6000000 INFO @ Tue, 30 Jun 2020 02:41:02: 1000000 INFO @ Tue, 30 Jun 2020 02:41:07: 7000000 INFO @ Tue, 30 Jun 2020 02:41:08: 2000000 INFO @ Tue, 30 Jun 2020 02:41:13: 8000000 INFO @ Tue, 30 Jun 2020 02:41:14: 3000000 INFO @ Tue, 30 Jun 2020 02:41:19: 9000000 INFO @ Tue, 30 Jun 2020 02:41:20: 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 02:41:24: 10000000 INFO @ Tue, 30 Jun 2020 02:41:26: 5000000 INFO @ Tue, 30 Jun 2020 02:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.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 02:41:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:30: 11000000 INFO @ Tue, 30 Jun 2020 02:41:32: 6000000 INFO @ Tue, 30 Jun 2020 02:41:32: 1000000 INFO @ Tue, 30 Jun 2020 02:41:36: 12000000 INFO @ Tue, 30 Jun 2020 02:41:37: 7000000 INFO @ Tue, 30 Jun 2020 02:41:38: 2000000 INFO @ Tue, 30 Jun 2020 02:41:42: 13000000 INFO @ Tue, 30 Jun 2020 02:41:43: 8000000 INFO @ Tue, 30 Jun 2020 02:41:44: 3000000 INFO @ Tue, 30 Jun 2020 02:41:48: 14000000 INFO @ Tue, 30 Jun 2020 02:41:49: 9000000 INFO @ Tue, 30 Jun 2020 02:41:50: 4000000 INFO @ Tue, 30 Jun 2020 02:41:54: 15000000 INFO @ Tue, 30 Jun 2020 02:41:55: 10000000 INFO @ Tue, 30 Jun 2020 02:41:56: 5000000 INFO @ Tue, 30 Jun 2020 02:42:01: 16000000 INFO @ Tue, 30 Jun 2020 02:42:01: 11000000 INFO @ Tue, 30 Jun 2020 02:42:02: 6000000 INFO @ Tue, 30 Jun 2020 02:42:07: 17000000 INFO @ Tue, 30 Jun 2020 02:42:07: 12000000 INFO @ Tue, 30 Jun 2020 02:42:08: 7000000 INFO @ Tue, 30 Jun 2020 02:42:13: 13000000 INFO @ Tue, 30 Jun 2020 02:42:13: 18000000 INFO @ Tue, 30 Jun 2020 02:42:14: 8000000 INFO @ Tue, 30 Jun 2020 02:42:19: 14000000 INFO @ Tue, 30 Jun 2020 02:42:20: 19000000 INFO @ Tue, 30 Jun 2020 02:42:20: 9000000 INFO @ Tue, 30 Jun 2020 02:42:25: 15000000 INFO @ Tue, 30 Jun 2020 02:42:26: 20000000 INFO @ Tue, 30 Jun 2020 02:42:26: 10000000 INFO @ Tue, 30 Jun 2020 02:42:31: 16000000 INFO @ Tue, 30 Jun 2020 02:42:32: 11000000 INFO @ Tue, 30 Jun 2020 02:42:32: 21000000 INFO @ Tue, 30 Jun 2020 02:42:37: 17000000 INFO @ Tue, 30 Jun 2020 02:42:38: 12000000 INFO @ Tue, 30 Jun 2020 02:42:38: 22000000 INFO @ Tue, 30 Jun 2020 02:42:43: 18000000 INFO @ Tue, 30 Jun 2020 02:42:44: 13000000 INFO @ Tue, 30 Jun 2020 02:42:44: 23000000 INFO @ Tue, 30 Jun 2020 02:42:48: 19000000 INFO @ Tue, 30 Jun 2020 02:42:49: 14000000 INFO @ Tue, 30 Jun 2020 02:42:50: 24000000 INFO @ Tue, 30 Jun 2020 02:42:54: 20000000 INFO @ Tue, 30 Jun 2020 02:42:55: 15000000 INFO @ Tue, 30 Jun 2020 02:42:56: 25000000 INFO @ Tue, 30 Jun 2020 02:43:00: 21000000 INFO @ Tue, 30 Jun 2020 02:43:01: 16000000 INFO @ Tue, 30 Jun 2020 02:43:02: 26000000 INFO @ Tue, 30 Jun 2020 02:43:06: 22000000 INFO @ Tue, 30 Jun 2020 02:43:07: 17000000 INFO @ Tue, 30 Jun 2020 02:43:08: 27000000 INFO @ Tue, 30 Jun 2020 02:43:11: 23000000 INFO @ Tue, 30 Jun 2020 02:43:13: 18000000 INFO @ Tue, 30 Jun 2020 02:43:14: 28000000 INFO @ Tue, 30 Jun 2020 02:43:17: 24000000 INFO @ Tue, 30 Jun 2020 02:43:19: 19000000 INFO @ Tue, 30 Jun 2020 02:43:20: 29000000 INFO @ Tue, 30 Jun 2020 02:43:23: 25000000 INFO @ Tue, 30 Jun 2020 02:43:25: 20000000 INFO @ Tue, 30 Jun 2020 02:43:26: 30000000 INFO @ Tue, 30 Jun 2020 02:43:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:43:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:43:27: #1 total tags in treatment: 30179370 INFO @ Tue, 30 Jun 2020 02:43:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:27: #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 02:43:28: #1 tags after filtering in treatment: 30179323 INFO @ Tue, 30 Jun 2020 02:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:29: 26000000 INFO @ Tue, 30 Jun 2020 02:43:30: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 02:43:30: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:30: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:43:30: #2 alternative fragment length(s) may be 2,53,71,592,598 bps INFO @ Tue, 30 Jun 2020 02:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.05_model.r WARNING @ Tue, 30 Jun 2020 02:43:30: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:30: #2 You may need to consider one of the other alternative d(s): 2,53,71,592,598 WARNING @ Tue, 30 Jun 2020 02:43:30: #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 02:43:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:31: 21000000 INFO @ Tue, 30 Jun 2020 02:43:34: 27000000 INFO @ Tue, 30 Jun 2020 02:43:37: 22000000 INFO @ Tue, 30 Jun 2020 02:43:40: 28000000 INFO @ Tue, 30 Jun 2020 02:43:43: 23000000 INFO @ Tue, 30 Jun 2020 02:43:46: 29000000 INFO @ Tue, 30 Jun 2020 02:43:49: 24000000 INFO @ Tue, 30 Jun 2020 02:43:52: 30000000 INFO @ Tue, 30 Jun 2020 02:43:53: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:43:53: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:43:53: #1 total tags in treatment: 30179370 INFO @ Tue, 30 Jun 2020 02:43:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:43:54: #1 tags after filtering in treatment: 30179323 INFO @ Tue, 30 Jun 2020 02:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:54: 25000000 INFO @ Tue, 30 Jun 2020 02:43:56: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 02:43:56: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:56: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:56: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:56: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:56: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:43:56: #2 alternative fragment length(s) may be 2,53,71,592,598 bps INFO @ Tue, 30 Jun 2020 02:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.10_model.r WARNING @ Tue, 30 Jun 2020 02:43:56: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:56: #2 You may need to consider one of the other alternative d(s): 2,53,71,592,598 WARNING @ Tue, 30 Jun 2020 02:43:56: #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 02:43:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:44:00: 26000000 INFO @ Tue, 30 Jun 2020 02:44:06: 27000000 INFO @ Tue, 30 Jun 2020 02:44:11: 28000000 INFO @ Tue, 30 Jun 2020 02:44:17: 29000000 INFO @ Tue, 30 Jun 2020 02:44:23: 30000000 INFO @ Tue, 30 Jun 2020 02:44:24: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:44:24: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:44:24: #1 total tags in treatment: 30179370 INFO @ Tue, 30 Jun 2020 02:44:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:44:24: #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 02:44:25: #1 tags after filtering in treatment: 30179323 INFO @ Tue, 30 Jun 2020 02:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:44:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:44:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:44:27: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 02:44:27: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 02:44:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:44:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:44:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:44:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:44:27: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:44:27: #2 alternative fragment length(s) may be 2,53,71,592,598 bps INFO @ Tue, 30 Jun 2020 02:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.20_model.r WARNING @ Tue, 30 Jun 2020 02:44:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:44:27: #2 You may need to consider one of the other alternative d(s): 2,53,71,592,598 WARNING @ Tue, 30 Jun 2020 02:44:27: #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 02:44:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:44:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.05_summits.bed INFO @ Tue, 30 Jun 2020 02:44:55: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (3138 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:44:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:45:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.10_summits.bed INFO @ Tue, 30 Jun 2020 02:45:25: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (1352 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981696/SRX3981696.20_summits.bed INFO @ Tue, 30 Jun 2020 02:45:55: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 8 millis CompletedMACS2peakCalling