Job ID = 6529246 SRX = SRX110791 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: 00:08:39 41972385 reads; of these: 41972385 (100.00%) were unpaired; of these: 2772642 (6.61%) aligned 0 times 33933107 (80.85%) aligned exactly 1 time 5266636 (12.55%) aligned >1 times 93.39% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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] 8633487 / 39199743 = 0.2202 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 01:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.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 01:54:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:54:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:54:21: 1000000 INFO @ Tue, 30 Jun 2020 01:54:27: 2000000 INFO @ Tue, 30 Jun 2020 01:54:33: 3000000 INFO @ Tue, 30 Jun 2020 01:54:39: 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 01:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.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 01:54:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:54:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:54:46: 5000000 INFO @ Tue, 30 Jun 2020 01:54:51: 1000000 INFO @ Tue, 30 Jun 2020 01:54:52: 6000000 INFO @ Tue, 30 Jun 2020 01:54:58: 2000000 INFO @ Tue, 30 Jun 2020 01:54:58: 7000000 INFO @ Tue, 30 Jun 2020 01:55:05: 3000000 INFO @ Tue, 30 Jun 2020 01:55:05: 8000000 INFO @ Tue, 30 Jun 2020 01:55:11: 9000000 INFO @ Tue, 30 Jun 2020 01:55:11: 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 01:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.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 01:55:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:55:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:55:17: 10000000 INFO @ Tue, 30 Jun 2020 01:55:18: 5000000 INFO @ Tue, 30 Jun 2020 01:55:21: 1000000 INFO @ Tue, 30 Jun 2020 01:55:23: 11000000 INFO @ Tue, 30 Jun 2020 01:55:25: 6000000 INFO @ Tue, 30 Jun 2020 01:55:28: 2000000 INFO @ Tue, 30 Jun 2020 01:55:29: 12000000 INFO @ Tue, 30 Jun 2020 01:55:32: 7000000 INFO @ Tue, 30 Jun 2020 01:55:35: 3000000 INFO @ Tue, 30 Jun 2020 01:55:35: 13000000 INFO @ Tue, 30 Jun 2020 01:55:39: 8000000 INFO @ Tue, 30 Jun 2020 01:55:41: 4000000 INFO @ Tue, 30 Jun 2020 01:55:42: 14000000 INFO @ Tue, 30 Jun 2020 01:55:45: 9000000 INFO @ Tue, 30 Jun 2020 01:55:47: 5000000 INFO @ Tue, 30 Jun 2020 01:55:48: 15000000 INFO @ Tue, 30 Jun 2020 01:55:51: 10000000 INFO @ Tue, 30 Jun 2020 01:55:53: 6000000 INFO @ Tue, 30 Jun 2020 01:55:54: 16000000 INFO @ Tue, 30 Jun 2020 01:55:57: 11000000 INFO @ Tue, 30 Jun 2020 01:56:00: 7000000 INFO @ Tue, 30 Jun 2020 01:56:00: 17000000 INFO @ Tue, 30 Jun 2020 01:56:03: 12000000 INFO @ Tue, 30 Jun 2020 01:56:06: 8000000 INFO @ Tue, 30 Jun 2020 01:56:07: 18000000 INFO @ Tue, 30 Jun 2020 01:56:09: 13000000 INFO @ Tue, 30 Jun 2020 01:56:12: 9000000 INFO @ Tue, 30 Jun 2020 01:56:13: 19000000 INFO @ Tue, 30 Jun 2020 01:56:15: 14000000 INFO @ Tue, 30 Jun 2020 01:56:19: 10000000 INFO @ Tue, 30 Jun 2020 01:56:19: 20000000 INFO @ Tue, 30 Jun 2020 01:56:21: 15000000 INFO @ Tue, 30 Jun 2020 01:56:25: 11000000 INFO @ Tue, 30 Jun 2020 01:56:26: 21000000 INFO @ Tue, 30 Jun 2020 01:56:27: 16000000 INFO @ Tue, 30 Jun 2020 01:56:31: 12000000 INFO @ Tue, 30 Jun 2020 01:56:32: 22000000 INFO @ Tue, 30 Jun 2020 01:56:33: 17000000 INFO @ Tue, 30 Jun 2020 01:56:37: 13000000 INFO @ Tue, 30 Jun 2020 01:56:38: 23000000 INFO @ Tue, 30 Jun 2020 01:56:39: 18000000 INFO @ Tue, 30 Jun 2020 01:56:43: 14000000 INFO @ Tue, 30 Jun 2020 01:56:44: 24000000 INFO @ Tue, 30 Jun 2020 01:56:45: 19000000 INFO @ Tue, 30 Jun 2020 01:56:49: 15000000 INFO @ Tue, 30 Jun 2020 01:56:51: 20000000 INFO @ Tue, 30 Jun 2020 01:56:51: 25000000 INFO @ Tue, 30 Jun 2020 01:56:56: 16000000 INFO @ Tue, 30 Jun 2020 01:56:57: 21000000 INFO @ Tue, 30 Jun 2020 01:56:58: 26000000 INFO @ Tue, 30 Jun 2020 01:57:02: 17000000 INFO @ Tue, 30 Jun 2020 01:57:03: 22000000 INFO @ Tue, 30 Jun 2020 01:57:04: 27000000 INFO @ Tue, 30 Jun 2020 01:57:08: 18000000 INFO @ Tue, 30 Jun 2020 01:57:09: 23000000 INFO @ Tue, 30 Jun 2020 01:57:10: 28000000 INFO @ Tue, 30 Jun 2020 01:57:14: 24000000 INFO @ Tue, 30 Jun 2020 01:57:14: 19000000 INFO @ Tue, 30 Jun 2020 01:57:16: 29000000 INFO @ Tue, 30 Jun 2020 01:57:21: 20000000 INFO @ Tue, 30 Jun 2020 01:57:21: 25000000 INFO @ Tue, 30 Jun 2020 01:57:23: 30000000 INFO @ Tue, 30 Jun 2020 01:57:27: 21000000 INFO @ Tue, 30 Jun 2020 01:57:27: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:57:27: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:57:27: #1 total tags in treatment: 30566256 INFO @ Tue, 30 Jun 2020 01:57:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:27: #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 01:57:27: 26000000 INFO @ Tue, 30 Jun 2020 01:57:28: #1 tags after filtering in treatment: 30566254 INFO @ Tue, 30 Jun 2020 01:57:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:28: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:30: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 01:57:30: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:30: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:30: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:30: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:30: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:30: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:57:30: #2 alternative fragment length(s) may be 3,41,56,73,89 bps INFO @ Tue, 30 Jun 2020 01:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:30: #2 You may need to consider one of the other alternative d(s): 3,41,56,73,89 WARNING @ Tue, 30 Jun 2020 01:57:30: #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 01:57:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:33: 22000000 INFO @ Tue, 30 Jun 2020 01:57:33: 27000000 INFO @ Tue, 30 Jun 2020 01:57:38: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:57:39: 28000000 INFO @ Tue, 30 Jun 2020 01:57:45: 24000000 INFO @ Tue, 30 Jun 2020 01:57:46: 29000000 INFO @ Tue, 30 Jun 2020 01:57:52: 25000000 INFO @ Tue, 30 Jun 2020 01:57:52: 30000000 INFO @ Tue, 30 Jun 2020 01:57:56: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:57:56: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:57:56: #1 total tags in treatment: 30566256 INFO @ Tue, 30 Jun 2020 01:57:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:56: #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 01:57:57: #1 tags after filtering in treatment: 30566254 INFO @ Tue, 30 Jun 2020 01:57:57: 26000000 INFO @ Tue, 30 Jun 2020 01:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:57: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:59: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 01:57:59: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:59: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:00: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:00: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:00: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:00: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:58:00: #2 alternative fragment length(s) may be 3,41,56,73,89 bps INFO @ Tue, 30 Jun 2020 01:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.10_model.r WARNING @ Tue, 30 Jun 2020 01:58:00: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:00: #2 You may need to consider one of the other alternative d(s): 3,41,56,73,89 WARNING @ Tue, 30 Jun 2020 01:58:00: #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 01:58:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:03: 27000000 INFO @ Tue, 30 Jun 2020 01:58:09: 28000000 INFO @ Tue, 30 Jun 2020 01:58:14: 29000000 INFO @ Tue, 30 Jun 2020 01:58:20: 30000000 INFO @ Tue, 30 Jun 2020 01:58:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:24: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:58:24: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:58:24: #1 total tags in treatment: 30566256 INFO @ Tue, 30 Jun 2020 01:58:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:24: #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 01:58:25: #1 tags after filtering in treatment: 30566254 INFO @ Tue, 30 Jun 2020 01:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:25: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:27: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 01:58:27: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:27: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:27: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:27: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:58:27: #2 alternative fragment length(s) may be 3,41,56,73,89 bps INFO @ Tue, 30 Jun 2020 01:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:27: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:27: #2 You may need to consider one of the other alternative d(s): 3,41,56,73,89 WARNING @ Tue, 30 Jun 2020 01:58:27: #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 01:58:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:51: Done! pass1 - making usageList (432 chroms): 3 millis pass2 - checking and writing primary data (11632 records, 4 fields): 37 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:59:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.10_summits.bed INFO @ Tue, 30 Jun 2020 01:59:19: Done! pass1 - making usageList (230 chroms): 1 millis pass2 - checking and writing primary data (3869 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110791/SRX110791.20_summits.bed INFO @ Tue, 30 Jun 2020 01:59:48: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 8 millis CompletedMACS2peakCalling