Job ID = 6529746 SRX = SRX4669049 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:02 32661237 reads; of these: 32661237 (100.00%) were unpaired; of these: 1783501 (5.46%) aligned 0 times 21144233 (64.74%) aligned exactly 1 time 9733503 (29.80%) aligned >1 times 94.54% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 12470428 / 30877736 = 0.4039 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 02:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.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 02:46:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:46: 1000000 INFO @ Tue, 30 Jun 2020 02:46:55: 2000000 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 02:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.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 02:47:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:07: 3000000 INFO @ Tue, 30 Jun 2020 02:47:15: 1000000 INFO @ Tue, 30 Jun 2020 02:47:17: 4000000 INFO @ Tue, 30 Jun 2020 02:47:24: 2000000 INFO @ Tue, 30 Jun 2020 02:47:26: 5000000 INFO @ Tue, 30 Jun 2020 02:47:33: 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 02:47:35: 6000000 INFO @ Tue, 30 Jun 2020 02:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.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 02:47:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:43: 4000000 INFO @ Tue, 30 Jun 2020 02:47:45: 7000000 INFO @ Tue, 30 Jun 2020 02:47:45: 1000000 INFO @ Tue, 30 Jun 2020 02:47:52: 5000000 INFO @ Tue, 30 Jun 2020 02:47:54: 2000000 INFO @ Tue, 30 Jun 2020 02:47:55: 8000000 INFO @ Tue, 30 Jun 2020 02:48:01: 6000000 INFO @ Tue, 30 Jun 2020 02:48:03: 3000000 INFO @ Tue, 30 Jun 2020 02:48:04: 9000000 INFO @ Tue, 30 Jun 2020 02:48:10: 7000000 INFO @ Tue, 30 Jun 2020 02:48:13: 4000000 INFO @ Tue, 30 Jun 2020 02:48:14: 10000000 INFO @ Tue, 30 Jun 2020 02:48:19: 8000000 INFO @ Tue, 30 Jun 2020 02:48:22: 5000000 INFO @ Tue, 30 Jun 2020 02:48:23: 11000000 INFO @ Tue, 30 Jun 2020 02:48:28: 9000000 INFO @ Tue, 30 Jun 2020 02:48:31: 6000000 INFO @ Tue, 30 Jun 2020 02:48:33: 12000000 INFO @ Tue, 30 Jun 2020 02:48:37: 10000000 INFO @ Tue, 30 Jun 2020 02:48:40: 7000000 INFO @ Tue, 30 Jun 2020 02:48:42: 13000000 INFO @ Tue, 30 Jun 2020 02:48:47: 11000000 INFO @ Tue, 30 Jun 2020 02:48:49: 8000000 INFO @ Tue, 30 Jun 2020 02:48:51: 14000000 INFO @ Tue, 30 Jun 2020 02:48:56: 12000000 INFO @ Tue, 30 Jun 2020 02:48:58: 9000000 INFO @ Tue, 30 Jun 2020 02:49:01: 15000000 INFO @ Tue, 30 Jun 2020 02:49:05: 13000000 INFO @ Tue, 30 Jun 2020 02:49:07: 10000000 INFO @ Tue, 30 Jun 2020 02:49:10: 16000000 INFO @ Tue, 30 Jun 2020 02:49:14: 14000000 INFO @ Tue, 30 Jun 2020 02:49:16: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:49:17: 17000000 INFO @ Tue, 30 Jun 2020 02:49:23: 15000000 INFO @ Tue, 30 Jun 2020 02:49:25: 12000000 INFO @ Tue, 30 Jun 2020 02:49:26: 18000000 INFO @ Tue, 30 Jun 2020 02:49:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:29: #1 total tags in treatment: 18407308 INFO @ Tue, 30 Jun 2020 02:49:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:29: #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 02:49:30: #1 tags after filtering in treatment: 18407308 INFO @ Tue, 30 Jun 2020 02:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:30: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:31: #2 number of paired peaks: 153 WARNING @ Tue, 30 Jun 2020 02:49:31: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:31: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 02:49:31: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 30 Jun 2020 02:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:31: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 30 Jun 2020 02:49:31: #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 02:49:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:32: 16000000 INFO @ Tue, 30 Jun 2020 02:49:33: 13000000 INFO @ Tue, 30 Jun 2020 02:49:40: 17000000 INFO @ Tue, 30 Jun 2020 02:49:41: 14000000 INFO @ Tue, 30 Jun 2020 02:49:49: 18000000 INFO @ Tue, 30 Jun 2020 02:49:50: 15000000 INFO @ Tue, 30 Jun 2020 02:49:52: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:52: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:52: #1 total tags in treatment: 18407308 INFO @ Tue, 30 Jun 2020 02:49:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:52: #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 02:49:53: #1 tags after filtering in treatment: 18407308 INFO @ Tue, 30 Jun 2020 02:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:54: #2 number of paired peaks: 153 WARNING @ Tue, 30 Jun 2020 02:49:54: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:54: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:54: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 02:49:54: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 30 Jun 2020 02:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.10_model.r WARNING @ Tue, 30 Jun 2020 02:49:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:54: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 30 Jun 2020 02:49:54: #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 02:49:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:58: 16000000 INFO @ Tue, 30 Jun 2020 02:50:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:06: 17000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:50:14: 18000000 INFO @ Tue, 30 Jun 2020 02:50:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:17: #1 total tags in treatment: 18407308 INFO @ Tue, 30 Jun 2020 02:50:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:17: #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: 18407308 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 02:50:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:18: Done! pass1 - making usageList (533 chroms): 2 millis pass2 - checking and writing primary data (2058 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:19: #2 number of paired peaks: 153 WARNING @ Tue, 30 Jun 2020 02:50:19: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 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 52 bps INFO @ Tue, 30 Jun 2020 02:50:19: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 30 Jun 2020 02:50:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:19: #2 Since the d (52) 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): 3,52 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 02:50:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.10_summits.bed INFO @ Tue, 30 Jun 2020 02:50:42: Done! pass1 - making usageList (440 chroms): 1 millis pass2 - checking and writing primary data (1441 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669049/SRX4669049.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:07: Done! pass1 - making usageList (249 chroms): 2 millis pass2 - checking and writing primary data (440 records, 4 fields): 14 millis CompletedMACS2peakCalling