Job ID = 6529987 SRX = SRX5736607 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: 00:06:47 25039537 reads; of these: 25039537 (100.00%) were unpaired; of these: 650470 (2.60%) aligned 0 times 18335249 (73.23%) aligned exactly 1 time 6053818 (24.18%) aligned >1 times 97.40% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 3570284 / 24389067 = 0.1464 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 03:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.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 03:08:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:35: 1000000 INFO @ Tue, 30 Jun 2020 03:08:41: 2000000 INFO @ Tue, 30 Jun 2020 03:08:46: 3000000 INFO @ Tue, 30 Jun 2020 03:08:52: 4000000 INFO @ Tue, 30 Jun 2020 03:08:57: 5000000 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 03:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.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 03:09:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:02: 6000000 INFO @ Tue, 30 Jun 2020 03:09:05: 1000000 INFO @ Tue, 30 Jun 2020 03:09:08: 7000000 INFO @ Tue, 30 Jun 2020 03:09:11: 2000000 INFO @ Tue, 30 Jun 2020 03:09:14: 8000000 INFO @ Tue, 30 Jun 2020 03:09:17: 3000000 INFO @ Tue, 30 Jun 2020 03:09:19: 9000000 INFO @ Tue, 30 Jun 2020 03:09:22: 4000000 INFO @ Tue, 30 Jun 2020 03:09:25: 10000000 INFO @ Tue, 30 Jun 2020 03:09:28: 5000000 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 03:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.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 03:09:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:31: 11000000 INFO @ Tue, 30 Jun 2020 03:09:33: 6000000 INFO @ Tue, 30 Jun 2020 03:09:35: 1000000 INFO @ Tue, 30 Jun 2020 03:09:36: 12000000 INFO @ Tue, 30 Jun 2020 03:09:39: 7000000 INFO @ Tue, 30 Jun 2020 03:09:41: 2000000 INFO @ Tue, 30 Jun 2020 03:09:42: 13000000 INFO @ Tue, 30 Jun 2020 03:09:45: 8000000 INFO @ Tue, 30 Jun 2020 03:09:46: 3000000 INFO @ Tue, 30 Jun 2020 03:09:48: 14000000 INFO @ Tue, 30 Jun 2020 03:09:51: 9000000 INFO @ Tue, 30 Jun 2020 03:09:51: 4000000 INFO @ Tue, 30 Jun 2020 03:09:53: 15000000 INFO @ Tue, 30 Jun 2020 03:09:56: 5000000 INFO @ Tue, 30 Jun 2020 03:09:57: 10000000 INFO @ Tue, 30 Jun 2020 03:09:59: 16000000 INFO @ Tue, 30 Jun 2020 03:10:01: 6000000 INFO @ Tue, 30 Jun 2020 03:10:02: 11000000 INFO @ Tue, 30 Jun 2020 03:10:05: 17000000 INFO @ Tue, 30 Jun 2020 03:10:06: 7000000 INFO @ Tue, 30 Jun 2020 03:10:08: 12000000 INFO @ Tue, 30 Jun 2020 03:10:11: 18000000 INFO @ Tue, 30 Jun 2020 03:10:11: 8000000 INFO @ Tue, 30 Jun 2020 03:10:14: 13000000 INFO @ Tue, 30 Jun 2020 03:10:17: 19000000 INFO @ Tue, 30 Jun 2020 03:10:17: 9000000 INFO @ Tue, 30 Jun 2020 03:10:19: 14000000 INFO @ Tue, 30 Jun 2020 03:10:22: 10000000 INFO @ Tue, 30 Jun 2020 03:10:22: 20000000 INFO @ Tue, 30 Jun 2020 03:10:25: 15000000 INFO @ Tue, 30 Jun 2020 03:10:28: 11000000 INFO @ Tue, 30 Jun 2020 03:10:28: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:10:28: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:10:28: #1 total tags in treatment: 20818783 INFO @ Tue, 30 Jun 2020 03:10:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:10:28: #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 03:10:28: #1 tags after filtering in treatment: 20818716 INFO @ Tue, 30 Jun 2020 03:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:10:28: #1 finished! INFO @ Tue, 30 Jun 2020 03:10:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:10:30: #2 number of paired peaks: 930 WARNING @ Tue, 30 Jun 2020 03:10:30: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 30 Jun 2020 03:10:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:10:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:10:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:10:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:10:30: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:10:30: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.05_model.r WARNING @ Tue, 30 Jun 2020 03:10:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:10:30: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:10:30: #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 03:10:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:10:32: 16000000 INFO @ Tue, 30 Jun 2020 03:10:33: 12000000 INFO @ Tue, 30 Jun 2020 03:10:38: 13000000 INFO @ Tue, 30 Jun 2020 03:10:38: 17000000 INFO @ Tue, 30 Jun 2020 03:10:43: 14000000 INFO @ Tue, 30 Jun 2020 03:10:44: 18000000 INFO @ Tue, 30 Jun 2020 03:10:48: 15000000 INFO @ Tue, 30 Jun 2020 03:10:49: 19000000 INFO @ Tue, 30 Jun 2020 03:10:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:10:55: 20000000 INFO @ Tue, 30 Jun 2020 03:10:59: 17000000 INFO @ Tue, 30 Jun 2020 03:11:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:00: #1 total tags in treatment: 20818783 INFO @ Tue, 30 Jun 2020 03:11:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:00: #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 03:11:01: #1 tags after filtering in treatment: 20818716 INFO @ Tue, 30 Jun 2020 03:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:02: #2 number of paired peaks: 930 WARNING @ Tue, 30 Jun 2020 03:11:02: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:02: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:02: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:02: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:11:02: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.10_model.r WARNING @ Tue, 30 Jun 2020 03:11:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:02: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:11:02: #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 03:11:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:04: 18000000 INFO @ Tue, 30 Jun 2020 03:11:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:09: 19000000 INFO @ Tue, 30 Jun 2020 03:11:14: 20000000 INFO @ Tue, 30 Jun 2020 03:11:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:18: #1 total tags in treatment: 20818783 INFO @ Tue, 30 Jun 2020 03:11:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:18: #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 03:11:19: #1 tags after filtering in treatment: 20818716 INFO @ Tue, 30 Jun 2020 03:11:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:19: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:20: #2 number of paired peaks: 930 WARNING @ Tue, 30 Jun 2020 03:11:20: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:20: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:21: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:21: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:21: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:21: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:11:21: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.20_model.r WARNING @ Tue, 30 Jun 2020 03:11:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:21: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:11:21: #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 03:11:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.05_summits.bed INFO @ Tue, 30 Jun 2020 03:11:28: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (3771 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:11:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:11:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:11:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.10_summits.bed INFO @ Tue, 30 Jun 2020 03:11:58: Done! pass1 - making usageList (402 chroms): 2 millis pass2 - checking and writing primary data (1518 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736607/SRX5736607.20_summits.bed INFO @ Tue, 30 Jun 2020 03:12:21: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 6 millis CompletedMACS2peakCalling