Job ID = 6529753 SRX = SRX4669061 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: 00:05:34 23934079 reads; of these: 23934079 (100.00%) were unpaired; of these: 1206238 (5.04%) aligned 0 times 19819517 (82.81%) aligned exactly 1 time 2908324 (12.15%) aligned >1 times 94.96% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 5271466 / 22727841 = 0.2319 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 02:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.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 02:57:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:53: 1000000 INFO @ Tue, 30 Jun 2020 02:57:59: 2000000 INFO @ Tue, 30 Jun 2020 02:58:06: 3000000 INFO @ Tue, 30 Jun 2020 02:58:13: 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 02:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.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 02:58:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:20: 5000000 INFO @ Tue, 30 Jun 2020 02:58:23: 1000000 INFO @ Tue, 30 Jun 2020 02:58:28: 6000000 INFO @ Tue, 30 Jun 2020 02:58:30: 2000000 INFO @ Tue, 30 Jun 2020 02:58:35: 7000000 INFO @ Tue, 30 Jun 2020 02:58:38: 3000000 INFO @ Tue, 30 Jun 2020 02:58:43: 8000000 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 02:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.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 02:58:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:46: 4000000 INFO @ Tue, 30 Jun 2020 02:58:50: 9000000 INFO @ Tue, 30 Jun 2020 02:58:52: 1000000 INFO @ Tue, 30 Jun 2020 02:58:54: 5000000 INFO @ Tue, 30 Jun 2020 02:58:58: 10000000 INFO @ Tue, 30 Jun 2020 02:58:59: 2000000 INFO @ Tue, 30 Jun 2020 02:59:02: 6000000 INFO @ Tue, 30 Jun 2020 02:59:05: 11000000 INFO @ Tue, 30 Jun 2020 02:59:06: 3000000 INFO @ Tue, 30 Jun 2020 02:59:09: 7000000 INFO @ Tue, 30 Jun 2020 02:59:13: 4000000 INFO @ Tue, 30 Jun 2020 02:59:13: 12000000 INFO @ Tue, 30 Jun 2020 02:59:17: 8000000 INFO @ Tue, 30 Jun 2020 02:59:20: 5000000 INFO @ Tue, 30 Jun 2020 02:59:21: 13000000 INFO @ Tue, 30 Jun 2020 02:59:25: 9000000 INFO @ Tue, 30 Jun 2020 02:59:27: 6000000 INFO @ Tue, 30 Jun 2020 02:59:28: 14000000 INFO @ Tue, 30 Jun 2020 02:59:33: 10000000 INFO @ Tue, 30 Jun 2020 02:59:34: 7000000 INFO @ Tue, 30 Jun 2020 02:59:36: 15000000 INFO @ Tue, 30 Jun 2020 02:59:41: 8000000 INFO @ Tue, 30 Jun 2020 02:59:41: 11000000 INFO @ Tue, 30 Jun 2020 02:59:44: 16000000 INFO @ Tue, 30 Jun 2020 02:59:48: 9000000 INFO @ Tue, 30 Jun 2020 02:59:49: 12000000 INFO @ Tue, 30 Jun 2020 02:59:52: 17000000 INFO @ Tue, 30 Jun 2020 02:59:55: 10000000 INFO @ Tue, 30 Jun 2020 02:59:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:55: #1 total tags in treatment: 17456375 INFO @ Tue, 30 Jun 2020 02:59:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:55: #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 02:59:56: #1 tags after filtering in treatment: 17456361 INFO @ Tue, 30 Jun 2020 02:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:57: 13000000 INFO @ Tue, 30 Jun 2020 02:59:57: #2 number of paired peaks: 121 WARNING @ Tue, 30 Jun 2020 02:59:57: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:57: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:59:57: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 02:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:57: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:57: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 02:59:57: #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 02:59:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:00:02: 11000000 INFO @ Tue, 30 Jun 2020 03:00:04: 14000000 INFO @ Tue, 30 Jun 2020 03:00:08: 12000000 INFO @ Tue, 30 Jun 2020 03:00:12: 15000000 INFO @ Tue, 30 Jun 2020 03:00:15: 13000000 INFO @ Tue, 30 Jun 2020 03:00:20: 16000000 INFO @ Tue, 30 Jun 2020 03:00:22: 14000000 INFO @ Tue, 30 Jun 2020 03:00:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:28: 17000000 INFO @ Tue, 30 Jun 2020 03:00:29: 15000000 INFO @ Tue, 30 Jun 2020 03:00:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:00:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:00:31: #1 total tags in treatment: 17456375 INFO @ Tue, 30 Jun 2020 03:00:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:31: #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 03:00:32: #1 tags after filtering in treatment: 17456361 INFO @ Tue, 30 Jun 2020 03:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:33: #2 number of paired peaks: 121 WARNING @ Tue, 30 Jun 2020 03:00:33: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:33: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:33: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:33: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:33: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:33: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:00:33: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 03:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.10_model.r WARNING @ Tue, 30 Jun 2020 03:00:33: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:00:33: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 03:00:33: #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 03:00:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:00:36: 16000000 INFO @ Tue, 30 Jun 2020 03:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.05_summits.bed INFO @ Tue, 30 Jun 2020 03:00:42: Done! INFO @ Tue, 30 Jun 2020 03:00:42: 17000000 pass1 - making usageList (425 chroms): 1 millis pass2 - checking and writing primary data (2760 records, 4 fields): 96 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:00:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:00:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:00:45: #1 total tags in treatment: 17456375 INFO @ Tue, 30 Jun 2020 03:00:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:45: #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 03:00:46: #1 tags after filtering in treatment: 17456361 INFO @ Tue, 30 Jun 2020 03:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:46: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:47: #2 number of paired peaks: 121 WARNING @ Tue, 30 Jun 2020 03:00:47: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:47: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:47: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:47: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:47: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:47: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:00:47: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 03:00:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:00:47: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 03:00:47: #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 03:00:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:01:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.10_summits.bed INFO @ Tue, 30 Jun 2020 03:01:20: Done! pass1 - making usageList (280 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669061/SRX4669061.20_summits.bed INFO @ Tue, 30 Jun 2020 03:01:33: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 4 millis CompletedMACS2peakCalling