Job ID = 6529712 SRX = SRX3989975 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: 00:04:05 13253228 reads; of these: 13253228 (100.00%) were unpaired; of these: 2258343 (17.04%) aligned 0 times 8008746 (60.43%) aligned exactly 1 time 2986139 (22.53%) aligned >1 times 82.96% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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 8 files... [bam_rmdupse_core] 2334774 / 10994885 = 0.2124 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 02:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.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 02:46:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:52: 1000000 INFO @ Tue, 30 Jun 2020 02:46:59: 2000000 INFO @ Tue, 30 Jun 2020 02:47:05: 3000000 INFO @ Tue, 30 Jun 2020 02:47:11: 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 02:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.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 02:47:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:18: 5000000 INFO @ Tue, 30 Jun 2020 02:47:23: 1000000 INFO @ Tue, 30 Jun 2020 02:47:25: 6000000 INFO @ Tue, 30 Jun 2020 02:47:30: 2000000 INFO @ Tue, 30 Jun 2020 02:47:32: 7000000 INFO @ Tue, 30 Jun 2020 02:47:36: 3000000 INFO @ Tue, 30 Jun 2020 02:47:38: 8000000 INFO @ Tue, 30 Jun 2020 02:47:43: 4000000 INFO @ Tue, 30 Jun 2020 02:47:43: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:47:43: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:47:43: #1 total tags in treatment: 8660111 INFO @ Tue, 30 Jun 2020 02:47:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:43: #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 02:47:44: #1 tags after filtering in treatment: 8660103 INFO @ Tue, 30 Jun 2020 02:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:44: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 02:47:44: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:44: start model_add_line... BedGraph に変換中... INFO @ Tue, 30 Jun 2020 02:47:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:44: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:47:44: #2 alternative fragment length(s) may be 4,45,579 bps INFO @ Tue, 30 Jun 2020 02:47:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:44: #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 02:47:44: #2 You may need to consider one of the other alternative d(s): 4,45,579 WARNING @ Tue, 30 Jun 2020 02:47:44: #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 02:47:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:44: #3 Pre-compute pvalue-qvalue table... 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 02:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.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 02:47:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:50: 5000000 INFO @ Tue, 30 Jun 2020 02:47:52: 1000000 INFO @ Tue, 30 Jun 2020 02:47:56: 6000000 INFO @ Tue, 30 Jun 2020 02:47:59: 2000000 INFO @ Tue, 30 Jun 2020 02:48:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:04: 7000000 INFO @ Tue, 30 Jun 2020 02:48:05: 3000000 INFO @ Tue, 30 Jun 2020 02:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.05_summits.bed INFO @ Tue, 30 Jun 2020 02:48:10: Done! pass1 - making usageList (256 chroms): 1 millis pass2 - checking and writing primary data (1011 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:11: 8000000 INFO @ Tue, 30 Jun 2020 02:48:11: 4000000 INFO @ Tue, 30 Jun 2020 02:48:15: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:48:15: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:48:15: #1 total tags in treatment: 8660111 INFO @ Tue, 30 Jun 2020 02:48:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:15: #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 02:48:16: #1 tags after filtering in treatment: 8660103 INFO @ Tue, 30 Jun 2020 02:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:16: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 02:48:16: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:16: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:48:16: #2 alternative fragment length(s) may be 4,45,579 bps INFO @ Tue, 30 Jun 2020 02:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:16: #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 02:48:16: #2 You may need to consider one of the other alternative d(s): 4,45,579 WARNING @ Tue, 30 Jun 2020 02:48:16: #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 02:48:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:17: 5000000 INFO @ Tue, 30 Jun 2020 02:48:23: 6000000 INFO @ Tue, 30 Jun 2020 02:48:30: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:48:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:35: 8000000 INFO @ Tue, 30 Jun 2020 02:48:39: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:48:39: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:48:39: #1 total tags in treatment: 8660111 INFO @ Tue, 30 Jun 2020 02:48:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:39: #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 02:48:40: #1 tags after filtering in treatment: 8660103 INFO @ Tue, 30 Jun 2020 02:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:40: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 02:48:40: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:40: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:48:40: #2 alternative fragment length(s) may be 4,45,579 bps INFO @ Tue, 30 Jun 2020 02:48:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:40: #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 02:48:40: #2 You may need to consider one of the other alternative d(s): 4,45,579 WARNING @ Tue, 30 Jun 2020 02:48:40: #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 02:48:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.10_summits.bed INFO @ Tue, 30 Jun 2020 02:48:42: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:48:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989975/SRX3989975.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:07: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 3 millis CompletedMACS2peakCalling