Job ID = 6529274 SRX = SRX1166570 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: 00:05:41 26749908 reads; of these: 26749908 (100.00%) were unpaired; of these: 553375 (2.07%) aligned 0 times 20910218 (78.17%) aligned exactly 1 time 5286315 (19.76%) aligned >1 times 97.93% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 7130042 / 26196533 = 0.2722 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 01:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.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 01:36:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:31: 1000000 INFO @ Tue, 30 Jun 2020 01:36:37: 2000000 INFO @ Tue, 30 Jun 2020 01:36:43: 3000000 INFO @ Tue, 30 Jun 2020 01:36:49: 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 01:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.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 01:36:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:55: 5000000 INFO @ Tue, 30 Jun 2020 01:37:02: 6000000 INFO @ Tue, 30 Jun 2020 01:37:03: 1000000 INFO @ Tue, 30 Jun 2020 01:37:10: 7000000 INFO @ Tue, 30 Jun 2020 01:37:11: 2000000 INFO @ Tue, 30 Jun 2020 01:37:17: 8000000 INFO @ Tue, 30 Jun 2020 01:37:19: 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 01:37:24: 9000000 INFO @ Tue, 30 Jun 2020 01:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.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 01:37:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:37:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:37:27: 4000000 INFO @ Tue, 30 Jun 2020 01:37:31: 10000000 INFO @ Tue, 30 Jun 2020 01:37:32: 1000000 INFO @ Tue, 30 Jun 2020 01:37:35: 5000000 INFO @ Tue, 30 Jun 2020 01:37:39: 11000000 INFO @ Tue, 30 Jun 2020 01:37:40: 2000000 INFO @ Tue, 30 Jun 2020 01:37:42: 6000000 INFO @ Tue, 30 Jun 2020 01:37:46: 12000000 INFO @ Tue, 30 Jun 2020 01:37:47: 3000000 INFO @ Tue, 30 Jun 2020 01:37:50: 7000000 INFO @ Tue, 30 Jun 2020 01:37:54: 13000000 INFO @ Tue, 30 Jun 2020 01:37:55: 4000000 INFO @ Tue, 30 Jun 2020 01:37:58: 8000000 INFO @ Tue, 30 Jun 2020 01:38:01: 14000000 INFO @ Tue, 30 Jun 2020 01:38:02: 5000000 INFO @ Tue, 30 Jun 2020 01:38:06: 9000000 INFO @ Tue, 30 Jun 2020 01:38:08: 15000000 INFO @ Tue, 30 Jun 2020 01:38:10: 6000000 INFO @ Tue, 30 Jun 2020 01:38:14: 10000000 INFO @ Tue, 30 Jun 2020 01:38:16: 16000000 INFO @ Tue, 30 Jun 2020 01:38:17: 7000000 INFO @ Tue, 30 Jun 2020 01:38:22: 11000000 INFO @ Tue, 30 Jun 2020 01:38:23: 17000000 INFO @ Tue, 30 Jun 2020 01:38:25: 8000000 INFO @ Tue, 30 Jun 2020 01:38:30: 12000000 INFO @ Tue, 30 Jun 2020 01:38:31: 18000000 INFO @ Tue, 30 Jun 2020 01:38:32: 9000000 INFO @ Tue, 30 Jun 2020 01:38:37: 13000000 INFO @ Tue, 30 Jun 2020 01:38:38: 19000000 INFO @ Tue, 30 Jun 2020 01:38:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:38:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:38:39: #1 total tags in treatment: 19066491 INFO @ Tue, 30 Jun 2020 01:38:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:38:39: #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 01:38:39: #1 tags after filtering in treatment: 19066412 INFO @ Tue, 30 Jun 2020 01:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:38:39: #1 finished! INFO @ Tue, 30 Jun 2020 01:38:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:38:40: 10000000 INFO @ Tue, 30 Jun 2020 01:38:40: #2 number of paired peaks: 280 WARNING @ Tue, 30 Jun 2020 01:38:40: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 30 Jun 2020 01:38:40: start model_add_line... INFO @ Tue, 30 Jun 2020 01:38:40: start X-correlation... INFO @ Tue, 30 Jun 2020 01:38:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:38:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:38:41: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 01:38:41: #2 alternative fragment length(s) may be 4,52,596 bps INFO @ Tue, 30 Jun 2020 01:38:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.05_model.r WARNING @ Tue, 30 Jun 2020 01:38:41: #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 01:38:41: #2 You may need to consider one of the other alternative d(s): 4,52,596 WARNING @ Tue, 30 Jun 2020 01:38:41: #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 01:38:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:38:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:38:45: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:38:47: 11000000 INFO @ Tue, 30 Jun 2020 01:38:53: 15000000 INFO @ Tue, 30 Jun 2020 01:38:55: 12000000 INFO @ Tue, 30 Jun 2020 01:39:01: 16000000 INFO @ Tue, 30 Jun 2020 01:39:02: 13000000 INFO @ Tue, 30 Jun 2020 01:39:09: 17000000 INFO @ Tue, 30 Jun 2020 01:39:09: 14000000 INFO @ Tue, 30 Jun 2020 01:39:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:39:17: 15000000 INFO @ Tue, 30 Jun 2020 01:39:17: 18000000 INFO @ Tue, 30 Jun 2020 01:39:24: 16000000 INFO @ Tue, 30 Jun 2020 01:39:25: 19000000 INFO @ Tue, 30 Jun 2020 01:39:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:39:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:39:25: #1 total tags in treatment: 19066491 INFO @ Tue, 30 Jun 2020 01:39:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:39:25: #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 01:39:26: #1 tags after filtering in treatment: 19066412 INFO @ Tue, 30 Jun 2020 01:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:39:26: #1 finished! INFO @ Tue, 30 Jun 2020 01:39:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:39:27: #2 number of paired peaks: 280 WARNING @ Tue, 30 Jun 2020 01:39:27: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 30 Jun 2020 01:39:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:39:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:39:27: end of X-cor INFO @ Tue, 30 Jun 2020 01:39:27: #2 finished! INFO @ Tue, 30 Jun 2020 01:39:27: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 01:39:27: #2 alternative fragment length(s) may be 4,52,596 bps INFO @ Tue, 30 Jun 2020 01:39:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.10_model.r WARNING @ Tue, 30 Jun 2020 01:39:27: #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 01:39:27: #2 You may need to consider one of the other alternative d(s): 4,52,596 WARNING @ Tue, 30 Jun 2020 01:39:27: #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 01:39:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:39:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.05_summits.bed INFO @ Tue, 30 Jun 2020 01:39:31: Done! pass1 - making usageList (504 chroms): 1 millis pass2 - checking and writing primary data (2135 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:39:31: 17000000 INFO @ Tue, 30 Jun 2020 01:39:38: 18000000 INFO @ Tue, 30 Jun 2020 01:39:45: 19000000 INFO @ Tue, 30 Jun 2020 01:39:46: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:39:46: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:39:46: #1 total tags in treatment: 19066491 INFO @ Tue, 30 Jun 2020 01:39:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:39:46: #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 01:39:46: #1 tags after filtering in treatment: 19066412 INFO @ Tue, 30 Jun 2020 01:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:39:46: #1 finished! INFO @ Tue, 30 Jun 2020 01:39:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:39:48: #2 number of paired peaks: 280 WARNING @ Tue, 30 Jun 2020 01:39:48: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 30 Jun 2020 01:39:48: start model_add_line... INFO @ Tue, 30 Jun 2020 01:39:48: start X-correlation... INFO @ Tue, 30 Jun 2020 01:39:48: end of X-cor INFO @ Tue, 30 Jun 2020 01:39:48: #2 finished! INFO @ Tue, 30 Jun 2020 01:39:48: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 01:39:48: #2 alternative fragment length(s) may be 4,52,596 bps INFO @ Tue, 30 Jun 2020 01:39:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.20_model.r WARNING @ Tue, 30 Jun 2020 01:39:48: #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 01:39:48: #2 You may need to consider one of the other alternative d(s): 4,52,596 WARNING @ Tue, 30 Jun 2020 01:39:48: #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 01:39:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:40:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:40:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:40:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:40:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.10_summits.bed INFO @ Tue, 30 Jun 2020 01:40:17: Done! pass1 - making usageList (306 chroms): 1 millis pass2 - checking and writing primary data (861 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:40:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:40:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:40:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:40:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166570/SRX1166570.20_summits.bed INFO @ Tue, 30 Jun 2020 01:40:39: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (333 records, 4 fields): 8 millis CompletedMACS2peakCalling