Job ID = 6529250 SRX = SRX110797 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: 00:06:50 23908946 reads; of these: 23908946 (100.00%) were unpaired; of these: 602948 (2.52%) aligned 0 times 12052792 (50.41%) aligned exactly 1 time 11253206 (47.07%) aligned >1 times 97.48% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 2197287 / 23305998 = 0.0943 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 01:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.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 01:39:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:39:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:02: 1000000 INFO @ Tue, 30 Jun 2020 01:40:07: 2000000 INFO @ Tue, 30 Jun 2020 01:40:12: 3000000 INFO @ Tue, 30 Jun 2020 01:40:17: 4000000 INFO @ Tue, 30 Jun 2020 01:40:22: 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 01:40:26: 6000000 INFO @ Tue, 30 Jun 2020 01:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.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 01:40:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:32: 7000000 INFO @ Tue, 30 Jun 2020 01:40:32: 1000000 INFO @ Tue, 30 Jun 2020 01:40:37: 8000000 INFO @ Tue, 30 Jun 2020 01:40:38: 2000000 INFO @ Tue, 30 Jun 2020 01:40:42: 9000000 INFO @ Tue, 30 Jun 2020 01:40:43: 3000000 INFO @ Tue, 30 Jun 2020 01:40:47: 10000000 INFO @ Tue, 30 Jun 2020 01:40:48: 4000000 INFO @ Tue, 30 Jun 2020 01:40:52: 11000000 INFO @ Tue, 30 Jun 2020 01:40:53: 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 01:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.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 01:40:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:58: 12000000 INFO @ Tue, 30 Jun 2020 01:40:59: 6000000 INFO @ Tue, 30 Jun 2020 01:41:03: 1000000 INFO @ Tue, 30 Jun 2020 01:41:03: 13000000 INFO @ Tue, 30 Jun 2020 01:41:04: 7000000 INFO @ Tue, 30 Jun 2020 01:41:08: 2000000 INFO @ Tue, 30 Jun 2020 01:41:08: 14000000 INFO @ Tue, 30 Jun 2020 01:41:09: 8000000 INFO @ Tue, 30 Jun 2020 01:41:14: 3000000 INFO @ Tue, 30 Jun 2020 01:41:14: 15000000 INFO @ Tue, 30 Jun 2020 01:41:15: 9000000 INFO @ Tue, 30 Jun 2020 01:41:19: 4000000 INFO @ Tue, 30 Jun 2020 01:41:19: 16000000 INFO @ Tue, 30 Jun 2020 01:41:20: 10000000 INFO @ Tue, 30 Jun 2020 01:41:25: 5000000 INFO @ Tue, 30 Jun 2020 01:41:25: 17000000 INFO @ Tue, 30 Jun 2020 01:41:26: 11000000 INFO @ Tue, 30 Jun 2020 01:41:30: 6000000 INFO @ Tue, 30 Jun 2020 01:41:31: 18000000 INFO @ Tue, 30 Jun 2020 01:41:31: 12000000 INFO @ Tue, 30 Jun 2020 01:41:36: 7000000 INFO @ Tue, 30 Jun 2020 01:41:36: 19000000 INFO @ Tue, 30 Jun 2020 01:41:37: 13000000 INFO @ Tue, 30 Jun 2020 01:41:41: 8000000 INFO @ Tue, 30 Jun 2020 01:41:42: 20000000 INFO @ Tue, 30 Jun 2020 01:41:42: 14000000 INFO @ Tue, 30 Jun 2020 01:41:46: 9000000 INFO @ Tue, 30 Jun 2020 01:41:47: 15000000 INFO @ Tue, 30 Jun 2020 01:41:48: 21000000 INFO @ Tue, 30 Jun 2020 01:41:48: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:41:48: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:41:48: #1 total tags in treatment: 21108711 INFO @ Tue, 30 Jun 2020 01:41:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:41:48: #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 01:41:49: #1 tags after filtering in treatment: 21108711 INFO @ Tue, 30 Jun 2020 01:41:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:41:49: #1 finished! INFO @ Tue, 30 Jun 2020 01:41:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:41:51: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 01:41:51: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 01:41:51: start model_add_line... INFO @ Tue, 30 Jun 2020 01:41:51: start X-correlation... INFO @ Tue, 30 Jun 2020 01:41:51: end of X-cor INFO @ Tue, 30 Jun 2020 01:41:51: #2 finished! INFO @ Tue, 30 Jun 2020 01:41:51: #2 predicted fragment length is 21 bps INFO @ Tue, 30 Jun 2020 01:41:51: #2 alternative fragment length(s) may be 4,21,47,484 bps INFO @ Tue, 30 Jun 2020 01:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.05_model.r WARNING @ Tue, 30 Jun 2020 01:41:51: #2 Since the d (21) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:41:51: #2 You may need to consider one of the other alternative d(s): 4,21,47,484 WARNING @ Tue, 30 Jun 2020 01:41:51: #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 01:41:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:41:52: 10000000 INFO @ Tue, 30 Jun 2020 01:41:53: 16000000 INFO @ Tue, 30 Jun 2020 01:41:57: 11000000 INFO @ Tue, 30 Jun 2020 01:41:58: 17000000 INFO @ Tue, 30 Jun 2020 01:42:02: 12000000 INFO @ Tue, 30 Jun 2020 01:42:04: 18000000 INFO @ Tue, 30 Jun 2020 01:42:08: 13000000 INFO @ Tue, 30 Jun 2020 01:42:09: 19000000 INFO @ Tue, 30 Jun 2020 01:42:13: 14000000 INFO @ Tue, 30 Jun 2020 01:42:15: 20000000 INFO @ Tue, 30 Jun 2020 01:42:18: 15000000 INFO @ Tue, 30 Jun 2020 01:42:20: 21000000 INFO @ Tue, 30 Jun 2020 01:42:21: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:42:21: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:42:21: #1 total tags in treatment: 21108711 INFO @ Tue, 30 Jun 2020 01:42:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:42:21: #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 01:42:22: #1 tags after filtering in treatment: 21108711 INFO @ Tue, 30 Jun 2020 01:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:42:22: #1 finished! INFO @ Tue, 30 Jun 2020 01:42:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:42:23: 16000000 INFO @ Tue, 30 Jun 2020 01:42:23: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 01:42:23: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 01:42:23: start model_add_line... INFO @ Tue, 30 Jun 2020 01:42:23: start X-correlation... INFO @ Tue, 30 Jun 2020 01:42:23: end of X-cor INFO @ Tue, 30 Jun 2020 01:42:23: #2 finished! INFO @ Tue, 30 Jun 2020 01:42:23: #2 predicted fragment length is 21 bps INFO @ Tue, 30 Jun 2020 01:42:23: #2 alternative fragment length(s) may be 4,21,47,484 bps INFO @ Tue, 30 Jun 2020 01:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.10_model.r WARNING @ Tue, 30 Jun 2020 01:42:23: #2 Since the d (21) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:42:23: #2 You may need to consider one of the other alternative d(s): 4,21,47,484 WARNING @ Tue, 30 Jun 2020 01:42:23: #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 01:42:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:42:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:42:29: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:42:34: 18000000 INFO @ Tue, 30 Jun 2020 01:42:40: 19000000 INFO @ Tue, 30 Jun 2020 01:42:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:42:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:42:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.05_summits.bed INFO @ Tue, 30 Jun 2020 01:42:43: Done! pass1 - making usageList (321 chroms): 1 millis pass2 - checking and writing primary data (1141 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:42:45: 20000000 INFO @ Tue, 30 Jun 2020 01:42:51: 21000000 INFO @ Tue, 30 Jun 2020 01:42:52: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:42:52: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:42:52: #1 total tags in treatment: 21108711 INFO @ Tue, 30 Jun 2020 01:42:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:42:52: #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 01:42:53: #1 tags after filtering in treatment: 21108711 INFO @ Tue, 30 Jun 2020 01:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:42:53: #1 finished! INFO @ Tue, 30 Jun 2020 01:42:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:42:54: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 01:42:54: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 01:42:54: start model_add_line... INFO @ Tue, 30 Jun 2020 01:42:54: start X-correlation... INFO @ Tue, 30 Jun 2020 01:42:54: end of X-cor INFO @ Tue, 30 Jun 2020 01:42:54: #2 finished! INFO @ Tue, 30 Jun 2020 01:42:54: #2 predicted fragment length is 21 bps INFO @ Tue, 30 Jun 2020 01:42:54: #2 alternative fragment length(s) may be 4,21,47,484 bps INFO @ Tue, 30 Jun 2020 01:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.20_model.r WARNING @ Tue, 30 Jun 2020 01:42:54: #2 Since the d (21) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:42:54: #2 You may need to consider one of the other alternative d(s): 4,21,47,484 WARNING @ Tue, 30 Jun 2020 01:42:54: #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 01:42:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:42:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:43:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:43:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:43:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.10_summits.bed INFO @ Tue, 30 Jun 2020 01:43:15: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (348 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:43:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110797/SRX110797.20_summits.bed INFO @ Tue, 30 Jun 2020 01:43:46: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 4 millis CompletedMACS2peakCalling