Job ID = 6529743 SRX = SRX4669037 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: 00:06:48 24849410 reads; of these: 24849410 (100.00%) were unpaired; of these: 794703 (3.20%) aligned 0 times 16860599 (67.85%) aligned exactly 1 time 7194108 (28.95%) aligned >1 times 96.80% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 4105773 / 24054707 = 0.1707 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 02:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.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 02:48:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:09: 1000000 INFO @ Tue, 30 Jun 2020 02:48:15: 2000000 INFO @ Tue, 30 Jun 2020 02:48:20: 3000000 INFO @ Tue, 30 Jun 2020 02:48:25: 4000000 INFO @ Tue, 30 Jun 2020 02:48:31: 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 02:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.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 02:48:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:37: 6000000 INFO @ Tue, 30 Jun 2020 02:48:39: 1000000 INFO @ Tue, 30 Jun 2020 02:48:42: 7000000 INFO @ Tue, 30 Jun 2020 02:48:45: 2000000 INFO @ Tue, 30 Jun 2020 02:48:48: 8000000 INFO @ Tue, 30 Jun 2020 02:48:51: 3000000 INFO @ Tue, 30 Jun 2020 02:48:54: 9000000 INFO @ Tue, 30 Jun 2020 02:48:57: 4000000 INFO @ Tue, 30 Jun 2020 02:49:00: 10000000 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 02:49:03: 5000000 INFO @ Tue, 30 Jun 2020 02:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.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 02:49:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:06: 11000000 INFO @ Tue, 30 Jun 2020 02:49:09: 6000000 INFO @ Tue, 30 Jun 2020 02:49:10: 1000000 INFO @ Tue, 30 Jun 2020 02:49:12: 12000000 INFO @ Tue, 30 Jun 2020 02:49:16: 7000000 INFO @ Tue, 30 Jun 2020 02:49:16: 2000000 INFO @ Tue, 30 Jun 2020 02:49:19: 13000000 INFO @ Tue, 30 Jun 2020 02:49:22: 8000000 INFO @ Tue, 30 Jun 2020 02:49:23: 3000000 INFO @ Tue, 30 Jun 2020 02:49:25: 14000000 INFO @ Tue, 30 Jun 2020 02:49:28: 9000000 INFO @ Tue, 30 Jun 2020 02:49:29: 4000000 INFO @ Tue, 30 Jun 2020 02:49:31: 15000000 INFO @ Tue, 30 Jun 2020 02:49:34: 10000000 INFO @ Tue, 30 Jun 2020 02:49:35: 5000000 INFO @ Tue, 30 Jun 2020 02:49:38: 16000000 INFO @ Tue, 30 Jun 2020 02:49:40: 11000000 INFO @ Tue, 30 Jun 2020 02:49:41: 6000000 INFO @ Tue, 30 Jun 2020 02:49:44: 17000000 INFO @ Tue, 30 Jun 2020 02:49:46: 12000000 INFO @ Tue, 30 Jun 2020 02:49:47: 7000000 INFO @ Tue, 30 Jun 2020 02:49:50: 18000000 INFO @ Tue, 30 Jun 2020 02:49:51: 13000000 INFO @ Tue, 30 Jun 2020 02:49:52: 8000000 INFO @ Tue, 30 Jun 2020 02:49:56: 19000000 INFO @ Tue, 30 Jun 2020 02:49:56: 14000000 INFO @ Tue, 30 Jun 2020 02:49:58: 9000000 INFO @ Tue, 30 Jun 2020 02:50:02: 15000000 INFO @ Tue, 30 Jun 2020 02:50:02: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:02: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:02: #1 total tags in treatment: 19948934 INFO @ Tue, 30 Jun 2020 02:50:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:02: #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 02:50:03: #1 tags after filtering in treatment: 19948934 INFO @ Tue, 30 Jun 2020 02:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:04: 10000000 INFO @ Tue, 30 Jun 2020 02:50:05: #2 number of paired peaks: 264 WARNING @ Tue, 30 Jun 2020 02:50:05: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:05: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:50:05: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.05_model.r WARNING @ Tue, 30 Jun 2020 02:50:05: #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 02:50:05: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:50:05: #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 02:50:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:08: 16000000 INFO @ Tue, 30 Jun 2020 02:50:09: 11000000 INFO @ Tue, 30 Jun 2020 02:50:13: 17000000 INFO @ Tue, 30 Jun 2020 02:50:14: 12000000 INFO @ Tue, 30 Jun 2020 02:50:18: 18000000 INFO @ Tue, 30 Jun 2020 02:50:20: 13000000 INFO @ Tue, 30 Jun 2020 02:50:24: 19000000 INFO @ Tue, 30 Jun 2020 02:50:25: 14000000 INFO @ Tue, 30 Jun 2020 02:50:30: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:30: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:30: #1 total tags in treatment: 19948934 INFO @ Tue, 30 Jun 2020 02:50:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:30: #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 02:50:30: 15000000 INFO @ Tue, 30 Jun 2020 02:50:31: #1 tags after filtering in treatment: 19948934 INFO @ Tue, 30 Jun 2020 02:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:33: #2 number of paired peaks: 264 WARNING @ Tue, 30 Jun 2020 02:50:33: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:33: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:50:33: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:33: #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 02:50:33: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:50:33: #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 02:50:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:37: 16000000 INFO @ Tue, 30 Jun 2020 02:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:43: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:50:49: 18000000 INFO @ Tue, 30 Jun 2020 02:50:55: 19000000 INFO @ Tue, 30 Jun 2020 02:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.05_summits.bed INFO @ Tue, 30 Jun 2020 02:51:00: Done! pass1 - making usageList (747 chroms): 1 millis pass2 - checking and writing primary data (3707 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:02: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:51:02: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:51:02: #1 total tags in treatment: 19948934 INFO @ Tue, 30 Jun 2020 02:51:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:02: #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 02:51:03: #1 tags after filtering in treatment: 19948934 INFO @ Tue, 30 Jun 2020 02:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:04: #2 number of paired peaks: 264 WARNING @ Tue, 30 Jun 2020 02:51:04: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:04: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:05: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:51:05: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.20_model.r WARNING @ Tue, 30 Jun 2020 02:51:05: #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 02:51:05: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:51:05: #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 02:51:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.10_summits.bed INFO @ Tue, 30 Jun 2020 02:51:24: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669037/SRX4669037.20_summits.bed INFO @ Tue, 30 Jun 2020 02:52:00: Done! pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (374 records, 4 fields): 11 millis CompletedMACS2peakCalling