Job ID = 6530103 SRX = SRX969914 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: 00:05:30 18510338 reads; of these: 18510338 (100.00%) were unpaired; of these: 610695 (3.30%) aligned 0 times 13268725 (71.68%) aligned exactly 1 time 4630918 (25.02%) aligned >1 times 96.70% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 2332653 / 17899643 = 0.1303 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 03:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.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 03:19:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:41: 1000000 INFO @ Tue, 30 Jun 2020 03:19:47: 2000000 INFO @ Tue, 30 Jun 2020 03:19:53: 3000000 INFO @ Tue, 30 Jun 2020 03:19:59: 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 03:20:05: 5000000 INFO @ Tue, 30 Jun 2020 03:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.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 03:20:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:11: 6000000 INFO @ Tue, 30 Jun 2020 03:20:12: 1000000 INFO @ Tue, 30 Jun 2020 03:20:18: 7000000 INFO @ Tue, 30 Jun 2020 03:20:18: 2000000 INFO @ Tue, 30 Jun 2020 03:20:24: 8000000 INFO @ Tue, 30 Jun 2020 03:20:24: 3000000 INFO @ Tue, 30 Jun 2020 03:20:30: 9000000 INFO @ Tue, 30 Jun 2020 03:20:31: 4000000 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 03:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.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 03:20:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:37: 10000000 INFO @ Tue, 30 Jun 2020 03:20:37: 5000000 INFO @ Tue, 30 Jun 2020 03:20:41: 1000000 INFO @ Tue, 30 Jun 2020 03:20:43: 11000000 INFO @ Tue, 30 Jun 2020 03:20:43: 6000000 INFO @ Tue, 30 Jun 2020 03:20:46: 2000000 INFO @ Tue, 30 Jun 2020 03:20:49: 12000000 INFO @ Tue, 30 Jun 2020 03:20:50: 7000000 INFO @ Tue, 30 Jun 2020 03:20:52: 3000000 INFO @ Tue, 30 Jun 2020 03:20:56: 8000000 INFO @ Tue, 30 Jun 2020 03:20:56: 13000000 INFO @ Tue, 30 Jun 2020 03:20:58: 4000000 INFO @ Tue, 30 Jun 2020 03:21:02: 9000000 INFO @ Tue, 30 Jun 2020 03:21:03: 14000000 INFO @ Tue, 30 Jun 2020 03:21:03: 5000000 INFO @ Tue, 30 Jun 2020 03:21:09: 10000000 INFO @ Tue, 30 Jun 2020 03:21:09: 6000000 INFO @ Tue, 30 Jun 2020 03:21:10: 15000000 INFO @ Tue, 30 Jun 2020 03:21:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:21:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:21:14: #1 total tags in treatment: 15566990 INFO @ Tue, 30 Jun 2020 03:21:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:14: #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 03:21:15: #1 tags after filtering in treatment: 15566984 INFO @ Tue, 30 Jun 2020 03:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:15: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:15: 11000000 INFO @ Tue, 30 Jun 2020 03:21:15: 7000000 INFO @ Tue, 30 Jun 2020 03:21:16: #2 number of paired peaks: 265 WARNING @ Tue, 30 Jun 2020 03:21:16: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:16: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:16: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:16: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:16: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:16: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:21:16: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 03:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.05_model.r WARNING @ Tue, 30 Jun 2020 03:21:16: #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 03:21:16: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 03:21:16: #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 03:21:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:21: 8000000 INFO @ Tue, 30 Jun 2020 03:21:21: 12000000 INFO @ Tue, 30 Jun 2020 03:21:26: 9000000 INFO @ Tue, 30 Jun 2020 03:21:28: 13000000 INFO @ Tue, 30 Jun 2020 03:21:32: 10000000 INFO @ Tue, 30 Jun 2020 03:21:34: 14000000 INFO @ Tue, 30 Jun 2020 03:21:38: 11000000 INFO @ Tue, 30 Jun 2020 03:21:40: 15000000 INFO @ Tue, 30 Jun 2020 03:21:43: 12000000 INFO @ Tue, 30 Jun 2020 03:21:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:21:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:21:44: #1 total tags in treatment: 15566990 INFO @ Tue, 30 Jun 2020 03:21:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:44: #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 03:21:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:45: #1 tags after filtering in treatment: 15566984 INFO @ Tue, 30 Jun 2020 03:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:45: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:46: #2 number of paired peaks: 265 WARNING @ Tue, 30 Jun 2020 03:21:46: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:46: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:46: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:46: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:46: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:46: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:21:46: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 03:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.10_model.r WARNING @ Tue, 30 Jun 2020 03:21:46: #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 03:21:46: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 03:21:46: #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 03:21:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:50: 13000000 INFO @ Tue, 30 Jun 2020 03:21:55: 14000000 INFO @ Tue, 30 Jun 2020 03:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.05_summits.bed INFO @ Tue, 30 Jun 2020 03:21:58: Done! pass1 - making usageList (641 chroms): 2 millis pass2 - checking and writing primary data (2840 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:01: 15000000 INFO @ Tue, 30 Jun 2020 03:22:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:22:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:22:05: #1 total tags in treatment: 15566990 INFO @ Tue, 30 Jun 2020 03:22:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:22:05: #1 tags after filtering in treatment: 15566984 INFO @ Tue, 30 Jun 2020 03:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:06: #2 number of paired peaks: 265 WARNING @ Tue, 30 Jun 2020 03:22:06: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:06: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:22:06: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 03:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.20_model.r WARNING @ Tue, 30 Jun 2020 03:22:06: #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 03:22:06: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 03:22:06: #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 03:22:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.10_summits.bed INFO @ Tue, 30 Jun 2020 03:22:27: Done! pass1 - making usageList (476 chroms): 1 millis pass2 - checking and writing primary data (1486 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969914/SRX969914.20_summits.bed INFO @ Tue, 30 Jun 2020 03:22:48: Done! pass1 - making usageList (181 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。