Job ID = 6456068 SRX = SRX3167246 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:21 prefetch.2.10.7: 1) Downloading 'SRR6014249'... 2020-06-21T10:30:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:52 prefetch.2.10.7: 'SRR6014249' is valid 2020-06-21T10:31:52 prefetch.2.10.7: 1) 'SRR6014249' was downloaded successfully Read 6376875 spots for SRR6014249/SRR6014249.sra Written 6376875 spots for SRR6014249/SRR6014249.sra 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: 00:01:52 6376875 reads; of these: 6376875 (100.00%) were unpaired; of these: 221988 (3.48%) aligned 0 times 4469301 (70.09%) aligned exactly 1 time 1685586 (26.43%) aligned >1 times 96.52% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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_rmdupse_core] 649870 / 6154887 = 0.1056 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 @ Sun, 21 Jun 2020 19:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.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 @ Sun, 21 Jun 2020 19:36:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:17: 1000000 INFO @ Sun, 21 Jun 2020 19:36:23: 2000000 INFO @ Sun, 21 Jun 2020 19:36:29: 3000000 INFO @ Sun, 21 Jun 2020 19:36:35: 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 @ Sun, 21 Jun 2020 19:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.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 @ Sun, 21 Jun 2020 19:36:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:42: 5000000 INFO @ Sun, 21 Jun 2020 19:36:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:45: #1 total tags in treatment: 5505017 INFO @ Sun, 21 Jun 2020 19:36:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:36:46: #1 tags after filtering in treatment: 5504858 INFO @ Sun, 21 Jun 2020 19:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:46: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 19:36:46: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:46: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 19:36:46: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 19:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.05_model.r WARNING @ Sun, 21 Jun 2020 19:36:46: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:46: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sun, 21 Jun 2020 19:36:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:36:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:46: 1000000 INFO @ Sun, 21 Jun 2020 19:36:51: 2000000 INFO @ Sun, 21 Jun 2020 19:36:57: 3000000 INFO @ Sun, 21 Jun 2020 19:36:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:02: 4000000 INFO @ Sun, 21 Jun 2020 19:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.05_summits.bed INFO @ Sun, 21 Jun 2020 19:37:05: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:07: 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 @ Sun, 21 Jun 2020 19:37:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:10: #1 total tags in treatment: 5505017 INFO @ Sun, 21 Jun 2020 19:37:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:37:11: #1 tags after filtering in treatment: 5504858 INFO @ Sun, 21 Jun 2020 19:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.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 @ Sun, 21 Jun 2020 19:37:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:11: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 19:37:11: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 19:37:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:11: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 19:37:11: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 19:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.10_model.r WARNING @ Sun, 21 Jun 2020 19:37:11: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:37:11: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sun, 21 Jun 2020 19:37:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:37:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:16: 1000000 INFO @ Sun, 21 Jun 2020 19:37:21: 2000000 INFO @ Sun, 21 Jun 2020 19:37:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:27: 3000000 INFO @ Sun, 21 Jun 2020 19:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:30: Done! pass1 - making usageList (163 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:32: 4000000 INFO @ Sun, 21 Jun 2020 19:37:38: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:37:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:40: #1 total tags in treatment: 5505017 INFO @ Sun, 21 Jun 2020 19:37:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:37:41: #1 tags after filtering in treatment: 5504858 INFO @ Sun, 21 Jun 2020 19:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:41: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 19:37:41: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 19:37:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:41: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 19:37:41: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 19:37:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.20_model.r WARNING @ Sun, 21 Jun 2020 19:37:41: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:37:41: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sun, 21 Jun 2020 19:37:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:37:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167246/SRX3167246.20_summits.bed INFO @ Sun, 21 Jun 2020 19:38:00: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 3 millis CompletedMACS2peakCalling