Job ID = 6627616 SRX = SRX8521383 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: 00:06:14 43761441 reads; of these: 43761441 (100.00%) were unpaired; of these: 40465350 (92.47%) aligned 0 times 2412527 (5.51%) aligned exactly 1 time 883564 (2.02%) aligned >1 times 7.53% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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] 423950 / 3296091 = 0.1286 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, 14 Jul 2020 12:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.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, 14 Jul 2020 12:22:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:36: 1000000 INFO @ Tue, 14 Jul 2020 12:22:41: 2000000 INFO @ Tue, 14 Jul 2020 12:22:46: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 12:22:46: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 12:22:46: #1 total tags in treatment: 2872141 INFO @ Tue, 14 Jul 2020 12:22:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:22:46: #1 tags after filtering in treatment: 2871869 INFO @ Tue, 14 Jul 2020 12:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:46: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:47: #2 number of paired peaks: 1031 INFO @ Tue, 14 Jul 2020 12:22:47: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:47: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:47: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:47: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:47: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 12:22:47: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 12:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.05_model.r WARNING @ Tue, 14 Jul 2020 12:22:47: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:47: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 12:22:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:22:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:22:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.05_summits.bed INFO @ Tue, 14 Jul 2020 12:22:56: Done! pass1 - making usageList (174 chroms): 2 millis pass2 - checking and writing primary data (850 records, 4 fields): 7 millis CompletedMACS2peakCalling 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, 14 Jul 2020 12:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.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, 14 Jul 2020 12:22:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:05: 1000000 INFO @ Tue, 14 Jul 2020 12:23:10: 2000000 INFO @ Tue, 14 Jul 2020 12:23:15: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 12:23:15: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 12:23:15: #1 total tags in treatment: 2872141 INFO @ Tue, 14 Jul 2020 12:23:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:23:15: #1 tags after filtering in treatment: 2871869 INFO @ Tue, 14 Jul 2020 12:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:15: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:16: #2 number of paired peaks: 1031 INFO @ Tue, 14 Jul 2020 12:23:16: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:16: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:16: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:16: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:16: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 12:23:16: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 12:23:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.10_model.r WARNING @ Tue, 14 Jul 2020 12:23:16: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:23:16: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 12:23:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:23:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.10_summits.bed INFO @ Tue, 14 Jul 2020 12:23:26: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 4 millis CompletedMACS2peakCalling 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, 14 Jul 2020 12:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.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, 14 Jul 2020 12:23:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:36: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:23:43: 2000000 INFO @ Tue, 14 Jul 2020 12:23:49: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 12:23:49: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 12:23:49: #1 total tags in treatment: 2872141 INFO @ Tue, 14 Jul 2020 12:23:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:23:49: #1 tags after filtering in treatment: 2871869 INFO @ Tue, 14 Jul 2020 12:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:49: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:49: #2 number of paired peaks: 1031 INFO @ Tue, 14 Jul 2020 12:23:49: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:49: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:49: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:49: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:49: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 12:23:49: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 12:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.20_model.r WARNING @ Tue, 14 Jul 2020 12:23:49: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:23:49: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 12:23:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:23:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:23:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521383/SRX8521383.20_summits.bed INFO @ Tue, 14 Jul 2020 12:23:59: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 3 millis CompletedMACS2peakCalling