Job ID = 6529755 SRX = SRX4669064 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: 00:02:36 10033179 reads; of these: 10033179 (100.00%) were unpaired; of these: 571304 (5.69%) aligned 0 times 8234232 (82.07%) aligned exactly 1 time 1227643 (12.24%) aligned >1 times 94.31% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 783830 / 9461875 = 0.0828 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 02:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.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 02:44:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:49: 1000000 INFO @ Tue, 30 Jun 2020 02:44:55: 2000000 INFO @ Tue, 30 Jun 2020 02:45:01: 3000000 INFO @ Tue, 30 Jun 2020 02:45:07: 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 02:45:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.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 02:45:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:13: 5000000 INFO @ Tue, 30 Jun 2020 02:45:20: 6000000 INFO @ Tue, 30 Jun 2020 02:45:20: 1000000 INFO @ Tue, 30 Jun 2020 02:45:27: 7000000 INFO @ Tue, 30 Jun 2020 02:45:27: 2000000 INFO @ Tue, 30 Jun 2020 02:45:34: 8000000 INFO @ Tue, 30 Jun 2020 02:45:35: 3000000 INFO @ Tue, 30 Jun 2020 02:45:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:45:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:45:39: #1 total tags in treatment: 8678045 INFO @ Tue, 30 Jun 2020 02:45:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:45:39: #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 02:45:39: #1 tags after filtering in treatment: 8677969 INFO @ Tue, 30 Jun 2020 02:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:45:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:45:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:45:40: #2 number of paired peaks: 119 WARNING @ Tue, 30 Jun 2020 02:45:40: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 30 Jun 2020 02:45:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:45:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:45:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:45:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:45:40: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:45:40: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 30 Jun 2020 02:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.05_model.r WARNING @ Tue, 30 Jun 2020 02:45:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:45:40: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 30 Jun 2020 02:45:40: #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 02:45:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:45:40: #3 Pre-compute pvalue-qvalue table... 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 02:45:42: 4000000 INFO @ Tue, 30 Jun 2020 02:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.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 02:45:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:49: 1000000 INFO @ Tue, 30 Jun 2020 02:45:50: 5000000 INFO @ Tue, 30 Jun 2020 02:45:56: 2000000 INFO @ Tue, 30 Jun 2020 02:45:57: 6000000 INFO @ Tue, 30 Jun 2020 02:46:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:46:03: 3000000 INFO @ Tue, 30 Jun 2020 02:46:04: 7000000 INFO @ Tue, 30 Jun 2020 02:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.05_summits.bed INFO @ Tue, 30 Jun 2020 02:46:10: Done! INFO @ Tue, 30 Jun 2020 02:46:10: 4000000 pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:46:12: 8000000 INFO @ Tue, 30 Jun 2020 02:46:16: 5000000 INFO @ Tue, 30 Jun 2020 02:46:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:46:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:46:17: #1 total tags in treatment: 8678045 INFO @ Tue, 30 Jun 2020 02:46:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:17: #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 02:46:17: #1 tags after filtering in treatment: 8677969 INFO @ Tue, 30 Jun 2020 02:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:46:18: #2 number of paired peaks: 119 WARNING @ Tue, 30 Jun 2020 02:46:18: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 30 Jun 2020 02:46:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:46:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:46:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:46:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:46:18: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:46:18: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 30 Jun 2020 02:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.10_model.r WARNING @ Tue, 30 Jun 2020 02:46:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:46:18: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 30 Jun 2020 02:46:18: #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 02:46:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:46:28: 7000000 INFO @ Tue, 30 Jun 2020 02:46:35: 8000000 INFO @ Tue, 30 Jun 2020 02:46:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:46:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:46:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:46:39: #1 total tags in treatment: 8678045 INFO @ Tue, 30 Jun 2020 02:46:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:39: #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 02:46:39: #1 tags after filtering in treatment: 8677969 INFO @ Tue, 30 Jun 2020 02:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:46:40: #2 number of paired peaks: 119 WARNING @ Tue, 30 Jun 2020 02:46:40: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 30 Jun 2020 02:46:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:46:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:46:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:46:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:46:40: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:46:40: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 30 Jun 2020 02:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.20_model.r WARNING @ Tue, 30 Jun 2020 02:46:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:46:40: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 30 Jun 2020 02:46:40: #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 02:46:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.10_summits.bed INFO @ Tue, 30 Jun 2020 02:46:48: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:47:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669064/SRX4669064.20_summits.bed INFO @ Tue, 30 Jun 2020 02:47:11: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling