Job ID = 6626963 SRX = SRX7351009 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: 00:05:15 16987695 reads; of these: 16987695 (100.00%) were unpaired; of these: 600246 (3.53%) aligned 0 times 13303460 (78.31%) aligned exactly 1 time 3083989 (18.15%) aligned >1 times 96.47% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 2398256 / 16387449 = 0.1463 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 09:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.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 09:11:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:11:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:11:55: 1000000 INFO @ Tue, 14 Jul 2020 09:12:00: 2000000 INFO @ Tue, 14 Jul 2020 09:12:06: 3000000 INFO @ Tue, 14 Jul 2020 09:12:11: 4000000 INFO @ Tue, 14 Jul 2020 09:12:16: 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, 14 Jul 2020 09:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.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 09:12:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:12:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:12:22: 6000000 INFO @ Tue, 14 Jul 2020 09:12:26: 1000000 INFO @ Tue, 14 Jul 2020 09:12:28: 7000000 INFO @ Tue, 14 Jul 2020 09:12:34: 2000000 INFO @ Tue, 14 Jul 2020 09:12:35: 8000000 INFO @ Tue, 14 Jul 2020 09:12:41: 9000000 INFO @ Tue, 14 Jul 2020 09:12:41: 3000000 INFO @ Tue, 14 Jul 2020 09:12:47: 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, 14 Jul 2020 09:12:48: 4000000 INFO @ Tue, 14 Jul 2020 09:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.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 09:12:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:12:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:12:53: 11000000 INFO @ Tue, 14 Jul 2020 09:12:55: 5000000 INFO @ Tue, 14 Jul 2020 09:12:56: 1000000 INFO @ Tue, 14 Jul 2020 09:13:00: 12000000 INFO @ Tue, 14 Jul 2020 09:13:02: 6000000 INFO @ Tue, 14 Jul 2020 09:13:04: 2000000 INFO @ Tue, 14 Jul 2020 09:13:06: 13000000 INFO @ Tue, 14 Jul 2020 09:13:10: 7000000 INFO @ Tue, 14 Jul 2020 09:13:11: 3000000 INFO @ Tue, 14 Jul 2020 09:13:13: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:13:13: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:13:13: #1 total tags in treatment: 13989193 INFO @ Tue, 14 Jul 2020 09:13:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:13:13: #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 09:13:13: #1 tags after filtering in treatment: 13989012 INFO @ Tue, 14 Jul 2020 09:13:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:13:13: #1 finished! INFO @ Tue, 14 Jul 2020 09:13:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:13:14: #2 number of paired peaks: 2354 INFO @ Tue, 14 Jul 2020 09:13:14: start model_add_line... INFO @ Tue, 14 Jul 2020 09:13:14: start X-correlation... INFO @ Tue, 14 Jul 2020 09:13:14: end of X-cor INFO @ Tue, 14 Jul 2020 09:13:14: #2 finished! INFO @ Tue, 14 Jul 2020 09:13:14: #2 predicted fragment length is 134 bps INFO @ Tue, 14 Jul 2020 09:13:14: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 14 Jul 2020 09:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.05_model.r WARNING @ Tue, 14 Jul 2020 09:13:14: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:13:14: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 14 Jul 2020 09:13:14: #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 09:13:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:13:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:13:17: 8000000 INFO @ Tue, 14 Jul 2020 09:13:18: 4000000 INFO @ Tue, 14 Jul 2020 09:13:24: 9000000 INFO @ Tue, 14 Jul 2020 09:13:25: 5000000 INFO @ Tue, 14 Jul 2020 09:13:32: 10000000 INFO @ Tue, 14 Jul 2020 09:13:32: 6000000 INFO @ Tue, 14 Jul 2020 09:13:39: 11000000 INFO @ Tue, 14 Jul 2020 09:13:39: 7000000 INFO @ Tue, 14 Jul 2020 09:13:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:13:46: 8000000 INFO @ Tue, 14 Jul 2020 09:13:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:13:53: 9000000 INFO @ Tue, 14 Jul 2020 09:13:53: 13000000 INFO @ Tue, 14 Jul 2020 09:14:00: 10000000 INFO @ Tue, 14 Jul 2020 09:14:00: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:14:00: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:14:00: #1 total tags in treatment: 13989193 INFO @ Tue, 14 Jul 2020 09:14:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:14:00: #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 09:14:01: #1 tags after filtering in treatment: 13989012 INFO @ Tue, 14 Jul 2020 09:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:14:01: #1 finished! INFO @ Tue, 14 Jul 2020 09:14:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.05_summits.bed INFO @ Tue, 14 Jul 2020 09:14:02: Done! INFO @ Tue, 14 Jul 2020 09:14:02: #2 number of paired peaks: 2354 INFO @ Tue, 14 Jul 2020 09:14:02: start model_add_line... INFO @ Tue, 14 Jul 2020 09:14:02: start X-correlation... INFO @ Tue, 14 Jul 2020 09:14:02: end of X-cor INFO @ Tue, 14 Jul 2020 09:14:02: #2 finished! INFO @ Tue, 14 Jul 2020 09:14:02: #2 predicted fragment length is 134 bps INFO @ Tue, 14 Jul 2020 09:14:02: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 14 Jul 2020 09:14:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.10_model.r WARNING @ Tue, 14 Jul 2020 09:14:02: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:14:02: #2 You may need to consider one of the other alternative d(s): 134 pass1 - making usageList (224 chroms): 2 millis WARNING @ Tue, 14 Jul 2020 09:14:02: #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 09:14:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:14:02: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (11424 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:14:07: 11000000 INFO @ Tue, 14 Jul 2020 09:14:14: 12000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:14:20: 13000000 INFO @ Tue, 14 Jul 2020 09:14:27: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:14:27: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:14:27: #1 total tags in treatment: 13989193 INFO @ Tue, 14 Jul 2020 09:14:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:14:27: #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 09:14:27: #1 tags after filtering in treatment: 13989012 INFO @ Tue, 14 Jul 2020 09:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:14:27: #1 finished! INFO @ Tue, 14 Jul 2020 09:14:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:14:28: #2 number of paired peaks: 2354 INFO @ Tue, 14 Jul 2020 09:14:28: start model_add_line... INFO @ Tue, 14 Jul 2020 09:14:29: start X-correlation... INFO @ Tue, 14 Jul 2020 09:14:29: end of X-cor INFO @ Tue, 14 Jul 2020 09:14:29: #2 finished! INFO @ Tue, 14 Jul 2020 09:14:29: #2 predicted fragment length is 134 bps INFO @ Tue, 14 Jul 2020 09:14:29: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 14 Jul 2020 09:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.20_model.r WARNING @ Tue, 14 Jul 2020 09:14:29: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:14:29: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 14 Jul 2020 09:14:29: #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 09:14:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:14:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.10_summits.bed INFO @ Tue, 14 Jul 2020 09:14:52: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (7001 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:15:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351009/SRX7351009.20_summits.bed INFO @ Tue, 14 Jul 2020 09:15:17: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (2739 records, 4 fields): 8 millis CompletedMACS2peakCalling