Job ID = 6626610 SRX = SRX1532033 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: 00:00:01 Multiseed full-index search: 00:05:28 18135121 reads; of these: 18135121 (100.00%) were unpaired; of these: 1188279 (6.55%) aligned 0 times 11809638 (65.12%) aligned exactly 1 time 5137204 (28.33%) aligned >1 times 93.45% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 2313526 / 16946842 = 0.1365 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 08:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.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 08:01:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:01:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:01:42: 1000000 INFO @ Tue, 14 Jul 2020 08:01:50: 2000000 INFO @ Tue, 14 Jul 2020 08:01:57: 3000000 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 08:02:04: 4000000 INFO @ Tue, 14 Jul 2020 08:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.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 08:02:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:02:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:02:11: 1000000 INFO @ Tue, 14 Jul 2020 08:02:12: 5000000 INFO @ Tue, 14 Jul 2020 08:02:17: 2000000 INFO @ Tue, 14 Jul 2020 08:02:19: 6000000 INFO @ Tue, 14 Jul 2020 08:02:24: 3000000 INFO @ Tue, 14 Jul 2020 08:02:25: 7000000 INFO @ Tue, 14 Jul 2020 08:02:30: 4000000 INFO @ Tue, 14 Jul 2020 08:02:32: 8000000 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 08:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.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 08:02:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:02:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:02:37: 5000000 INFO @ Tue, 14 Jul 2020 08:02:39: 9000000 INFO @ Tue, 14 Jul 2020 08:02:42: 1000000 INFO @ Tue, 14 Jul 2020 08:02:44: 6000000 INFO @ Tue, 14 Jul 2020 08:02:46: 10000000 INFO @ Tue, 14 Jul 2020 08:02:49: 2000000 INFO @ Tue, 14 Jul 2020 08:02:51: 7000000 INFO @ Tue, 14 Jul 2020 08:02:53: 11000000 INFO @ Tue, 14 Jul 2020 08:02:56: 3000000 INFO @ Tue, 14 Jul 2020 08:02:58: 8000000 INFO @ Tue, 14 Jul 2020 08:03:00: 12000000 INFO @ Tue, 14 Jul 2020 08:03:04: 4000000 INFO @ Tue, 14 Jul 2020 08:03:05: 9000000 INFO @ Tue, 14 Jul 2020 08:03:07: 13000000 INFO @ Tue, 14 Jul 2020 08:03:11: 5000000 INFO @ Tue, 14 Jul 2020 08:03:12: 10000000 INFO @ Tue, 14 Jul 2020 08:03:14: 14000000 INFO @ Tue, 14 Jul 2020 08:03:18: 6000000 INFO @ Tue, 14 Jul 2020 08:03:18: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:03:18: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:03:18: #1 total tags in treatment: 14633316 INFO @ Tue, 14 Jul 2020 08:03:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:18: #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 08:03:19: 11000000 INFO @ Tue, 14 Jul 2020 08:03:19: #1 tags after filtering in treatment: 14633233 INFO @ Tue, 14 Jul 2020 08:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:03:19: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:20: #2 number of paired peaks: 1671 INFO @ Tue, 14 Jul 2020 08:03:20: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:20: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:20: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:20: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:20: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 08:03:20: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 14 Jul 2020 08:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.05_model.r WARNING @ Tue, 14 Jul 2020 08:03:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:20: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 14 Jul 2020 08:03:20: #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 08:03:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:03:25: 7000000 INFO @ Tue, 14 Jul 2020 08:03:25: 12000000 INFO @ Tue, 14 Jul 2020 08:03:32: 13000000 INFO @ Tue, 14 Jul 2020 08:03:33: 8000000 INFO @ Tue, 14 Jul 2020 08:03:39: 14000000 INFO @ Tue, 14 Jul 2020 08:03:40: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:03:43: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:03:43: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:03:43: #1 total tags in treatment: 14633316 INFO @ Tue, 14 Jul 2020 08:03:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:43: #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 08:03:44: #1 tags after filtering in treatment: 14633233 INFO @ Tue, 14 Jul 2020 08:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:03:44: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:45: #2 number of paired peaks: 1671 INFO @ Tue, 14 Jul 2020 08:03:45: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:45: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:45: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:45: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:45: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 08:03:45: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 14 Jul 2020 08:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.10_model.r WARNING @ Tue, 14 Jul 2020 08:03:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:45: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 14 Jul 2020 08:03:45: #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 08:03:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:03:47: 10000000 INFO @ Tue, 14 Jul 2020 08:03:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:03:53: 11000000 INFO @ Tue, 14 Jul 2020 08:04:01: 12000000 INFO @ Tue, 14 Jul 2020 08:04:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.05_summits.bed INFO @ Tue, 14 Jul 2020 08:04:03: Done! pass1 - making usageList (594 chroms): 2 millis pass2 - checking and writing primary data (3123 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:04:07: 13000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:04:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:04:14: 14000000 INFO @ Tue, 14 Jul 2020 08:04:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:04:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:04:19: #1 total tags in treatment: 14633316 INFO @ Tue, 14 Jul 2020 08:04:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:04:19: #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 08:04:19: #1 tags after filtering in treatment: 14633233 INFO @ Tue, 14 Jul 2020 08:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:04:19: #1 finished! INFO @ Tue, 14 Jul 2020 08:04:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:04:20: #2 number of paired peaks: 1671 INFO @ Tue, 14 Jul 2020 08:04:20: start model_add_line... INFO @ Tue, 14 Jul 2020 08:04:20: start X-correlation... INFO @ Tue, 14 Jul 2020 08:04:20: end of X-cor INFO @ Tue, 14 Jul 2020 08:04:20: #2 finished! INFO @ Tue, 14 Jul 2020 08:04:20: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 08:04:20: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 14 Jul 2020 08:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.20_model.r WARNING @ Tue, 14 Jul 2020 08:04:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:04:20: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 14 Jul 2020 08:04:20: #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 08:04:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.10_summits.bed INFO @ Tue, 14 Jul 2020 08:04:27: Done! pass1 - making usageList (516 chroms): 1 millis pass2 - checking and writing primary data (2252 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:04:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1532033/SRX1532033.20_summits.bed INFO @ Tue, 14 Jul 2020 08:05:02: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (1407 records, 4 fields): 12 millis CompletedMACS2peakCalling