Job ID = 1295422 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,065,384 reads read : 16,130,768 reads written : 16,130,768 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 01:10:37 8065384 reads; of these: 8065384 (100.00%) were paired; of these: 1358638 (16.85%) aligned concordantly 0 times 2986454 (37.03%) aligned concordantly exactly 1 time 3720292 (46.13%) aligned concordantly >1 times ---- 1358638 pairs aligned concordantly 0 times; of these: 93707 (6.90%) aligned discordantly 1 time ---- 1264931 pairs aligned 0 times concordantly or discordantly; of these: 2529862 mates make up the pairs; of these: 1692680 (66.91%) aligned 0 times 261692 (10.34%) aligned exactly 1 time 575490 (22.75%) aligned >1 times 89.51% overall alignment rate Time searching: 01:10:37 Overall time: 01:10:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 951957 / 6756925 = 0.1409 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 15:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.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 @ Mon, 03 Jun 2019 15:00:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.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 @ Mon, 03 Jun 2019 15:00:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:00:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:00:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.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 @ Mon, 03 Jun 2019 15:00:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:00:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:00:33: 1000000 INFO @ Mon, 03 Jun 2019 15:00:33: 1000000 INFO @ Mon, 03 Jun 2019 15:00:34: 1000000 INFO @ Mon, 03 Jun 2019 15:00:47: 2000000 INFO @ Mon, 03 Jun 2019 15:00:47: 2000000 INFO @ Mon, 03 Jun 2019 15:00:50: 2000000 INFO @ Mon, 03 Jun 2019 15:01:01: 3000000 INFO @ Mon, 03 Jun 2019 15:01:02: 3000000 INFO @ Mon, 03 Jun 2019 15:01:06: 3000000 INFO @ Mon, 03 Jun 2019 15:01:16: 4000000 INFO @ Mon, 03 Jun 2019 15:01:16: 4000000 INFO @ Mon, 03 Jun 2019 15:01:21: 4000000 INFO @ Mon, 03 Jun 2019 15:01:30: 5000000 INFO @ Mon, 03 Jun 2019 15:01:30: 5000000 INFO @ Mon, 03 Jun 2019 15:01:37: 5000000 INFO @ Mon, 03 Jun 2019 15:01:44: 6000000 INFO @ Mon, 03 Jun 2019 15:01:44: 6000000 INFO @ Mon, 03 Jun 2019 15:01:52: 6000000 INFO @ Mon, 03 Jun 2019 15:01:58: 7000000 INFO @ Mon, 03 Jun 2019 15:01:58: 7000000 INFO @ Mon, 03 Jun 2019 15:02:08: 7000000 INFO @ Mon, 03 Jun 2019 15:02:12: 8000000 INFO @ Mon, 03 Jun 2019 15:02:12: 8000000 INFO @ Mon, 03 Jun 2019 15:02:24: 8000000 INFO @ Mon, 03 Jun 2019 15:02:26: 9000000 INFO @ Mon, 03 Jun 2019 15:02:26: 9000000 INFO @ Mon, 03 Jun 2019 15:02:39: 9000000 INFO @ Mon, 03 Jun 2019 15:02:40: 10000000 INFO @ Mon, 03 Jun 2019 15:02:40: 10000000 INFO @ Mon, 03 Jun 2019 15:02:54: 11000000 INFO @ Mon, 03 Jun 2019 15:02:54: 11000000 INFO @ Mon, 03 Jun 2019 15:02:55: 10000000 INFO @ Mon, 03 Jun 2019 15:03:08: 12000000 INFO @ Mon, 03 Jun 2019 15:03:08: 12000000 INFO @ Mon, 03 Jun 2019 15:03:10: 11000000 INFO @ Mon, 03 Jun 2019 15:03:15: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:03:15: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:03:15: #1 total tags in treatment: 5761043 INFO @ Mon, 03 Jun 2019 15:03:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:03:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:03:16: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:03:16: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:03:16: #1 total tags in treatment: 5761043 INFO @ Mon, 03 Jun 2019 15:03:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:03:16: #1 tags after filtering in treatment: 5188794 INFO @ Mon, 03 Jun 2019 15:03:16: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 15:03:16: #1 finished! INFO @ Mon, 03 Jun 2019 15:03:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:03:16: #1 tags after filtering in treatment: 5188794 INFO @ Mon, 03 Jun 2019 15:03:16: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 15:03:16: #1 finished! INFO @ Mon, 03 Jun 2019 15:03:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:03:17: #2 number of paired peaks: 3164 INFO @ Mon, 03 Jun 2019 15:03:17: start model_add_line... INFO @ Mon, 03 Jun 2019 15:03:17: #2 number of paired peaks: 3164 INFO @ Mon, 03 Jun 2019 15:03:17: start model_add_line... INFO @ Mon, 03 Jun 2019 15:03:17: start X-correlation... INFO @ Mon, 03 Jun 2019 15:03:17: end of X-cor INFO @ Mon, 03 Jun 2019 15:03:17: #2 finished! INFO @ Mon, 03 Jun 2019 15:03:17: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 15:03:17: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 15:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.05_model.r INFO @ Mon, 03 Jun 2019 15:03:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:03:18: start X-correlation... INFO @ Mon, 03 Jun 2019 15:03:18: end of X-cor INFO @ Mon, 03 Jun 2019 15:03:18: #2 finished! INFO @ Mon, 03 Jun 2019 15:03:18: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 15:03:18: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 15:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.10_model.r INFO @ Mon, 03 Jun 2019 15:03:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:03:25: 12000000 INFO @ Mon, 03 Jun 2019 15:03:33: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:03:33: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:03:33: #1 total tags in treatment: 5761043 INFO @ Mon, 03 Jun 2019 15:03:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:03:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:03:34: #1 tags after filtering in treatment: 5188794 INFO @ Mon, 03 Jun 2019 15:03:34: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 15:03:34: #1 finished! INFO @ Mon, 03 Jun 2019 15:03:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:03:35: #2 number of paired peaks: 3164 INFO @ Mon, 03 Jun 2019 15:03:35: start model_add_line... INFO @ Mon, 03 Jun 2019 15:03:35: start X-correlation... INFO @ Mon, 03 Jun 2019 15:03:35: end of X-cor INFO @ Mon, 03 Jun 2019 15:03:35: #2 finished! INFO @ Mon, 03 Jun 2019 15:03:35: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 15:03:35: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 15:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.20_model.r INFO @ Mon, 03 Jun 2019 15:03:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:03:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:03:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:04:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:04:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.10_summits.bed INFO @ Mon, 03 Jun 2019 15:04:14: Done! INFO @ Mon, 03 Jun 2019 15:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.05_summits.bed INFO @ Mon, 03 Jun 2019 15:04:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3544 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6678 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393642/SRX3393642.20_summits.bed INFO @ Mon, 03 Jun 2019 15:04:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1462 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。