Job ID = 1295835 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,551,557 reads read : 43,103,114 reads written : 43,103,114 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: 00:51:11 21551557 reads; of these: 21551557 (100.00%) were paired; of these: 14456452 (67.08%) aligned concordantly 0 times 4995709 (23.18%) aligned concordantly exactly 1 time 2099396 (9.74%) aligned concordantly >1 times ---- 14456452 pairs aligned concordantly 0 times; of these: 4929319 (34.10%) aligned discordantly 1 time ---- 9527133 pairs aligned 0 times concordantly or discordantly; of these: 19054266 mates make up the pairs; of these: 7397096 (38.82%) aligned 0 times 5576776 (29.27%) aligned exactly 1 time 6080394 (31.91%) aligned >1 times 82.84% overall alignment rate Time searching: 00:51:11 Overall time: 00:51:11 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 16 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] 7240684 / 11815945 = 0.6128 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 16:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.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 16:56:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:56:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.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 16:56:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:56:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.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 16:56:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:56:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:56:18: 1000000 INFO @ Mon, 03 Jun 2019 16:56:20: 1000000 INFO @ Mon, 03 Jun 2019 16:56:20: 1000000 INFO @ Mon, 03 Jun 2019 16:56:25: 2000000 INFO @ Mon, 03 Jun 2019 16:56:29: 2000000 INFO @ Mon, 03 Jun 2019 16:56:29: 2000000 INFO @ Mon, 03 Jun 2019 16:56:31: 3000000 INFO @ Mon, 03 Jun 2019 16:56:37: 3000000 INFO @ Mon, 03 Jun 2019 16:56:37: 3000000 INFO @ Mon, 03 Jun 2019 16:56:38: 4000000 INFO @ Mon, 03 Jun 2019 16:56:44: 5000000 INFO @ Mon, 03 Jun 2019 16:56:46: 4000000 INFO @ Mon, 03 Jun 2019 16:56:46: 4000000 INFO @ Mon, 03 Jun 2019 16:56:51: 6000000 INFO @ Mon, 03 Jun 2019 16:56:55: 5000000 INFO @ Mon, 03 Jun 2019 16:56:55: 5000000 INFO @ Mon, 03 Jun 2019 16:56:58: 7000000 INFO @ Mon, 03 Jun 2019 16:57:03: 6000000 INFO @ Mon, 03 Jun 2019 16:57:03: 6000000 INFO @ Mon, 03 Jun 2019 16:57:04: 8000000 INFO @ Mon, 03 Jun 2019 16:57:11: 9000000 INFO @ Mon, 03 Jun 2019 16:57:12: 7000000 INFO @ Mon, 03 Jun 2019 16:57:12: 7000000 INFO @ Mon, 03 Jun 2019 16:57:17: 10000000 INFO @ Mon, 03 Jun 2019 16:57:21: 8000000 INFO @ Mon, 03 Jun 2019 16:57:21: 8000000 INFO @ Mon, 03 Jun 2019 16:57:24: 11000000 INFO @ Mon, 03 Jun 2019 16:57:29: 9000000 INFO @ Mon, 03 Jun 2019 16:57:29: 9000000 INFO @ Mon, 03 Jun 2019 16:57:31: 12000000 INFO @ Mon, 03 Jun 2019 16:57:37: 13000000 INFO @ Mon, 03 Jun 2019 16:57:38: 10000000 INFO @ Mon, 03 Jun 2019 16:57:38: 10000000 INFO @ Mon, 03 Jun 2019 16:57:44: 14000000 INFO @ Mon, 03 Jun 2019 16:57:46: 11000000 INFO @ Mon, 03 Jun 2019 16:57:46: 11000000 INFO @ Mon, 03 Jun 2019 16:57:50: 15000000 INFO @ Mon, 03 Jun 2019 16:57:55: 12000000 INFO @ Mon, 03 Jun 2019 16:57:55: 12000000 INFO @ Mon, 03 Jun 2019 16:57:57: 16000000 INFO @ Mon, 03 Jun 2019 16:58:04: 13000000 INFO @ Mon, 03 Jun 2019 16:58:04: 13000000 INFO @ Mon, 03 Jun 2019 16:58:04: 17000000 INFO @ Mon, 03 Jun 2019 16:58:10: 18000000 INFO @ Mon, 03 Jun 2019 16:58:12: 14000000 INFO @ Mon, 03 Jun 2019 16:58:12: 14000000 INFO @ Mon, 03 Jun 2019 16:58:17: 19000000 INFO @ Mon, 03 Jun 2019 16:58:21: 15000000 INFO @ Mon, 03 Jun 2019 16:58:21: 15000000 INFO @ Mon, 03 Jun 2019 16:58:24: 20000000 INFO @ Mon, 03 Jun 2019 16:58:30: 16000000 INFO @ Mon, 03 Jun 2019 16:58:30: 16000000 INFO @ Mon, 03 Jun 2019 16:58:30: 21000000 INFO @ Mon, 03 Jun 2019 16:58:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:58:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:58:31: #1 total tags in treatment: 3136087 INFO @ Mon, 03 Jun 2019 16:58:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:58:31: #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 16:58:32: #1 tags after filtering in treatment: 2540493 INFO @ Mon, 03 Jun 2019 16:58:32: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 16:58:32: #1 finished! INFO @ Mon, 03 Jun 2019 16:58:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:58:32: #2 number of paired peaks: 3477 INFO @ Mon, 03 Jun 2019 16:58:32: start model_add_line... INFO @ Mon, 03 Jun 2019 16:58:32: start X-correlation... INFO @ Mon, 03 Jun 2019 16:58:32: end of X-cor INFO @ Mon, 03 Jun 2019 16:58:32: #2 finished! INFO @ Mon, 03 Jun 2019 16:58:32: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 16:58:32: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 16:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.05_model.r INFO @ Mon, 03 Jun 2019 16:58:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:58:38: 17000000 INFO @ Mon, 03 Jun 2019 16:58:38: 17000000 INFO @ Mon, 03 Jun 2019 16:58:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.05_summits.bed INFO @ Mon, 03 Jun 2019 16:58:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7073 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:58:47: 18000000 INFO @ Mon, 03 Jun 2019 16:58:47: 18000000 INFO @ Mon, 03 Jun 2019 16:58:55: 19000000 INFO @ Mon, 03 Jun 2019 16:58:55: 19000000 INFO @ Mon, 03 Jun 2019 16:59:03: 20000000 INFO @ Mon, 03 Jun 2019 16:59:03: 20000000 INFO @ Mon, 03 Jun 2019 16:59:11: 21000000 INFO @ Mon, 03 Jun 2019 16:59:11: 21000000 INFO @ Mon, 03 Jun 2019 16:59:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:59:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:59:13: #1 total tags in treatment: 3136087 INFO @ Mon, 03 Jun 2019 16:59:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:59:13: #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 16:59:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:59:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:59:13: #1 total tags in treatment: 3136087 INFO @ Mon, 03 Jun 2019 16:59:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:59:13: #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 16:59:13: #1 tags after filtering in treatment: 2540493 INFO @ Mon, 03 Jun 2019 16:59:13: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 16:59:13: #1 finished! INFO @ Mon, 03 Jun 2019 16:59:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:59:13: #1 tags after filtering in treatment: 2540493 INFO @ Mon, 03 Jun 2019 16:59:13: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 16:59:13: #1 finished! INFO @ Mon, 03 Jun 2019 16:59:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:59:14: #2 number of paired peaks: 3477 INFO @ Mon, 03 Jun 2019 16:59:14: start model_add_line... INFO @ Mon, 03 Jun 2019 16:59:14: #2 number of paired peaks: 3477 INFO @ Mon, 03 Jun 2019 16:59:14: start model_add_line... INFO @ Mon, 03 Jun 2019 16:59:14: start X-correlation... INFO @ Mon, 03 Jun 2019 16:59:14: start X-correlation... INFO @ Mon, 03 Jun 2019 16:59:14: end of X-cor INFO @ Mon, 03 Jun 2019 16:59:14: #2 finished! INFO @ Mon, 03 Jun 2019 16:59:14: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 16:59:14: end of X-cor INFO @ Mon, 03 Jun 2019 16:59:14: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 16:59:14: #2 finished! INFO @ Mon, 03 Jun 2019 16:59:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.20_model.r INFO @ Mon, 03 Jun 2019 16:59:14: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 16:59:14: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 16:59:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.10_model.r INFO @ Mon, 03 Jun 2019 16:59:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:59:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:59:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:59:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:59:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:59:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.20_summits.bed INFO @ Mon, 03 Jun 2019 16:59:26: Done! INFO @ Mon, 03 Jun 2019 16:59:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:59:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577933/SRX4577933.10_summits.bed pass1 - making usageList (13 chroms): 1 millis INFO @ Mon, 03 Jun 2019 16:59:26: Done! pass2 - checking and writing primary data (673 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2562 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。