Job ID = 1295844 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,022,343 reads read : 24,044,686 reads written : 24,044,686 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: 00:27:47 12022343 reads; of these: 12022343 (100.00%) were paired; of these: 1367006 (11.37%) aligned concordantly 0 times 8432404 (70.14%) aligned concordantly exactly 1 time 2222933 (18.49%) aligned concordantly >1 times ---- 1367006 pairs aligned concordantly 0 times; of these: 515657 (37.72%) aligned discordantly 1 time ---- 851349 pairs aligned 0 times concordantly or discordantly; of these: 1702698 mates make up the pairs; of these: 700944 (41.17%) aligned 0 times 484763 (28.47%) aligned exactly 1 time 516991 (30.36%) aligned >1 times 97.08% overall alignment rate Time searching: 00:27:47 Overall time: 00:27:47 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 12 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] 950429 / 11163826 = 0.0851 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 16:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.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 16:25:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:25:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.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 16:25:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:25:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.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 16:25:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:25:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:25:20: 1000000 INFO @ Mon, 03 Jun 2019 16:25:21: 1000000 INFO @ Mon, 03 Jun 2019 16:25:22: 1000000 INFO @ Mon, 03 Jun 2019 16:25:26: 2000000 INFO @ Mon, 03 Jun 2019 16:25:28: 2000000 INFO @ Mon, 03 Jun 2019 16:25:32: 2000000 INFO @ Mon, 03 Jun 2019 16:25:33: 3000000 INFO @ Mon, 03 Jun 2019 16:25:36: 3000000 INFO @ Mon, 03 Jun 2019 16:25:40: 4000000 INFO @ Mon, 03 Jun 2019 16:25:41: 3000000 INFO @ Mon, 03 Jun 2019 16:25:44: 4000000 INFO @ Mon, 03 Jun 2019 16:25:47: 5000000 INFO @ Mon, 03 Jun 2019 16:25:50: 4000000 INFO @ Mon, 03 Jun 2019 16:25:51: 5000000 INFO @ Mon, 03 Jun 2019 16:25:53: 6000000 INFO @ Mon, 03 Jun 2019 16:25:59: 6000000 INFO @ Mon, 03 Jun 2019 16:25:59: 5000000 INFO @ Mon, 03 Jun 2019 16:26:00: 7000000 INFO @ Mon, 03 Jun 2019 16:26:07: 7000000 INFO @ Mon, 03 Jun 2019 16:26:07: 8000000 INFO @ Mon, 03 Jun 2019 16:26:09: 6000000 INFO @ Mon, 03 Jun 2019 16:26:14: 9000000 INFO @ Mon, 03 Jun 2019 16:26:14: 8000000 INFO @ Mon, 03 Jun 2019 16:26:18: 7000000 INFO @ Mon, 03 Jun 2019 16:26:20: 10000000 INFO @ Mon, 03 Jun 2019 16:26:22: 9000000 INFO @ Mon, 03 Jun 2019 16:26:27: 11000000 INFO @ Mon, 03 Jun 2019 16:26:28: 8000000 INFO @ Mon, 03 Jun 2019 16:26:30: 10000000 INFO @ Mon, 03 Jun 2019 16:26:34: 12000000 INFO @ Mon, 03 Jun 2019 16:26:37: 9000000 INFO @ Mon, 03 Jun 2019 16:26:37: 11000000 INFO @ Mon, 03 Jun 2019 16:26:40: 13000000 INFO @ Mon, 03 Jun 2019 16:26:45: 12000000 INFO @ Mon, 03 Jun 2019 16:26:46: 10000000 INFO @ Mon, 03 Jun 2019 16:26:47: 14000000 INFO @ Mon, 03 Jun 2019 16:26:52: 13000000 INFO @ Mon, 03 Jun 2019 16:26:54: 15000000 INFO @ Mon, 03 Jun 2019 16:26:55: 11000000 INFO @ Mon, 03 Jun 2019 16:27:00: 14000000 INFO @ Mon, 03 Jun 2019 16:27:00: 16000000 INFO @ Mon, 03 Jun 2019 16:27:05: 12000000 INFO @ Mon, 03 Jun 2019 16:27:07: 17000000 INFO @ Mon, 03 Jun 2019 16:27:07: 15000000 INFO @ Mon, 03 Jun 2019 16:27:14: 18000000 INFO @ Mon, 03 Jun 2019 16:27:14: 13000000 INFO @ Mon, 03 Jun 2019 16:27:15: 16000000 INFO @ Mon, 03 Jun 2019 16:27:20: 19000000 INFO @ Mon, 03 Jun 2019 16:27:22: 17000000 INFO @ Mon, 03 Jun 2019 16:27:23: 14000000 INFO @ Mon, 03 Jun 2019 16:27:27: 20000000 INFO @ Mon, 03 Jun 2019 16:27:30: 18000000 INFO @ Mon, 03 Jun 2019 16:27:32: 15000000 INFO @ Mon, 03 Jun 2019 16:27:34: 21000000 INFO @ Mon, 03 Jun 2019 16:27:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:27:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:27:37: #1 total tags in treatment: 9729685 INFO @ Mon, 03 Jun 2019 16:27:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:37: #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 16:27:37: #1 tags after filtering in treatment: 7063950 INFO @ Mon, 03 Jun 2019 16:27:37: #1 Redundant rate of treatment: 0.27 INFO @ Mon, 03 Jun 2019 16:27:37: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:37: 19000000 INFO @ Mon, 03 Jun 2019 16:27:38: #2 number of paired peaks: 9437 INFO @ Mon, 03 Jun 2019 16:27:38: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:38: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:39: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:39: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:39: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 16:27:39: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 16:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.10_model.r INFO @ Mon, 03 Jun 2019 16:27:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:41: 16000000 INFO @ Mon, 03 Jun 2019 16:27:45: 20000000 INFO @ Mon, 03 Jun 2019 16:27:50: 17000000 INFO @ Mon, 03 Jun 2019 16:27:52: 21000000 INFO @ Mon, 03 Jun 2019 16:27:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:27:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:27:56: #1 total tags in treatment: 9729685 INFO @ Mon, 03 Jun 2019 16:27:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:56: #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 16:27:56: #1 tags after filtering in treatment: 7063950 INFO @ Mon, 03 Jun 2019 16:27:56: #1 Redundant rate of treatment: 0.27 INFO @ Mon, 03 Jun 2019 16:27:56: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:57: #2 number of paired peaks: 9437 INFO @ Mon, 03 Jun 2019 16:27:57: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:57: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:57: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:57: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:57: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 16:27:57: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 16:27:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.05_model.r INFO @ Mon, 03 Jun 2019 16:27:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:59: 18000000 INFO @ Mon, 03 Jun 2019 16:28:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:28:08: 19000000 INFO @ Mon, 03 Jun 2019 16:28:17: 20000000 INFO @ Mon, 03 Jun 2019 16:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.10_summits.bed INFO @ Mon, 03 Jun 2019 16:28:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7968 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:28:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:28:25: 21000000 INFO @ Mon, 03 Jun 2019 16:28:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:28:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:28:29: #1 total tags in treatment: 9729685 INFO @ Mon, 03 Jun 2019 16:28:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:28:29: #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 16:28:29: #1 tags after filtering in treatment: 7063950 INFO @ Mon, 03 Jun 2019 16:28:29: #1 Redundant rate of treatment: 0.27 INFO @ Mon, 03 Jun 2019 16:28:29: #1 finished! INFO @ Mon, 03 Jun 2019 16:28:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:28:31: #2 number of paired peaks: 9437 INFO @ Mon, 03 Jun 2019 16:28:31: start model_add_line... INFO @ Mon, 03 Jun 2019 16:28:31: start X-correlation... INFO @ Mon, 03 Jun 2019 16:28:31: end of X-cor INFO @ Mon, 03 Jun 2019 16:28:31: #2 finished! INFO @ Mon, 03 Jun 2019 16:28:31: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 16:28:31: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 16:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.20_model.r INFO @ Mon, 03 Jun 2019 16:28:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.05_summits.bed INFO @ Mon, 03 Jun 2019 16:28:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8982 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:28:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 16:29:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:29:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:29:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577937/SRX4577937.20_summits.bed INFO @ Mon, 03 Jun 2019 16:29:09: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6468 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。