Job ID = 11158500 sra ファイルのダウンロード中... Completed: 1498017K bytes transferred in 41 seconds (296636K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 23009151 spots for /home/okishinya/chipatlas/results/dm3/SRX4279686/SRR7408116.sra Written 23009151 spots for /home/okishinya/chipatlas/results/dm3/SRX4279686/SRR7408116.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 02:01:30 23009151 reads; of these: 23009151 (100.00%) were paired; of these: 9890388 (42.98%) aligned concordantly 0 times 9898269 (43.02%) aligned concordantly exactly 1 time 3220494 (14.00%) aligned concordantly >1 times ---- 9890388 pairs aligned concordantly 0 times; of these: 1371260 (13.86%) aligned discordantly 1 time ---- 8519128 pairs aligned 0 times concordantly or discordantly; of these: 17038256 mates make up the pairs; of these: 9067048 (53.22%) aligned 0 times 3101973 (18.21%) aligned exactly 1 time 4869235 (28.58%) aligned >1 times 80.30% overall alignment rate Time searching: 02:01:30 Overall time: 02:01:30 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] 5967566 / 13467718 = 0.4431 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 @ Tue, 04 Sep 2018 11:53:35: # Command line: callpeak -t SRX4279686.bam -f BAM -g dm -n SRX4279686.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279686.20 # format = BAM # ChIP-seq file = ['SRX4279686.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, 04 Sep 2018 11:53:35: # Command line: callpeak -t SRX4279686.bam -f BAM -g dm -n SRX4279686.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279686.05 # format = BAM # ChIP-seq file = ['SRX4279686.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, 04 Sep 2018 11:53:35: # Command line: callpeak -t SRX4279686.bam -f BAM -g dm -n SRX4279686.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279686.10 # format = BAM # ChIP-seq file = ['SRX4279686.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, 04 Sep 2018 11:53:35: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:53:35: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:53:35: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:53:35: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:53:35: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:53:35: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:53:42: 1000000 INFO @ Tue, 04 Sep 2018 11:53:43: 1000000 INFO @ Tue, 04 Sep 2018 11:53:43: 1000000 INFO @ Tue, 04 Sep 2018 11:53:49: 2000000 INFO @ Tue, 04 Sep 2018 11:53:50: 2000000 INFO @ Tue, 04 Sep 2018 11:53:50: 2000000 INFO @ Tue, 04 Sep 2018 11:53:56: 3000000 INFO @ Tue, 04 Sep 2018 11:53:57: 3000000 INFO @ Tue, 04 Sep 2018 11:53:57: 3000000 INFO @ Tue, 04 Sep 2018 11:54:02: 4000000 INFO @ Tue, 04 Sep 2018 11:54:04: 4000000 INFO @ Tue, 04 Sep 2018 11:54:04: 4000000 INFO @ Tue, 04 Sep 2018 11:54:09: 5000000 INFO @ Tue, 04 Sep 2018 11:54:12: 5000000 INFO @ Tue, 04 Sep 2018 11:54:12: 5000000 INFO @ Tue, 04 Sep 2018 11:54:16: 6000000 INFO @ Tue, 04 Sep 2018 11:54:19: 6000000 INFO @ Tue, 04 Sep 2018 11:54:19: 6000000 INFO @ Tue, 04 Sep 2018 11:54:22: 7000000 INFO @ Tue, 04 Sep 2018 11:54:26: 7000000 INFO @ Tue, 04 Sep 2018 11:54:26: 7000000 INFO @ Tue, 04 Sep 2018 11:54:29: 8000000 INFO @ Tue, 04 Sep 2018 11:54:34: 8000000 INFO @ Tue, 04 Sep 2018 11:54:34: 8000000 INFO @ Tue, 04 Sep 2018 11:54:35: 9000000 INFO @ Tue, 04 Sep 2018 11:54:41: 9000000 INFO @ Tue, 04 Sep 2018 11:54:41: 9000000 INFO @ Tue, 04 Sep 2018 11:54:42: 10000000 INFO @ Tue, 04 Sep 2018 11:54:48: 10000000 INFO @ Tue, 04 Sep 2018 11:54:48: 10000000 INFO @ Tue, 04 Sep 2018 11:54:49: 11000000 INFO @ Tue, 04 Sep 2018 11:54:55: 11000000 INFO @ Tue, 04 Sep 2018 11:54:55: 11000000 INFO @ Tue, 04 Sep 2018 11:54:55: 12000000 INFO @ Tue, 04 Sep 2018 11:55:02: 13000000 INFO @ Tue, 04 Sep 2018 11:55:03: 12000000 INFO @ Tue, 04 Sep 2018 11:55:03: 12000000 INFO @ Tue, 04 Sep 2018 11:55:09: 14000000 INFO @ Tue, 04 Sep 2018 11:55:10: 13000000 INFO @ Tue, 04 Sep 2018 11:55:10: 13000000 INFO @ Tue, 04 Sep 2018 11:55:15: 15000000 INFO @ Tue, 04 Sep 2018 11:55:17: 14000000 INFO @ Tue, 04 Sep 2018 11:55:17: 14000000 INFO @ Tue, 04 Sep 2018 11:55:22: 16000000 INFO @ Tue, 04 Sep 2018 11:55:24: 15000000 INFO @ Tue, 04 Sep 2018 11:55:24: 15000000 INFO @ Tue, 04 Sep 2018 11:55:29: 17000000 INFO @ Tue, 04 Sep 2018 11:55:31: 16000000 INFO @ Tue, 04 Sep 2018 11:55:32: 16000000 INFO @ Tue, 04 Sep 2018 11:55:35: 18000000 INFO @ Tue, 04 Sep 2018 11:55:39: 17000000 INFO @ Tue, 04 Sep 2018 11:55:39: 17000000 INFO @ Tue, 04 Sep 2018 11:55:42: 19000000 INFO @ Tue, 04 Sep 2018 11:55:46: 18000000 INFO @ Tue, 04 Sep 2018 11:55:46: 18000000 INFO @ Tue, 04 Sep 2018 11:55:48: 20000000 INFO @ Tue, 04 Sep 2018 11:55:53: 19000000 INFO @ Tue, 04 Sep 2018 11:55:53: 19000000 INFO @ Tue, 04 Sep 2018 11:55:55: 21000000 INFO @ Tue, 04 Sep 2018 11:56:00: 20000000 INFO @ Tue, 04 Sep 2018 11:56:00: 20000000 INFO @ Tue, 04 Sep 2018 11:56:01: 22000000 INFO @ Tue, 04 Sep 2018 11:56:07: 21000000 INFO @ Tue, 04 Sep 2018 11:56:08: 21000000 INFO @ Tue, 04 Sep 2018 11:56:08: 23000000 INFO @ Tue, 04 Sep 2018 11:56:14: 22000000 INFO @ Tue, 04 Sep 2018 11:56:15: 24000000 INFO @ Tue, 04 Sep 2018 11:56:15: 22000000 INFO @ Tue, 04 Sep 2018 11:56:21: 25000000 INFO @ Tue, 04 Sep 2018 11:56:21: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:56:21: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:56:21: #1 total tags in treatment: 7327301 INFO @ Tue, 04 Sep 2018 11:56:21: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 11:56:21: #1 tags after filtering in treatment: 6658299 INFO @ Tue, 04 Sep 2018 11:56:21: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 04 Sep 2018 11:56:21: #1 finished! INFO @ Tue, 04 Sep 2018 11:56:21: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:56:22: 23000000 INFO @ Tue, 04 Sep 2018 11:56:22: #2 number of paired peaks: 625 WARNING @ Tue, 04 Sep 2018 11:56:22: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 04 Sep 2018 11:56:22: start model_add_line... INFO @ Tue, 04 Sep 2018 11:56:22: start X-correlation... INFO @ Tue, 04 Sep 2018 11:56:22: 23000000 INFO @ Tue, 04 Sep 2018 11:56:22: end of X-cor INFO @ Tue, 04 Sep 2018 11:56:22: #2 finished! INFO @ Tue, 04 Sep 2018 11:56:22: #2 predicted fragment length is 169 bps INFO @ Tue, 04 Sep 2018 11:56:22: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 04 Sep 2018 11:56:22: #2.2 Generate R script for model : SRX4279686.10_model.r INFO @ Tue, 04 Sep 2018 11:56:22: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:56:29: 24000000 INFO @ Tue, 04 Sep 2018 11:56:30: 24000000 INFO @ Tue, 04 Sep 2018 11:56:36: 25000000 INFO @ Tue, 04 Sep 2018 11:56:37: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:56:37: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:56:37: #1 total tags in treatment: 7327301 INFO @ Tue, 04 Sep 2018 11:56:37: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:56:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 11:56:37: #1 tags after filtering in treatment: 6658299 INFO @ Tue, 04 Sep 2018 11:56:37: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 04 Sep 2018 11:56:37: #1 finished! INFO @ Tue, 04 Sep 2018 11:56:37: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:56:37: 25000000 INFO @ Tue, 04 Sep 2018 11:56:37: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:56:37: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:56:37: #1 total tags in treatment: 7327301 INFO @ Tue, 04 Sep 2018 11:56:37: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:56:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 11:56:37: #1 tags after filtering in treatment: 6658299 INFO @ Tue, 04 Sep 2018 11:56:37: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 04 Sep 2018 11:56:37: #1 finished! INFO @ Tue, 04 Sep 2018 11:56:37: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:56:37: #2 number of paired peaks: 625 WARNING @ Tue, 04 Sep 2018 11:56:37: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 04 Sep 2018 11:56:37: start model_add_line... INFO @ Tue, 04 Sep 2018 11:56:37: start X-correlation... INFO @ Tue, 04 Sep 2018 11:56:37: end of X-cor INFO @ Tue, 04 Sep 2018 11:56:37: #2 finished! INFO @ Tue, 04 Sep 2018 11:56:37: #2 predicted fragment length is 169 bps INFO @ Tue, 04 Sep 2018 11:56:37: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 04 Sep 2018 11:56:37: #2.2 Generate R script for model : SRX4279686.05_model.r INFO @ Tue, 04 Sep 2018 11:56:37: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:56:38: #2 number of paired peaks: 625 WARNING @ Tue, 04 Sep 2018 11:56:38: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 04 Sep 2018 11:56:38: start model_add_line... INFO @ Tue, 04 Sep 2018 11:56:38: start X-correlation... INFO @ Tue, 04 Sep 2018 11:56:38: end of X-cor INFO @ Tue, 04 Sep 2018 11:56:38: #2 finished! INFO @ Tue, 04 Sep 2018 11:56:38: #2 predicted fragment length is 169 bps INFO @ Tue, 04 Sep 2018 11:56:38: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 04 Sep 2018 11:56:38: #2.2 Generate R script for model : SRX4279686.20_model.r INFO @ Tue, 04 Sep 2018 11:56:38: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:56:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:56:40: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:56:48: #4 Write output xls file... SRX4279686.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:56:48: #4 Write peak in narrowPeak format file... SRX4279686.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:56:48: #4 Write summits bed file... SRX4279686.10_summits.bed INFO @ Tue, 04 Sep 2018 11:56:48: Done! pass1 - making usageList (15 chroms): 13 millis pass2 - checking and writing primary data (1231 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:56:54: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:56:55: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:57:02: #4 Write output xls file... SRX4279686.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:57:02: #4 Write peak in narrowPeak format file... SRX4279686.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:57:02: #4 Write summits bed file... SRX4279686.05_summits.bed INFO @ Tue, 04 Sep 2018 11:57:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1928 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:57:04: #4 Write output xls file... SRX4279686.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:57:04: #4 Write peak in narrowPeak format file... SRX4279686.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:57:04: #4 Write summits bed file... SRX4279686.20_summits.bed INFO @ Tue, 04 Sep 2018 11:57:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (822 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。