Job ID = 11158489 sra ファイルのダウンロード中... Completed: 1352136K bytes transferred in 154 seconds (71579K 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 20460530 spots for /home/okishinya/chipatlas/results/dm3/SRX4279659/SRR7408143.sra Written 20460530 spots for /home/okishinya/chipatlas/results/dm3/SRX4279659/SRR7408143.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:39:34 20460530 reads; of these: 20460530 (100.00%) were paired; of these: 13456589 (65.77%) aligned concordantly 0 times 4262035 (20.83%) aligned concordantly exactly 1 time 2741906 (13.40%) aligned concordantly >1 times ---- 13456589 pairs aligned concordantly 0 times; of these: 2559763 (19.02%) aligned discordantly 1 time ---- 10896826 pairs aligned 0 times concordantly or discordantly; of these: 21793652 mates make up the pairs; of these: 10518800 (48.27%) aligned 0 times 5428911 (24.91%) aligned exactly 1 time 5845941 (26.82%) aligned >1 times 74.29% overall alignment rate Time searching: 01:39:35 Overall time: 01:39:35 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] 1897912 / 7457576 = 0.2545 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 11:32:17: # Command line: callpeak -t SRX4279659.bam -f BAM -g dm -n SRX4279659.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279659.10 # format = BAM # ChIP-seq file = ['SRX4279659.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 11:32:17: # Command line: callpeak -t SRX4279659.bam -f BAM -g dm -n SRX4279659.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279659.05 # format = BAM # ChIP-seq file = ['SRX4279659.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 11:32:17: # Command line: callpeak -t SRX4279659.bam -f BAM -g dm -n SRX4279659.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279659.20 # format = BAM # ChIP-seq file = ['SRX4279659.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 11:32:17: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:32:17: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:32:17: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:32:17: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:32:17: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:32:17: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:32:25: 1000000 INFO @ Tue, 04 Sep 2018 11:32:25: 1000000 INFO @ Tue, 04 Sep 2018 11:32:25: 1000000 INFO @ Tue, 04 Sep 2018 11:32:31: 2000000 INFO @ Tue, 04 Sep 2018 11:32:32: 2000000 INFO @ Tue, 04 Sep 2018 11:32:32: 2000000 INFO @ Tue, 04 Sep 2018 11:32:38: 3000000 INFO @ Tue, 04 Sep 2018 11:32:39: 3000000 INFO @ Tue, 04 Sep 2018 11:32:40: 3000000 INFO @ Tue, 04 Sep 2018 11:32:46: 4000000 INFO @ Tue, 04 Sep 2018 11:32:46: 4000000 INFO @ Tue, 04 Sep 2018 11:32:47: 4000000 INFO @ Tue, 04 Sep 2018 11:32:53: 5000000 INFO @ Tue, 04 Sep 2018 11:32:54: 5000000 INFO @ Tue, 04 Sep 2018 11:32:55: 5000000 INFO @ Tue, 04 Sep 2018 11:33:00: 6000000 INFO @ Tue, 04 Sep 2018 11:33:02: 6000000 INFO @ Tue, 04 Sep 2018 11:33:03: 6000000 INFO @ Tue, 04 Sep 2018 11:33:07: 7000000 INFO @ Tue, 04 Sep 2018 11:33:09: 7000000 INFO @ Tue, 04 Sep 2018 11:33:10: 7000000 INFO @ Tue, 04 Sep 2018 11:33:14: 8000000 INFO @ Tue, 04 Sep 2018 11:33:17: 8000000 INFO @ Tue, 04 Sep 2018 11:33:18: 8000000 INFO @ Tue, 04 Sep 2018 11:33:20: 9000000 INFO @ Tue, 04 Sep 2018 11:33:25: 9000000 INFO @ Tue, 04 Sep 2018 11:33:26: 9000000 INFO @ Tue, 04 Sep 2018 11:33:27: 10000000 INFO @ Tue, 04 Sep 2018 11:33:33: 10000000 INFO @ Tue, 04 Sep 2018 11:33:34: 11000000 INFO @ Tue, 04 Sep 2018 11:33:34: 10000000 INFO @ Tue, 04 Sep 2018 11:33:41: 12000000 INFO @ Tue, 04 Sep 2018 11:33:41: 11000000 INFO @ Tue, 04 Sep 2018 11:33:42: 11000000 INFO @ Tue, 04 Sep 2018 11:33:48: 13000000 INFO @ Tue, 04 Sep 2018 11:33:49: 12000000 INFO @ Tue, 04 Sep 2018 11:33:50: 12000000 INFO @ Tue, 04 Sep 2018 11:33:54: 14000000 INFO @ Tue, 04 Sep 2018 11:33:57: 13000000 INFO @ Tue, 04 Sep 2018 11:33:58: 13000000 INFO @ Tue, 04 Sep 2018 11:34:01: 15000000 INFO @ Tue, 04 Sep 2018 11:34:05: 14000000 INFO @ Tue, 04 Sep 2018 11:34:06: 14000000 INFO @ Tue, 04 Sep 2018 11:34:08: 16000000 INFO @ Tue, 04 Sep 2018 11:34:13: 15000000 INFO @ Tue, 04 Sep 2018 11:34:14: 15000000 INFO @ Tue, 04 Sep 2018 11:34:15: 17000000 INFO @ Tue, 04 Sep 2018 11:34:20: 16000000 INFO @ Tue, 04 Sep 2018 11:34:21: 16000000 INFO @ Tue, 04 Sep 2018 11:34:21: 18000000 INFO @ Tue, 04 Sep 2018 11:34:28: 17000000 INFO @ Tue, 04 Sep 2018 11:34:28: 19000000 INFO @ Tue, 04 Sep 2018 11:34:29: 17000000 INFO @ Tue, 04 Sep 2018 11:34:35: 20000000 INFO @ Tue, 04 Sep 2018 11:34:36: 18000000 INFO @ Tue, 04 Sep 2018 11:34:37: 18000000 INFO @ Tue, 04 Sep 2018 11:34:42: 21000000 INFO @ Tue, 04 Sep 2018 11:34:44: 19000000 INFO @ Tue, 04 Sep 2018 11:34:45: 19000000 INFO @ Tue, 04 Sep 2018 11:34:48: 22000000 INFO @ Tue, 04 Sep 2018 11:34:52: 20000000 INFO @ Tue, 04 Sep 2018 11:34:53: 20000000 INFO @ Tue, 04 Sep 2018 11:34:55: 23000000 INFO @ Tue, 04 Sep 2018 11:35:00: 21000000 INFO @ Tue, 04 Sep 2018 11:35:01: 21000000 INFO @ Tue, 04 Sep 2018 11:35:02: 24000000 INFO @ Tue, 04 Sep 2018 11:35:08: 22000000 INFO @ Tue, 04 Sep 2018 11:35:08: 22000000 INFO @ Tue, 04 Sep 2018 11:35:08: 25000000 INFO @ Tue, 04 Sep 2018 11:35:15: 26000000 INFO @ Tue, 04 Sep 2018 11:35:15: 23000000 INFO @ Tue, 04 Sep 2018 11:35:16: 23000000 INFO @ Tue, 04 Sep 2018 11:35:19: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:35:19: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:35:19: #1 total tags in treatment: 5144733 INFO @ Tue, 04 Sep 2018 11:35:19: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:35:19: #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 11:35:19: #1 tags after filtering in treatment: 4621076 INFO @ Tue, 04 Sep 2018 11:35:19: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 04 Sep 2018 11:35:19: #1 finished! INFO @ Tue, 04 Sep 2018 11:35:19: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:35:20: #2 number of paired peaks: 841 WARNING @ Tue, 04 Sep 2018 11:35:20: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 04 Sep 2018 11:35:20: start model_add_line... INFO @ Tue, 04 Sep 2018 11:35:20: start X-correlation... INFO @ Tue, 04 Sep 2018 11:35:20: end of X-cor INFO @ Tue, 04 Sep 2018 11:35:20: #2 finished! INFO @ Tue, 04 Sep 2018 11:35:20: #2 predicted fragment length is 161 bps INFO @ Tue, 04 Sep 2018 11:35:20: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 04 Sep 2018 11:35:20: #2.2 Generate R script for model : SRX4279659.10_model.r INFO @ Tue, 04 Sep 2018 11:35:20: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:35:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:35:23: 24000000 INFO @ Tue, 04 Sep 2018 11:35:24: 24000000 INFO @ Tue, 04 Sep 2018 11:35:31: 25000000 INFO @ Tue, 04 Sep 2018 11:35:32: 25000000 INFO @ Tue, 04 Sep 2018 11:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:35:39: #4 Write output xls file... SRX4279659.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:35:39: #4 Write peak in narrowPeak format file... SRX4279659.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:35:39: #4 Write summits bed file... SRX4279659.10_summits.bed INFO @ Tue, 04 Sep 2018 11:35:39: Done! INFO @ Tue, 04 Sep 2018 11:35:39: 26000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1982 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:35:40: 26000000 INFO @ Tue, 04 Sep 2018 11:35:44: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:35:44: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:35:44: #1 total tags in treatment: 5144733 INFO @ Tue, 04 Sep 2018 11:35:44: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:35:44: #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 11:35:44: #1 tags after filtering in treatment: 4621076 INFO @ Tue, 04 Sep 2018 11:35:44: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 04 Sep 2018 11:35:44: #1 finished! INFO @ Tue, 04 Sep 2018 11:35:44: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:35:44: #2 number of paired peaks: 841 WARNING @ Tue, 04 Sep 2018 11:35:44: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 04 Sep 2018 11:35:44: start model_add_line... INFO @ Tue, 04 Sep 2018 11:35:44: start X-correlation... INFO @ Tue, 04 Sep 2018 11:35:44: end of X-cor INFO @ Tue, 04 Sep 2018 11:35:44: #2 finished! INFO @ Tue, 04 Sep 2018 11:35:44: #2 predicted fragment length is 161 bps INFO @ Tue, 04 Sep 2018 11:35:44: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 04 Sep 2018 11:35:44: #2.2 Generate R script for model : SRX4279659.20_model.r INFO @ Tue, 04 Sep 2018 11:35:44: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:35:44: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:35:44: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:35:44: #1 total tags in treatment: 5144733 INFO @ Tue, 04 Sep 2018 11:35:44: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:35:44: #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 11:35:44: #1 tags after filtering in treatment: 4621076 INFO @ Tue, 04 Sep 2018 11:35:44: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 04 Sep 2018 11:35:44: #1 finished! INFO @ Tue, 04 Sep 2018 11:35:44: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:35:45: #2 number of paired peaks: 841 WARNING @ Tue, 04 Sep 2018 11:35:45: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 04 Sep 2018 11:35:45: start model_add_line... INFO @ Tue, 04 Sep 2018 11:35:45: start X-correlation... INFO @ Tue, 04 Sep 2018 11:35:45: end of X-cor INFO @ Tue, 04 Sep 2018 11:35:45: #2 finished! INFO @ Tue, 04 Sep 2018 11:35:45: #2 predicted fragment length is 161 bps INFO @ Tue, 04 Sep 2018 11:35:45: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 04 Sep 2018 11:35:45: #2.2 Generate R script for model : SRX4279659.05_model.r INFO @ Tue, 04 Sep 2018 11:35:45: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:35:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:35:55: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:35:56: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:36:01: #4 Write output xls file... SRX4279659.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:36:01: #4 Write peak in narrowPeak format file... SRX4279659.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:36:01: #4 Write summits bed file... SRX4279659.20_summits.bed INFO @ Tue, 04 Sep 2018 11:36:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:36:03: #4 Write output xls file... SRX4279659.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:36:03: #4 Write peak in narrowPeak format file... SRX4279659.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:36:03: #4 Write summits bed file... SRX4279659.05_summits.bed INFO @ Tue, 04 Sep 2018 11:36:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3398 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。