Job ID = 11158503 sra ファイルのダウンロード中... Completed: 2114440K bytes transferred in 48 seconds (359190K 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 32026579 spots for /home/okishinya/chipatlas/results/dm3/SRX4279689/SRR7408113.sra Written 32026579 spots for /home/okishinya/chipatlas/results/dm3/SRX4279689/SRR7408113.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: 04:55:01 32026579 reads; of these: 32026579 (100.00%) were paired; of these: 18702245 (58.40%) aligned concordantly 0 times 10676739 (33.34%) aligned concordantly exactly 1 time 2647595 (8.27%) aligned concordantly >1 times ---- 18702245 pairs aligned concordantly 0 times; of these: 10417 (0.06%) aligned discordantly 1 time ---- 18691828 pairs aligned 0 times concordantly or discordantly; of these: 37383656 mates make up the pairs; of these: 30995696 (82.91%) aligned 0 times 709229 (1.90%) aligned exactly 1 time 5678731 (15.19%) aligned >1 times 51.61% overall alignment rate Time searching: 04:55:02 Overall time: 04:55:02 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] 9212556 / 13291477 = 0.6931 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 14:45:56: # Command line: callpeak -t SRX4279689.bam -f BAM -g dm -n SRX4279689.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279689.05 # format = BAM # ChIP-seq file = ['SRX4279689.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 14:45:56: # Command line: callpeak -t SRX4279689.bam -f BAM -g dm -n SRX4279689.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279689.20 # format = BAM # ChIP-seq file = ['SRX4279689.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 14:45:56: # Command line: callpeak -t SRX4279689.bam -f BAM -g dm -n SRX4279689.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279689.10 # format = BAM # ChIP-seq file = ['SRX4279689.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 14:45:56: #1 read tag files... INFO @ Tue, 04 Sep 2018 14:45:56: #1 read tag files... INFO @ Tue, 04 Sep 2018 14:45:56: #1 read tag files... INFO @ Tue, 04 Sep 2018 14:45:56: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 14:45:56: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 14:45:56: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 14:46:03: 1000000 INFO @ Tue, 04 Sep 2018 14:46:04: 1000000 INFO @ Tue, 04 Sep 2018 14:46:04: 1000000 INFO @ Tue, 04 Sep 2018 14:46:10: 2000000 INFO @ Tue, 04 Sep 2018 14:46:11: 2000000 INFO @ Tue, 04 Sep 2018 14:46:11: 2000000 INFO @ Tue, 04 Sep 2018 14:46:16: 3000000 INFO @ Tue, 04 Sep 2018 14:46:19: 3000000 INFO @ Tue, 04 Sep 2018 14:46:19: 3000000 INFO @ Tue, 04 Sep 2018 14:46:23: 4000000 INFO @ Tue, 04 Sep 2018 14:46:26: 4000000 INFO @ Tue, 04 Sep 2018 14:46:26: 4000000 INFO @ Tue, 04 Sep 2018 14:46:29: 5000000 INFO @ Tue, 04 Sep 2018 14:46:33: 5000000 INFO @ Tue, 04 Sep 2018 14:46:33: 5000000 INFO @ Tue, 04 Sep 2018 14:46:36: 6000000 INFO @ Tue, 04 Sep 2018 14:46:41: 6000000 INFO @ Tue, 04 Sep 2018 14:46:41: 6000000 INFO @ Tue, 04 Sep 2018 14:46:42: 7000000 INFO @ Tue, 04 Sep 2018 14:46:47: 7000000 INFO @ Tue, 04 Sep 2018 14:46:47: 7000000 INFO @ Tue, 04 Sep 2018 14:46:47: 8000000 INFO @ Tue, 04 Sep 2018 14:46:53: 8000000 INFO @ Tue, 04 Sep 2018 14:46:53: 8000000 INFO @ Tue, 04 Sep 2018 14:46:53: 9000000 INFO @ Tue, 04 Sep 2018 14:46:59: 9000000 INFO @ Tue, 04 Sep 2018 14:46:59: 9000000 INFO @ Tue, 04 Sep 2018 14:47:00: 10000000 INFO @ Tue, 04 Sep 2018 14:47:06: 11000000 INFO @ Tue, 04 Sep 2018 14:47:07: 10000000 INFO @ Tue, 04 Sep 2018 14:47:07: 10000000 INFO @ Tue, 04 Sep 2018 14:47:12: 12000000 INFO @ Tue, 04 Sep 2018 14:47:13: 11000000 INFO @ Tue, 04 Sep 2018 14:47:13: 11000000 INFO @ Tue, 04 Sep 2018 14:47:17: 13000000 INFO @ Tue, 04 Sep 2018 14:47:19: 12000000 INFO @ Tue, 04 Sep 2018 14:47:19: 12000000 INFO @ Tue, 04 Sep 2018 14:47:23: 14000000 INFO @ Tue, 04 Sep 2018 14:47:25: 13000000 INFO @ Tue, 04 Sep 2018 14:47:25: 13000000 INFO @ Tue, 04 Sep 2018 14:47:28: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 14:47:28: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 14:47:28: #1 total tags in treatment: 4115124 INFO @ Tue, 04 Sep 2018 14:47:28: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 14:47:28: #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 14:47:28: #1 tags after filtering in treatment: 3967438 INFO @ Tue, 04 Sep 2018 14:47:28: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 04 Sep 2018 14:47:28: #1 finished! INFO @ Tue, 04 Sep 2018 14:47:28: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 14:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 14:47:28: #2 number of paired peaks: 816 WARNING @ Tue, 04 Sep 2018 14:47:28: Fewer paired peaks (816) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 816 pairs to build model! INFO @ Tue, 04 Sep 2018 14:47:28: start model_add_line... INFO @ Tue, 04 Sep 2018 14:47:28: start X-correlation... INFO @ Tue, 04 Sep 2018 14:47:28: end of X-cor INFO @ Tue, 04 Sep 2018 14:47:28: #2 finished! INFO @ Tue, 04 Sep 2018 14:47:28: #2 predicted fragment length is 166 bps INFO @ Tue, 04 Sep 2018 14:47:28: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 04 Sep 2018 14:47:28: #2.2 Generate R script for model : SRX4279689.05_model.r INFO @ Tue, 04 Sep 2018 14:47:28: #3 Call peaks... INFO @ Tue, 04 Sep 2018 14:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 14:47:32: 14000000 INFO @ Tue, 04 Sep 2018 14:47:32: 14000000 INFO @ Tue, 04 Sep 2018 14:47:37: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 14:47:37: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 14:47:37: #1 total tags in treatment: 4115124 INFO @ Tue, 04 Sep 2018 14:47:37: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 14:47:37: #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 14:47:37: #1 tags after filtering in treatment: 3967438 INFO @ Tue, 04 Sep 2018 14:47:37: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 04 Sep 2018 14:47:37: #1 finished! INFO @ Tue, 04 Sep 2018 14:47:37: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 14:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 14:47:37: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 14:47:37: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 14:47:37: #1 total tags in treatment: 4115124 INFO @ Tue, 04 Sep 2018 14:47:37: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 14:47:37: #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 14:47:37: #1 tags after filtering in treatment: 3967438 INFO @ Tue, 04 Sep 2018 14:47:37: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 04 Sep 2018 14:47:37: #1 finished! INFO @ Tue, 04 Sep 2018 14:47:37: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 14:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 14:47:37: #2 number of paired peaks: 816 WARNING @ Tue, 04 Sep 2018 14:47:37: Fewer paired peaks (816) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 816 pairs to build model! INFO @ Tue, 04 Sep 2018 14:47:37: start model_add_line... INFO @ Tue, 04 Sep 2018 14:47:37: start X-correlation... INFO @ Tue, 04 Sep 2018 14:47:37: end of X-cor INFO @ Tue, 04 Sep 2018 14:47:37: #2 finished! INFO @ Tue, 04 Sep 2018 14:47:37: #2 predicted fragment length is 166 bps INFO @ Tue, 04 Sep 2018 14:47:37: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 04 Sep 2018 14:47:37: #2.2 Generate R script for model : SRX4279689.10_model.r INFO @ Tue, 04 Sep 2018 14:47:37: #3 Call peaks... INFO @ Tue, 04 Sep 2018 14:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 14:47:37: #2 number of paired peaks: 816 WARNING @ Tue, 04 Sep 2018 14:47:37: Fewer paired peaks (816) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 816 pairs to build model! INFO @ Tue, 04 Sep 2018 14:47:37: start model_add_line... INFO @ Tue, 04 Sep 2018 14:47:37: start X-correlation... INFO @ Tue, 04 Sep 2018 14:47:37: end of X-cor INFO @ Tue, 04 Sep 2018 14:47:37: #2 finished! INFO @ Tue, 04 Sep 2018 14:47:37: #2 predicted fragment length is 166 bps INFO @ Tue, 04 Sep 2018 14:47:37: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 04 Sep 2018 14:47:37: #2.2 Generate R script for model : SRX4279689.20_model.r INFO @ Tue, 04 Sep 2018 14:47:37: #3 Call peaks... INFO @ Tue, 04 Sep 2018 14:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 14:47:38: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 14:47:44: #4 Write output xls file... SRX4279689.05_peaks.xls INFO @ Tue, 04 Sep 2018 14:47:44: #4 Write peak in narrowPeak format file... SRX4279689.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 14:47:44: #4 Write summits bed file... SRX4279689.05_summits.bed INFO @ Tue, 04 Sep 2018 14:47:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2131 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 14:47:47: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 14:47:48: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 14:47:52: #4 Write output xls file... SRX4279689.10_peaks.xls INFO @ Tue, 04 Sep 2018 14:47:52: #4 Write peak in narrowPeak format file... SRX4279689.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 14:47:52: #4 Write summits bed file... SRX4279689.10_summits.bed INFO @ Tue, 04 Sep 2018 14:47:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 14:47:53: #4 Write output xls file... SRX4279689.20_peaks.xls INFO @ Tue, 04 Sep 2018 14:47:53: #4 Write peak in narrowPeak format file... SRX4279689.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 14:47:53: #4 Write summits bed file... SRX4279689.20_summits.bed INFO @ Tue, 04 Sep 2018 14:47:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。