Job ID = 11158502 sra ファイルのダウンロード中... Completed: 1366197K bytes transferred in 38 seconds (286982K 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 20592334 spots for /home/okishinya/chipatlas/results/dm3/SRX4279688/SRR7408114.sra Written 20592334 spots for /home/okishinya/chipatlas/results/dm3/SRX4279688/SRR7408114.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: 00:00:01 Multiseed full-index search: 02:03:41 20592334 reads; of these: 20592334 (100.00%) were paired; of these: 11503098 (55.86%) aligned concordantly 0 times 6555951 (31.84%) aligned concordantly exactly 1 time 2533285 (12.30%) aligned concordantly >1 times ---- 11503098 pairs aligned concordantly 0 times; of these: 1681845 (14.62%) aligned discordantly 1 time ---- 9821253 pairs aligned 0 times concordantly or discordantly; of these: 19642506 mates make up the pairs; of these: 10519667 (53.56%) aligned 0 times 3435291 (17.49%) aligned exactly 1 time 5687548 (28.96%) aligned >1 times 74.46% overall alignment rate Time searching: 02:03:42 Overall time: 02:03:42 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] 4306856 / 9529510 = 0.4519 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 11:54:01: # Command line: callpeak -t SRX4279688.bam -f BAM -g dm -n SRX4279688.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279688.20 # format = BAM # ChIP-seq file = ['SRX4279688.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 11:54:01: # Command line: callpeak -t SRX4279688.bam -f BAM -g dm -n SRX4279688.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279688.10 # format = BAM # ChIP-seq file = ['SRX4279688.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 11:54:01: # Command line: callpeak -t SRX4279688.bam -f BAM -g dm -n SRX4279688.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279688.05 # format = BAM # ChIP-seq file = ['SRX4279688.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 11:54:01: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:54:01: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:54:01: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:54:01: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:54:01: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:54:01: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:54:07: 1000000 INFO @ Tue, 04 Sep 2018 11:54:07: 1000000 INFO @ Tue, 04 Sep 2018 11:54:08: 1000000 INFO @ Tue, 04 Sep 2018 11:54:14: 2000000 INFO @ Tue, 04 Sep 2018 11:54:14: 2000000 INFO @ Tue, 04 Sep 2018 11:54:15: 2000000 INFO @ Tue, 04 Sep 2018 11:54:21: 3000000 INFO @ Tue, 04 Sep 2018 11:54:21: 3000000 INFO @ Tue, 04 Sep 2018 11:54:22: 3000000 INFO @ Tue, 04 Sep 2018 11:54:27: 4000000 INFO @ Tue, 04 Sep 2018 11:54:27: 4000000 INFO @ Tue, 04 Sep 2018 11:54:29: 4000000 INFO @ Tue, 04 Sep 2018 11:54:34: 5000000 INFO @ Tue, 04 Sep 2018 11:54:34: 5000000 INFO @ Tue, 04 Sep 2018 11:54:37: 5000000 INFO @ Tue, 04 Sep 2018 11:54:41: 6000000 INFO @ Tue, 04 Sep 2018 11:54:41: 6000000 INFO @ Tue, 04 Sep 2018 11:54:44: 6000000 INFO @ Tue, 04 Sep 2018 11:54:47: 7000000 INFO @ Tue, 04 Sep 2018 11:54:47: 7000000 INFO @ Tue, 04 Sep 2018 11:54:51: 7000000 INFO @ Tue, 04 Sep 2018 11:54:54: 8000000 INFO @ Tue, 04 Sep 2018 11:54:54: 8000000 INFO @ Tue, 04 Sep 2018 11:54:59: 8000000 INFO @ Tue, 04 Sep 2018 11:55:01: 9000000 INFO @ Tue, 04 Sep 2018 11:55:01: 9000000 INFO @ Tue, 04 Sep 2018 11:55:06: 9000000 INFO @ Tue, 04 Sep 2018 11:55:08: 10000000 INFO @ Tue, 04 Sep 2018 11:55:08: 10000000 INFO @ Tue, 04 Sep 2018 11:55:13: 10000000 INFO @ Tue, 04 Sep 2018 11:55:15: 11000000 INFO @ Tue, 04 Sep 2018 11:55:15: 11000000 INFO @ Tue, 04 Sep 2018 11:55:21: 11000000 INFO @ Tue, 04 Sep 2018 11:55:21: 12000000 INFO @ Tue, 04 Sep 2018 11:55:21: 12000000 INFO @ Tue, 04 Sep 2018 11:55:28: 13000000 INFO @ Tue, 04 Sep 2018 11:55:28: 13000000 INFO @ Tue, 04 Sep 2018 11:55:28: 12000000 INFO @ Tue, 04 Sep 2018 11:55:35: 14000000 INFO @ Tue, 04 Sep 2018 11:55:35: 14000000 INFO @ Tue, 04 Sep 2018 11:55:36: 13000000 INFO @ Tue, 04 Sep 2018 11:55:42: 15000000 INFO @ Tue, 04 Sep 2018 11:55:42: 15000000 INFO @ Tue, 04 Sep 2018 11:55:43: 14000000 INFO @ Tue, 04 Sep 2018 11:55:49: 16000000 INFO @ Tue, 04 Sep 2018 11:55:49: 16000000 INFO @ Tue, 04 Sep 2018 11:55:51: 15000000 INFO @ Tue, 04 Sep 2018 11:55:55: 17000000 INFO @ Tue, 04 Sep 2018 11:55:55: 17000000 INFO @ Tue, 04 Sep 2018 11:55:58: 16000000 INFO @ Tue, 04 Sep 2018 11:56:02: 18000000 INFO @ Tue, 04 Sep 2018 11:56:02: 18000000 INFO @ Tue, 04 Sep 2018 11:56:05: 17000000 INFO @ Tue, 04 Sep 2018 11:56:09: 19000000 INFO @ Tue, 04 Sep 2018 11:56:09: 19000000 INFO @ Tue, 04 Sep 2018 11:56:13: 18000000 INFO @ Tue, 04 Sep 2018 11:56:16: 20000000 INFO @ Tue, 04 Sep 2018 11:56:16: 20000000 INFO @ Tue, 04 Sep 2018 11:56:20: 19000000 INFO @ Tue, 04 Sep 2018 11:56:22: 21000000 INFO @ Tue, 04 Sep 2018 11:56:22: 21000000 INFO @ Tue, 04 Sep 2018 11:56:27: 20000000 INFO @ Tue, 04 Sep 2018 11:56:29: 22000000 INFO @ Tue, 04 Sep 2018 11:56:29: 22000000 INFO @ Tue, 04 Sep 2018 11:56:30: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:56:30: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:56:30: #1 total tags in treatment: 4996638 INFO @ Tue, 04 Sep 2018 11:56:30: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:56:30: #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 11:56:30: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:56:30: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:56:30: #1 total tags in treatment: 4996638 INFO @ Tue, 04 Sep 2018 11:56:30: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:56:30: #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 11:56:30: #1 tags after filtering in treatment: 4478865 INFO @ Tue, 04 Sep 2018 11:56:30: #1 tags after filtering in treatment: 4478865 INFO @ Tue, 04 Sep 2018 11:56:30: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 04 Sep 2018 11:56:30: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 04 Sep 2018 11:56:30: #1 finished! INFO @ Tue, 04 Sep 2018 11:56:30: #1 finished! INFO @ Tue, 04 Sep 2018 11:56:30: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:56:30: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:56:30: #2 number of paired peaks: 752 WARNING @ Tue, 04 Sep 2018 11:56:30: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Tue, 04 Sep 2018 11:56:30: #2 number of paired peaks: 752 WARNING @ Tue, 04 Sep 2018 11:56:30: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Tue, 04 Sep 2018 11:56:30: start model_add_line... INFO @ Tue, 04 Sep 2018 11:56:30: start model_add_line... INFO @ Tue, 04 Sep 2018 11:56:30: start X-correlation... INFO @ Tue, 04 Sep 2018 11:56:30: start X-correlation... INFO @ Tue, 04 Sep 2018 11:56:31: end of X-cor INFO @ Tue, 04 Sep 2018 11:56:31: #2 finished! INFO @ Tue, 04 Sep 2018 11:56:31: end of X-cor INFO @ Tue, 04 Sep 2018 11:56:31: #2 finished! INFO @ Tue, 04 Sep 2018 11:56:31: #2 predicted fragment length is 157 bps INFO @ Tue, 04 Sep 2018 11:56:31: #2 predicted fragment length is 157 bps INFO @ Tue, 04 Sep 2018 11:56:31: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 04 Sep 2018 11:56:31: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 04 Sep 2018 11:56:31: #2.2 Generate R script for model : SRX4279688.10_model.r INFO @ Tue, 04 Sep 2018 11:56:31: #2.2 Generate R script for model : SRX4279688.05_model.r INFO @ Tue, 04 Sep 2018 11:56:31: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:56:31: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:56:34: 21000000 INFO @ Tue, 04 Sep 2018 11:56:40: 22000000 INFO @ Tue, 04 Sep 2018 11:56:40: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:56:40: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:56:40: #1 total tags in treatment: 4996638 INFO @ Tue, 04 Sep 2018 11:56:40: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:56:40: #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 11:56:40: #1 tags after filtering in treatment: 4478865 INFO @ Tue, 04 Sep 2018 11:56:40: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 04 Sep 2018 11:56:40: #1 finished! INFO @ Tue, 04 Sep 2018 11:56:40: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:56:41: #2 number of paired peaks: 752 WARNING @ Tue, 04 Sep 2018 11:56:41: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Tue, 04 Sep 2018 11:56:41: start model_add_line... INFO @ Tue, 04 Sep 2018 11:56:41: start X-correlation... INFO @ Tue, 04 Sep 2018 11:56:41: end of X-cor INFO @ Tue, 04 Sep 2018 11:56:41: #2 finished! INFO @ Tue, 04 Sep 2018 11:56:41: #2 predicted fragment length is 157 bps INFO @ Tue, 04 Sep 2018 11:56:41: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 04 Sep 2018 11:56:41: #2.2 Generate R script for model : SRX4279688.20_model.r INFO @ Tue, 04 Sep 2018 11:56:41: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:56:42: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:56:43: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:56:50: #4 Write output xls file... SRX4279688.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:56:50: #4 Write peak in narrowPeak format file... SRX4279688.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:56:50: #4 Write summits bed file... SRX4279688.10_summits.bed INFO @ Tue, 04 Sep 2018 11:56:50: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1037 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:56:50: #4 Write output xls file... SRX4279688.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:56:50: #4 Write peak in narrowPeak format file... SRX4279688.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:56:50: #4 Write summits bed file... SRX4279688.05_summits.bed INFO @ Tue, 04 Sep 2018 11:56:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1428 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:56:52: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:56:58: #4 Write output xls file... SRX4279688.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:56:58: #4 Write peak in narrowPeak format file... SRX4279688.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:56:58: #4 Write summits bed file... SRX4279688.20_summits.bed INFO @ Tue, 04 Sep 2018 11:56:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (709 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。