Job ID = 11171255 sra ファイルのダウンロード中... Completed: 2098070K bytes transferred in 66 seconds (260017K 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 31814615 spots for /home/okishinya/chipatlas/results/dm3/SRX2982442/SRR5803103.sra Written 31814615 spots for /home/okishinya/chipatlas/results/dm3/SRX2982442/SRR5803103.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: 01:10:42 31814615 reads; of these: 31814615 (100.00%) were paired; of these: 4135252 (13.00%) aligned concordantly 0 times 23306553 (73.26%) aligned concordantly exactly 1 time 4372810 (13.74%) aligned concordantly >1 times ---- 4135252 pairs aligned concordantly 0 times; of these: 25604 (0.62%) aligned discordantly 1 time ---- 4109648 pairs aligned 0 times concordantly or discordantly; of these: 8219296 mates make up the pairs; of these: 6923924 (84.24%) aligned 0 times 875513 (10.65%) aligned exactly 1 time 419859 (5.11%) aligned >1 times 89.12% overall alignment rate Time searching: 01:10:42 Overall time: 01:10:42 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 24 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] 14949808 / 27681168 = 0.5401 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 @ Sat, 08 Sep 2018 14:47:47: # Command line: callpeak -t SRX2982442.bam -f BAM -g dm -n SRX2982442.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2982442.20 # format = BAM # ChIP-seq file = ['SRX2982442.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 @ Sat, 08 Sep 2018 14:47:47: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:47:47: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:47:47: # Command line: callpeak -t SRX2982442.bam -f BAM -g dm -n SRX2982442.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2982442.05 # format = BAM # ChIP-seq file = ['SRX2982442.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 @ Sat, 08 Sep 2018 14:47:47: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:47:47: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:47:47: # Command line: callpeak -t SRX2982442.bam -f BAM -g dm -n SRX2982442.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2982442.10 # format = BAM # ChIP-seq file = ['SRX2982442.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 @ Sat, 08 Sep 2018 14:47:47: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:47:47: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:47:55: 1000000 INFO @ Sat, 08 Sep 2018 14:47:55: 1000000 INFO @ Sat, 08 Sep 2018 14:47:55: 1000000 INFO @ Sat, 08 Sep 2018 14:48:02: 2000000 INFO @ Sat, 08 Sep 2018 14:48:03: 2000000 INFO @ Sat, 08 Sep 2018 14:48:03: 2000000 INFO @ Sat, 08 Sep 2018 14:48:09: 3000000 INFO @ Sat, 08 Sep 2018 14:48:11: 3000000 INFO @ Sat, 08 Sep 2018 14:48:11: 3000000 INFO @ Sat, 08 Sep 2018 14:48:16: 4000000 INFO @ Sat, 08 Sep 2018 14:48:19: 4000000 INFO @ Sat, 08 Sep 2018 14:48:19: 4000000 INFO @ Sat, 08 Sep 2018 14:48:24: 5000000 INFO @ Sat, 08 Sep 2018 14:48:27: 5000000 INFO @ Sat, 08 Sep 2018 14:48:27: 5000000 INFO @ Sat, 08 Sep 2018 14:48:31: 6000000 INFO @ Sat, 08 Sep 2018 14:48:35: 6000000 INFO @ Sat, 08 Sep 2018 14:48:35: 6000000 INFO @ Sat, 08 Sep 2018 14:48:39: 7000000 INFO @ Sat, 08 Sep 2018 14:48:43: 7000000 INFO @ Sat, 08 Sep 2018 14:48:43: 7000000 INFO @ Sat, 08 Sep 2018 14:48:46: 8000000 INFO @ Sat, 08 Sep 2018 14:48:50: 8000000 INFO @ Sat, 08 Sep 2018 14:48:50: 8000000 INFO @ Sat, 08 Sep 2018 14:48:53: 9000000 INFO @ Sat, 08 Sep 2018 14:48:58: 9000000 INFO @ Sat, 08 Sep 2018 14:48:58: 9000000 INFO @ Sat, 08 Sep 2018 14:49:01: 10000000 INFO @ Sat, 08 Sep 2018 14:49:06: 10000000 INFO @ Sat, 08 Sep 2018 14:49:06: 10000000 INFO @ Sat, 08 Sep 2018 14:49:08: 11000000 INFO @ Sat, 08 Sep 2018 14:49:14: 11000000 INFO @ Sat, 08 Sep 2018 14:49:14: 11000000 INFO @ Sat, 08 Sep 2018 14:49:16: 12000000 INFO @ Sat, 08 Sep 2018 14:49:21: 12000000 INFO @ Sat, 08 Sep 2018 14:49:21: 12000000 INFO @ Sat, 08 Sep 2018 14:49:23: 13000000 INFO @ Sat, 08 Sep 2018 14:49:29: 13000000 INFO @ Sat, 08 Sep 2018 14:49:29: 13000000 INFO @ Sat, 08 Sep 2018 14:49:31: 14000000 INFO @ Sat, 08 Sep 2018 14:49:37: 14000000 INFO @ Sat, 08 Sep 2018 14:49:37: 14000000 INFO @ Sat, 08 Sep 2018 14:49:38: 15000000 INFO @ Sat, 08 Sep 2018 14:49:45: 15000000 INFO @ Sat, 08 Sep 2018 14:49:45: 15000000 INFO @ Sat, 08 Sep 2018 14:49:45: 16000000 INFO @ Sat, 08 Sep 2018 14:49:53: 16000000 INFO @ Sat, 08 Sep 2018 14:49:53: 16000000 INFO @ Sat, 08 Sep 2018 14:49:53: 17000000 INFO @ Sat, 08 Sep 2018 14:50:00: 17000000 INFO @ Sat, 08 Sep 2018 14:50:00: 17000000 INFO @ Sat, 08 Sep 2018 14:50:00: 18000000 INFO @ Sat, 08 Sep 2018 14:50:08: 19000000 INFO @ Sat, 08 Sep 2018 14:50:08: 18000000 INFO @ Sat, 08 Sep 2018 14:50:08: 18000000 INFO @ Sat, 08 Sep 2018 14:50:15: 20000000 INFO @ Sat, 08 Sep 2018 14:50:16: 19000000 INFO @ Sat, 08 Sep 2018 14:50:16: 19000000 INFO @ Sat, 08 Sep 2018 14:50:23: 21000000 INFO @ Sat, 08 Sep 2018 14:50:24: 20000000 INFO @ Sat, 08 Sep 2018 14:50:24: 20000000 INFO @ Sat, 08 Sep 2018 14:50:30: 22000000 INFO @ Sat, 08 Sep 2018 14:50:31: 21000000 INFO @ Sat, 08 Sep 2018 14:50:31: 21000000 INFO @ Sat, 08 Sep 2018 14:50:38: 23000000 INFO @ Sat, 08 Sep 2018 14:50:39: 22000000 INFO @ Sat, 08 Sep 2018 14:50:39: 22000000 INFO @ Sat, 08 Sep 2018 14:50:45: 24000000 INFO @ Sat, 08 Sep 2018 14:50:47: 23000000 INFO @ Sat, 08 Sep 2018 14:50:47: 23000000 INFO @ Sat, 08 Sep 2018 14:50:53: 25000000 INFO @ Sat, 08 Sep 2018 14:50:55: 24000000 INFO @ Sat, 08 Sep 2018 14:50:55: 24000000 INFO @ Sat, 08 Sep 2018 14:51:00: 26000000 INFO @ Sat, 08 Sep 2018 14:51:03: 25000000 INFO @ Sat, 08 Sep 2018 14:51:03: 25000000 INFO @ Sat, 08 Sep 2018 14:51:06: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:51:06: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:51:06: #1 total tags in treatment: 12739660 INFO @ Sat, 08 Sep 2018 14:51:06: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:51:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:51:07: #1 tags after filtering in treatment: 12095162 INFO @ Sat, 08 Sep 2018 14:51:07: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 08 Sep 2018 14:51:07: #1 finished! INFO @ Sat, 08 Sep 2018 14:51:07: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:51:08: #2 number of paired peaks: 164 WARNING @ Sat, 08 Sep 2018 14:51:08: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 08 Sep 2018 14:51:08: start model_add_line... INFO @ Sat, 08 Sep 2018 14:51:08: start X-correlation... INFO @ Sat, 08 Sep 2018 14:51:08: end of X-cor INFO @ Sat, 08 Sep 2018 14:51:08: #2 finished! INFO @ Sat, 08 Sep 2018 14:51:08: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Sep 2018 14:51:08: #2 alternative fragment length(s) may be 2,192,524 bps INFO @ Sat, 08 Sep 2018 14:51:08: #2.2 Generate R script for model : SRX2982442.10_model.r INFO @ Sat, 08 Sep 2018 14:51:08: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:51:11: 26000000 INFO @ Sat, 08 Sep 2018 14:51:11: 26000000 INFO @ Sat, 08 Sep 2018 14:51:17: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:51:17: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:51:17: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:51:17: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:51:17: #1 total tags in treatment: 12739660 INFO @ Sat, 08 Sep 2018 14:51:17: #1 total tags in treatment: 12739660 INFO @ Sat, 08 Sep 2018 14:51:17: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:51:17: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:51:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:51:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:51:17: #1 tags after filtering in treatment: 12095162 INFO @ Sat, 08 Sep 2018 14:51:17: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 08 Sep 2018 14:51:17: #1 finished! INFO @ Sat, 08 Sep 2018 14:51:17: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:51:17: #1 tags after filtering in treatment: 12095162 INFO @ Sat, 08 Sep 2018 14:51:17: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 08 Sep 2018 14:51:17: #1 finished! INFO @ Sat, 08 Sep 2018 14:51:17: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:51:18: #2 number of paired peaks: 164 WARNING @ Sat, 08 Sep 2018 14:51:18: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 08 Sep 2018 14:51:18: start model_add_line... INFO @ Sat, 08 Sep 2018 14:51:18: #2 number of paired peaks: 164 WARNING @ Sat, 08 Sep 2018 14:51:18: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 08 Sep 2018 14:51:18: start model_add_line... INFO @ Sat, 08 Sep 2018 14:51:18: start X-correlation... INFO @ Sat, 08 Sep 2018 14:51:18: end of X-cor INFO @ Sat, 08 Sep 2018 14:51:18: #2 finished! INFO @ Sat, 08 Sep 2018 14:51:18: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Sep 2018 14:51:18: #2 alternative fragment length(s) may be 2,192,524 bps INFO @ Sat, 08 Sep 2018 14:51:18: #2.2 Generate R script for model : SRX2982442.20_model.r INFO @ Sat, 08 Sep 2018 14:51:18: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:51:18: start X-correlation... INFO @ Sat, 08 Sep 2018 14:51:18: end of X-cor INFO @ Sat, 08 Sep 2018 14:51:18: #2 finished! INFO @ Sat, 08 Sep 2018 14:51:18: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Sep 2018 14:51:18: #2 alternative fragment length(s) may be 2,192,524 bps INFO @ Sat, 08 Sep 2018 14:51:18: #2.2 Generate R script for model : SRX2982442.05_model.r INFO @ Sat, 08 Sep 2018 14:51:18: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:51:37: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:51:45: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:51:46: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:51:51: #4 Write output xls file... SRX2982442.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:51:51: #4 Write peak in narrowPeak format file... SRX2982442.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:51:51: #4 Write summits bed file... SRX2982442.10_summits.bed INFO @ Sat, 08 Sep 2018 14:51:51: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (793 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:52:00: #4 Write output xls file... SRX2982442.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:52:00: #4 Write peak in narrowPeak format file... SRX2982442.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:52:00: #4 Write summits bed file... SRX2982442.20_summits.bed INFO @ Sat, 08 Sep 2018 14:52:00: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:52:02: #4 Write output xls file... SRX2982442.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:52:02: #4 Write peak in narrowPeak format file... SRX2982442.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:52:02: #4 Write summits bed file... SRX2982442.05_summits.bed INFO @ Sat, 08 Sep 2018 14:52:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2111 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。