Job ID = 10845212 sra ファイルのダウンロード中... Completed: 274935K bytes transferred in 29 seconds (76805K bits/sec), in 1 file. Completed: 276938K bytes transferred in 5 seconds (397265K 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 4725851 spots for /home/okishinya/chipatlas/results/dm3/SRX3632908/SRR6655551.sra Written 4725851 spots for /home/okishinya/chipatlas/results/dm3/SRX3632908/SRR6655551.sra Read 5152228 spots for /home/okishinya/chipatlas/results/dm3/SRX3632908/SRR6655552.sra Written 5152228 spots for /home/okishinya/chipatlas/results/dm3/SRX3632908/SRR6655552.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 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: 00:18:26 9878079 reads; of these: 9878079 (100.00%) were paired; of these: 991040 (10.03%) aligned concordantly 0 times 8056538 (81.56%) aligned concordantly exactly 1 time 830501 (8.41%) aligned concordantly >1 times ---- 991040 pairs aligned concordantly 0 times; of these: 407715 (41.14%) aligned discordantly 1 time ---- 583325 pairs aligned 0 times concordantly or discordantly; of these: 1166650 mates make up the pairs; of these: 694208 (59.50%) aligned 0 times 343671 (29.46%) aligned exactly 1 time 128771 (11.04%) aligned >1 times 96.49% overall alignment rate Time searching: 00:18:26 Overall time: 00:18:26 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 8 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] 427341 / 9204998 = 0.0464 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 @ Wed, 04 Jul 2018 09:52:35: # Command line: callpeak -t SRX3632908.bam -f BAM -g dm -n SRX3632908.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632908.20 # format = BAM # ChIP-seq file = ['SRX3632908.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 @ Wed, 04 Jul 2018 09:52:35: # Command line: callpeak -t SRX3632908.bam -f BAM -g dm -n SRX3632908.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632908.10 # format = BAM # ChIP-seq file = ['SRX3632908.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 @ Wed, 04 Jul 2018 09:52:35: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:52:35: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:52:35: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:52:35: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:52:35: # Command line: callpeak -t SRX3632908.bam -f BAM -g dm -n SRX3632908.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632908.05 # format = BAM # ChIP-seq file = ['SRX3632908.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 @ Wed, 04 Jul 2018 09:52:35: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:52:35: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:52:42: 1000000 INFO @ Wed, 04 Jul 2018 09:52:42: 1000000 INFO @ Wed, 04 Jul 2018 09:52:42: 1000000 INFO @ Wed, 04 Jul 2018 09:52:48: 2000000 INFO @ Wed, 04 Jul 2018 09:52:49: 2000000 INFO @ Wed, 04 Jul 2018 09:52:49: 2000000 INFO @ Wed, 04 Jul 2018 09:52:54: 3000000 INFO @ Wed, 04 Jul 2018 09:52:56: 3000000 INFO @ Wed, 04 Jul 2018 09:52:56: 3000000 INFO @ Wed, 04 Jul 2018 09:53:01: 4000000 INFO @ Wed, 04 Jul 2018 09:53:03: 4000000 INFO @ Wed, 04 Jul 2018 09:53:03: 4000000 INFO @ Wed, 04 Jul 2018 09:53:07: 5000000 INFO @ Wed, 04 Jul 2018 09:53:10: 5000000 INFO @ Wed, 04 Jul 2018 09:53:11: 5000000 INFO @ Wed, 04 Jul 2018 09:53:13: 6000000 INFO @ Wed, 04 Jul 2018 09:53:17: 6000000 INFO @ Wed, 04 Jul 2018 09:53:18: 6000000 INFO @ Wed, 04 Jul 2018 09:53:20: 7000000 INFO @ Wed, 04 Jul 2018 09:53:24: 7000000 INFO @ Wed, 04 Jul 2018 09:53:26: 7000000 INFO @ Wed, 04 Jul 2018 09:53:26: 8000000 INFO @ Wed, 04 Jul 2018 09:53:32: 8000000 INFO @ Wed, 04 Jul 2018 09:53:32: 9000000 INFO @ Wed, 04 Jul 2018 09:53:33: 8000000 INFO @ Wed, 04 Jul 2018 09:53:39: 10000000 INFO @ Wed, 04 Jul 2018 09:53:39: 9000000 INFO @ Wed, 04 Jul 2018 09:53:41: 9000000 INFO @ Wed, 04 Jul 2018 09:53:45: 11000000 INFO @ Wed, 04 Jul 2018 09:53:46: 10000000 INFO @ Wed, 04 Jul 2018 09:53:48: 10000000 INFO @ Wed, 04 Jul 2018 09:53:52: 12000000 INFO @ Wed, 04 Jul 2018 09:53:53: 11000000 INFO @ Wed, 04 Jul 2018 09:53:56: 11000000 INFO @ Wed, 04 Jul 2018 09:53:59: 13000000 INFO @ Wed, 04 Jul 2018 09:53:59: 12000000 INFO @ Wed, 04 Jul 2018 09:54:05: 12000000 INFO @ Wed, 04 Jul 2018 09:54:06: 13000000 INFO @ Wed, 04 Jul 2018 09:54:06: 14000000 INFO @ Wed, 04 Jul 2018 09:54:12: 14000000 INFO @ Wed, 04 Jul 2018 09:54:13: 15000000 INFO @ Wed, 04 Jul 2018 09:54:13: 13000000 INFO @ Wed, 04 Jul 2018 09:54:19: 15000000 INFO @ Wed, 04 Jul 2018 09:54:20: 16000000 INFO @ Wed, 04 Jul 2018 09:54:21: 14000000 INFO @ Wed, 04 Jul 2018 09:54:25: 16000000 INFO @ Wed, 04 Jul 2018 09:54:27: 17000000 INFO @ Wed, 04 Jul 2018 09:54:30: 15000000 INFO @ Wed, 04 Jul 2018 09:54:32: 17000000 INFO @ Wed, 04 Jul 2018 09:54:34: 18000000 INFO @ Wed, 04 Jul 2018 09:54:36: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:54:36: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:54:36: #1 total tags in treatment: 8475110 INFO @ Wed, 04 Jul 2018 09:54:36: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:54:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:54:36: #1 tags after filtering in treatment: 7510961 INFO @ Wed, 04 Jul 2018 09:54:36: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 04 Jul 2018 09:54:36: #1 finished! INFO @ Wed, 04 Jul 2018 09:54:36: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:54:36: #2 number of paired peaks: 687 WARNING @ Wed, 04 Jul 2018 09:54:36: Fewer paired peaks (687) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 687 pairs to build model! INFO @ Wed, 04 Jul 2018 09:54:36: start model_add_line... INFO @ Wed, 04 Jul 2018 09:54:37: start X-correlation... INFO @ Wed, 04 Jul 2018 09:54:37: end of X-cor INFO @ Wed, 04 Jul 2018 09:54:37: #2 finished! INFO @ Wed, 04 Jul 2018 09:54:37: #2 predicted fragment length is 150 bps INFO @ Wed, 04 Jul 2018 09:54:37: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 04 Jul 2018 09:54:37: #2.2 Generate R script for model : SRX3632908.05_model.r INFO @ Wed, 04 Jul 2018 09:54:37: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:54:38: 16000000 INFO @ Wed, 04 Jul 2018 09:54:38: 18000000 INFO @ Wed, 04 Jul 2018 09:54:40: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:54:40: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:54:40: #1 total tags in treatment: 8475110 INFO @ Wed, 04 Jul 2018 09:54:40: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:54:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:54:40: #1 tags after filtering in treatment: 7510961 INFO @ Wed, 04 Jul 2018 09:54:40: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 04 Jul 2018 09:54:40: #1 finished! INFO @ Wed, 04 Jul 2018 09:54:40: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:54:40: #2 number of paired peaks: 687 WARNING @ Wed, 04 Jul 2018 09:54:40: Fewer paired peaks (687) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 687 pairs to build model! INFO @ Wed, 04 Jul 2018 09:54:40: start model_add_line... INFO @ Wed, 04 Jul 2018 09:54:40: start X-correlation... INFO @ Wed, 04 Jul 2018 09:54:40: end of X-cor INFO @ Wed, 04 Jul 2018 09:54:40: #2 finished! INFO @ Wed, 04 Jul 2018 09:54:40: #2 predicted fragment length is 150 bps INFO @ Wed, 04 Jul 2018 09:54:40: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 04 Jul 2018 09:54:40: #2.2 Generate R script for model : SRX3632908.20_model.r INFO @ Wed, 04 Jul 2018 09:54:40: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:54:45: 17000000 INFO @ Wed, 04 Jul 2018 09:54:52: 18000000 INFO @ Wed, 04 Jul 2018 09:54:53: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:54:53: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:54:53: #1 total tags in treatment: 8475110 INFO @ Wed, 04 Jul 2018 09:54:53: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:54:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:54:53: #1 tags after filtering in treatment: 7510961 INFO @ Wed, 04 Jul 2018 09:54:53: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 04 Jul 2018 09:54:53: #1 finished! INFO @ Wed, 04 Jul 2018 09:54:53: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:54:54: #2 number of paired peaks: 687 WARNING @ Wed, 04 Jul 2018 09:54:54: Fewer paired peaks (687) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 687 pairs to build model! INFO @ Wed, 04 Jul 2018 09:54:54: start model_add_line... INFO @ Wed, 04 Jul 2018 09:54:54: start X-correlation... INFO @ Wed, 04 Jul 2018 09:54:54: end of X-cor INFO @ Wed, 04 Jul 2018 09:54:54: #2 finished! INFO @ Wed, 04 Jul 2018 09:54:54: #2 predicted fragment length is 150 bps INFO @ Wed, 04 Jul 2018 09:54:54: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 04 Jul 2018 09:54:54: #2.2 Generate R script for model : SRX3632908.10_model.r INFO @ Wed, 04 Jul 2018 09:54:54: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:54:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:54:56: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:55:00: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:55:08: #4 Write output xls file... SRX3632908.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:55:08: #4 Write peak in narrowPeak format file... SRX3632908.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:55:08: #4 Write summits bed file... SRX3632908.05_summits.bed INFO @ Wed, 04 Jul 2018 09:55:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5539 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:55:10: #4 Write output xls file... SRX3632908.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:55:10: #4 Write peak in narrowPeak format file... SRX3632908.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:55:10: #4 Write summits bed file... SRX3632908.20_summits.bed INFO @ Wed, 04 Jul 2018 09:55:10: Done! pass1 - making usageList (12 chroms): 6 millis pass2 - checking and writing primary data (716 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:55:13: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:55:23: #4 Write output xls file... SRX3632908.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:55:23: #4 Write peak in narrowPeak format file... SRX3632908.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:55:23: #4 Write summits bed file... SRX3632908.10_summits.bed INFO @ Wed, 04 Jul 2018 09:55:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2803 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。