Job ID = 10714547 sra ファイルのダウンロード中... Completed: 1961636K bytes transferred in 12 seconds (1296183K 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 33313025 spots for /home/okishinya/chipatlas/results/dm3/SRX1704850/SRR3383184.sra Written 33313025 spots for /home/okishinya/chipatlas/results/dm3/SRX1704850/SRR3383184.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: 01:20:02 33313025 reads; of these: 33313025 (100.00%) were paired; of these: 6103018 (18.32%) aligned concordantly 0 times 20203563 (60.65%) aligned concordantly exactly 1 time 7006444 (21.03%) aligned concordantly >1 times ---- 6103018 pairs aligned concordantly 0 times; of these: 2327431 (38.14%) aligned discordantly 1 time ---- 3775587 pairs aligned 0 times concordantly or discordantly; of these: 7551174 mates make up the pairs; of these: 4233813 (56.07%) aligned 0 times 1749290 (23.17%) aligned exactly 1 time 1568071 (20.77%) aligned >1 times 93.65% overall alignment rate Time searching: 01:20:02 Overall time: 01:20:02 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 28 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] 12383906 / 29447626 = 0.4205 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 @ Sun, 03 Jun 2018 14:57:39: # Command line: callpeak -t SRX1704850.bam -f BAM -g dm -n SRX1704850.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1704850.05 # format = BAM # ChIP-seq file = ['SRX1704850.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 @ Sun, 03 Jun 2018 14:57:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:57:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:57:39: # Command line: callpeak -t SRX1704850.bam -f BAM -g dm -n SRX1704850.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1704850.10 # format = BAM # ChIP-seq file = ['SRX1704850.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 @ Sun, 03 Jun 2018 14:57:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:57:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:57:39: # Command line: callpeak -t SRX1704850.bam -f BAM -g dm -n SRX1704850.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1704850.20 # format = BAM # ChIP-seq file = ['SRX1704850.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 @ Sun, 03 Jun 2018 14:57:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:57:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:57:44: 1000000 INFO @ Sun, 03 Jun 2018 14:57:45: 1000000 INFO @ Sun, 03 Jun 2018 14:57:45: 1000000 INFO @ Sun, 03 Jun 2018 14:57:50: 2000000 INFO @ Sun, 03 Jun 2018 14:57:51: 2000000 INFO @ Sun, 03 Jun 2018 14:57:51: 2000000 INFO @ Sun, 03 Jun 2018 14:57:56: 3000000 INFO @ Sun, 03 Jun 2018 14:57:57: 3000000 INFO @ Sun, 03 Jun 2018 14:57:57: 3000000 INFO @ Sun, 03 Jun 2018 14:58:02: 4000000 INFO @ Sun, 03 Jun 2018 14:58:03: 4000000 INFO @ Sun, 03 Jun 2018 14:58:03: 4000000 INFO @ Sun, 03 Jun 2018 14:58:07: 5000000 INFO @ Sun, 03 Jun 2018 14:58:09: 5000000 INFO @ Sun, 03 Jun 2018 14:58:09: 5000000 INFO @ Sun, 03 Jun 2018 14:58:13: 6000000 INFO @ Sun, 03 Jun 2018 14:58:15: 6000000 INFO @ Sun, 03 Jun 2018 14:58:15: 6000000 INFO @ Sun, 03 Jun 2018 14:58:19: 7000000 INFO @ Sun, 03 Jun 2018 14:58:21: 7000000 INFO @ Sun, 03 Jun 2018 14:58:21: 7000000 INFO @ Sun, 03 Jun 2018 14:58:25: 8000000 INFO @ Sun, 03 Jun 2018 14:58:27: 8000000 INFO @ Sun, 03 Jun 2018 14:58:27: 8000000 INFO @ Sun, 03 Jun 2018 14:58:31: 9000000 INFO @ Sun, 03 Jun 2018 14:58:33: 9000000 INFO @ Sun, 03 Jun 2018 14:58:33: 9000000 INFO @ Sun, 03 Jun 2018 14:58:36: 10000000 INFO @ Sun, 03 Jun 2018 14:58:39: 10000000 INFO @ Sun, 03 Jun 2018 14:58:39: 10000000 INFO @ Sun, 03 Jun 2018 14:58:42: 11000000 INFO @ Sun, 03 Jun 2018 14:58:45: 11000000 INFO @ Sun, 03 Jun 2018 14:58:45: 11000000 INFO @ Sun, 03 Jun 2018 14:58:48: 12000000 INFO @ Sun, 03 Jun 2018 14:58:51: 12000000 INFO @ Sun, 03 Jun 2018 14:58:51: 12000000 INFO @ Sun, 03 Jun 2018 14:58:54: 13000000 INFO @ Sun, 03 Jun 2018 14:58:58: 13000000 INFO @ Sun, 03 Jun 2018 14:58:58: 13000000 INFO @ Sun, 03 Jun 2018 14:59:00: 14000000 INFO @ Sun, 03 Jun 2018 14:59:03: 14000000 INFO @ Sun, 03 Jun 2018 14:59:04: 14000000 INFO @ Sun, 03 Jun 2018 14:59:06: 15000000 INFO @ Sun, 03 Jun 2018 14:59:09: 15000000 INFO @ Sun, 03 Jun 2018 14:59:10: 15000000 INFO @ Sun, 03 Jun 2018 14:59:12: 16000000 INFO @ Sun, 03 Jun 2018 14:59:15: 16000000 INFO @ Sun, 03 Jun 2018 14:59:16: 16000000 INFO @ Sun, 03 Jun 2018 14:59:18: 17000000 INFO @ Sun, 03 Jun 2018 14:59:21: 17000000 INFO @ Sun, 03 Jun 2018 14:59:22: 17000000 INFO @ Sun, 03 Jun 2018 14:59:24: 18000000 INFO @ Sun, 03 Jun 2018 14:59:27: 18000000 INFO @ Sun, 03 Jun 2018 14:59:29: 18000000 INFO @ Sun, 03 Jun 2018 14:59:30: 19000000 INFO @ Sun, 03 Jun 2018 14:59:32: 19000000 INFO @ Sun, 03 Jun 2018 14:59:35: 19000000 INFO @ Sun, 03 Jun 2018 14:59:37: 20000000 INFO @ Sun, 03 Jun 2018 14:59:38: 20000000 INFO @ Sun, 03 Jun 2018 14:59:41: 20000000 INFO @ Sun, 03 Jun 2018 14:59:43: 21000000 INFO @ Sun, 03 Jun 2018 14:59:44: 21000000 INFO @ Sun, 03 Jun 2018 14:59:47: 21000000 INFO @ Sun, 03 Jun 2018 14:59:49: 22000000 INFO @ Sun, 03 Jun 2018 14:59:50: 22000000 INFO @ Sun, 03 Jun 2018 14:59:54: 22000000 INFO @ Sun, 03 Jun 2018 14:59:55: 23000000 INFO @ Sun, 03 Jun 2018 14:59:55: 23000000 INFO @ Sun, 03 Jun 2018 15:00:00: 23000000 INFO @ Sun, 03 Jun 2018 15:00:01: 24000000 INFO @ Sun, 03 Jun 2018 15:00:01: 24000000 INFO @ Sun, 03 Jun 2018 15:00:06: 24000000 INFO @ Sun, 03 Jun 2018 15:00:07: 25000000 INFO @ Sun, 03 Jun 2018 15:00:07: 25000000 INFO @ Sun, 03 Jun 2018 15:00:11: 25000000 INFO @ Sun, 03 Jun 2018 15:00:13: 26000000 INFO @ Sun, 03 Jun 2018 15:00:13: 26000000 INFO @ Sun, 03 Jun 2018 15:00:17: 26000000 INFO @ Sun, 03 Jun 2018 15:00:19: 27000000 INFO @ Sun, 03 Jun 2018 15:00:19: 27000000 INFO @ Sun, 03 Jun 2018 15:00:23: 27000000 INFO @ Sun, 03 Jun 2018 15:00:25: 28000000 INFO @ Sun, 03 Jun 2018 15:00:25: 28000000 INFO @ Sun, 03 Jun 2018 15:00:29: 28000000 INFO @ Sun, 03 Jun 2018 15:00:31: 29000000 INFO @ Sun, 03 Jun 2018 15:00:32: 29000000 INFO @ Sun, 03 Jun 2018 15:00:35: 29000000 INFO @ Sun, 03 Jun 2018 15:00:37: 30000000 INFO @ Sun, 03 Jun 2018 15:00:39: 30000000 INFO @ Sun, 03 Jun 2018 15:00:41: 30000000 INFO @ Sun, 03 Jun 2018 15:00:42: 31000000 INFO @ Sun, 03 Jun 2018 15:00:46: 31000000 INFO @ Sun, 03 Jun 2018 15:00:48: 31000000 INFO @ Sun, 03 Jun 2018 15:00:48: 32000000 INFO @ Sun, 03 Jun 2018 15:00:53: 32000000 INFO @ Sun, 03 Jun 2018 15:00:54: 32000000 INFO @ Sun, 03 Jun 2018 15:00:54: 33000000 INFO @ Sun, 03 Jun 2018 15:01:00: 34000000 INFO @ Sun, 03 Jun 2018 15:01:00: 33000000 INFO @ Sun, 03 Jun 2018 15:01:01: 33000000 INFO @ Sun, 03 Jun 2018 15:01:06: 35000000 INFO @ Sun, 03 Jun 2018 15:01:06: 34000000 INFO @ Sun, 03 Jun 2018 15:01:08: 34000000 INFO @ Sun, 03 Jun 2018 15:01:12: 36000000 INFO @ Sun, 03 Jun 2018 15:01:13: 35000000 INFO @ Sun, 03 Jun 2018 15:01:15: 35000000 INFO @ Sun, 03 Jun 2018 15:01:17: 37000000 INFO @ Sun, 03 Jun 2018 15:01:19: 36000000 INFO @ Sun, 03 Jun 2018 15:01:21: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 15:01:21: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 15:01:21: #1 total tags in treatment: 15459710 INFO @ Sun, 03 Jun 2018 15:01:21: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 15:01:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 15:01:22: #1 tags after filtering in treatment: 12640439 INFO @ Sun, 03 Jun 2018 15:01:22: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 15:01:22: #1 finished! INFO @ Sun, 03 Jun 2018 15:01:22: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 15:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 15:01:22: #2 number of paired peaks: 440 WARNING @ Sun, 03 Jun 2018 15:01:22: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Sun, 03 Jun 2018 15:01:22: start model_add_line... INFO @ Sun, 03 Jun 2018 15:01:23: start X-correlation... INFO @ Sun, 03 Jun 2018 15:01:23: end of X-cor INFO @ Sun, 03 Jun 2018 15:01:23: #2 finished! INFO @ Sun, 03 Jun 2018 15:01:23: #2 predicted fragment length is 194 bps INFO @ Sun, 03 Jun 2018 15:01:23: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 03 Jun 2018 15:01:23: #2.2 Generate R script for model : SRX1704850.20_model.r INFO @ Sun, 03 Jun 2018 15:01:23: #3 Call peaks... INFO @ Sun, 03 Jun 2018 15:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 15:01:23: 36000000 INFO @ Sun, 03 Jun 2018 15:01:25: 37000000 INFO @ Sun, 03 Jun 2018 15:01:29: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 15:01:29: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 15:01:29: #1 total tags in treatment: 15459710 INFO @ Sun, 03 Jun 2018 15:01:29: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 15:01:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 15:01:29: #1 tags after filtering in treatment: 12640439 INFO @ Sun, 03 Jun 2018 15:01:29: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 15:01:29: #1 finished! INFO @ Sun, 03 Jun 2018 15:01:29: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 15:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 15:01:30: #2 number of paired peaks: 440 WARNING @ Sun, 03 Jun 2018 15:01:30: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Sun, 03 Jun 2018 15:01:30: start model_add_line... INFO @ Sun, 03 Jun 2018 15:01:30: 37000000 INFO @ Sun, 03 Jun 2018 15:01:30: start X-correlation... INFO @ Sun, 03 Jun 2018 15:01:30: end of X-cor INFO @ Sun, 03 Jun 2018 15:01:30: #2 finished! INFO @ Sun, 03 Jun 2018 15:01:30: #2 predicted fragment length is 194 bps INFO @ Sun, 03 Jun 2018 15:01:30: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 03 Jun 2018 15:01:30: #2.2 Generate R script for model : SRX1704850.05_model.r INFO @ Sun, 03 Jun 2018 15:01:30: #3 Call peaks... INFO @ Sun, 03 Jun 2018 15:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 15:01:35: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 15:01:35: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 15:01:35: #1 total tags in treatment: 15459710 INFO @ Sun, 03 Jun 2018 15:01:35: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 15:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 15:01:35: #1 tags after filtering in treatment: 12640439 INFO @ Sun, 03 Jun 2018 15:01:35: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 15:01:35: #1 finished! INFO @ Sun, 03 Jun 2018 15:01:35: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 15:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 15:01:37: #2 number of paired peaks: 440 WARNING @ Sun, 03 Jun 2018 15:01:37: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Sun, 03 Jun 2018 15:01:37: start model_add_line... INFO @ Sun, 03 Jun 2018 15:01:37: start X-correlation... INFO @ Sun, 03 Jun 2018 15:01:37: end of X-cor INFO @ Sun, 03 Jun 2018 15:01:37: #2 finished! INFO @ Sun, 03 Jun 2018 15:01:37: #2 predicted fragment length is 194 bps INFO @ Sun, 03 Jun 2018 15:01:37: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 03 Jun 2018 15:01:37: #2.2 Generate R script for model : SRX1704850.10_model.r INFO @ Sun, 03 Jun 2018 15:01:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 15:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 15:01:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 15:02:01: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 15:02:07: #4 Write output xls file... SRX1704850.20_peaks.xls INFO @ Sun, 03 Jun 2018 15:02:07: #4 Write peak in narrowPeak format file... SRX1704850.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 15:02:07: #4 Write summits bed file... SRX1704850.20_summits.bed INFO @ Sun, 03 Jun 2018 15:02:07: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (752 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 15:02:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 15:02:18: #4 Write output xls file... SRX1704850.05_peaks.xls INFO @ Sun, 03 Jun 2018 15:02:18: #4 Write peak in narrowPeak format file... SRX1704850.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 15:02:18: #4 Write summits bed file... SRX1704850.05_summits.bed INFO @ Sun, 03 Jun 2018 15:02:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2564 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 15:02:29: #4 Write output xls file... SRX1704850.10_peaks.xls INFO @ Sun, 03 Jun 2018 15:02:29: #4 Write peak in narrowPeak format file... SRX1704850.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 15:02:29: #4 Write summits bed file... SRX1704850.10_summits.bed INFO @ Sun, 03 Jun 2018 15:02:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1373 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。