Job ID = 10714516 sra ファイルのダウンロード中... Completed: 1154364K bytes transferred in 18 seconds (501321K 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 16787610 spots for /home/okishinya/chipatlas/results/ce10/SRX4085430/SRR7167459.sra Written 16787610 spots for /home/okishinya/chipatlas/results/ce10/SRX4085430/SRR7167459.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: 00:17:47 16787610 reads; of these: 16787610 (100.00%) were paired; of these: 920102 (5.48%) aligned concordantly 0 times 13816079 (82.30%) aligned concordantly exactly 1 time 2051429 (12.22%) aligned concordantly >1 times ---- 920102 pairs aligned concordantly 0 times; of these: 97758 (10.62%) aligned discordantly 1 time ---- 822344 pairs aligned 0 times concordantly or discordantly; of these: 1644688 mates make up the pairs; of these: 1109813 (67.48%) aligned 0 times 416782 (25.34%) aligned exactly 1 time 118093 (7.18%) aligned >1 times 96.69% overall alignment rate Time searching: 00:17:47 Overall time: 00:17:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1739328 / 15935925 = 0.1091 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 13:33:11: # Command line: callpeak -t SRX4085430.bam -f BAM -g ce -n SRX4085430.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085430.20 # format = BAM # ChIP-seq file = ['SRX4085430.bam'] # control file = None # effective genome size = 9.00e+07 # 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 13:33:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:33:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:33:11: # Command line: callpeak -t SRX4085430.bam -f BAM -g ce -n SRX4085430.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085430.10 # format = BAM # ChIP-seq file = ['SRX4085430.bam'] # control file = None # effective genome size = 9.00e+07 # 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 13:33:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:33:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:33:11: # Command line: callpeak -t SRX4085430.bam -f BAM -g ce -n SRX4085430.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085430.05 # format = BAM # ChIP-seq file = ['SRX4085430.bam'] # control file = None # effective genome size = 9.00e+07 # 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 13:33:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:33:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:33:17: 1000000 INFO @ Sun, 03 Jun 2018 13:33:17: 1000000 INFO @ Sun, 03 Jun 2018 13:33:17: 1000000 INFO @ Sun, 03 Jun 2018 13:33:23: 2000000 INFO @ Sun, 03 Jun 2018 13:33:23: 2000000 INFO @ Sun, 03 Jun 2018 13:33:23: 2000000 INFO @ Sun, 03 Jun 2018 13:33:28: 3000000 INFO @ Sun, 03 Jun 2018 13:33:28: 3000000 INFO @ Sun, 03 Jun 2018 13:33:28: 3000000 INFO @ Sun, 03 Jun 2018 13:33:34: 4000000 INFO @ Sun, 03 Jun 2018 13:33:34: 4000000 INFO @ Sun, 03 Jun 2018 13:33:34: 4000000 INFO @ Sun, 03 Jun 2018 13:33:39: 5000000 INFO @ Sun, 03 Jun 2018 13:33:39: 5000000 INFO @ Sun, 03 Jun 2018 13:33:39: 5000000 INFO @ Sun, 03 Jun 2018 13:33:45: 6000000 INFO @ Sun, 03 Jun 2018 13:33:45: 6000000 INFO @ Sun, 03 Jun 2018 13:33:45: 6000000 INFO @ Sun, 03 Jun 2018 13:33:50: 7000000 INFO @ Sun, 03 Jun 2018 13:33:51: 7000000 INFO @ Sun, 03 Jun 2018 13:33:51: 7000000 INFO @ Sun, 03 Jun 2018 13:33:56: 8000000 INFO @ Sun, 03 Jun 2018 13:33:56: 8000000 INFO @ Sun, 03 Jun 2018 13:33:56: 8000000 INFO @ Sun, 03 Jun 2018 13:34:01: 9000000 INFO @ Sun, 03 Jun 2018 13:34:02: 9000000 INFO @ Sun, 03 Jun 2018 13:34:02: 9000000 INFO @ Sun, 03 Jun 2018 13:34:07: 10000000 INFO @ Sun, 03 Jun 2018 13:34:07: 10000000 INFO @ Sun, 03 Jun 2018 13:34:07: 10000000 INFO @ Sun, 03 Jun 2018 13:34:12: 11000000 INFO @ Sun, 03 Jun 2018 13:34:13: 11000000 INFO @ Sun, 03 Jun 2018 13:34:13: 11000000 INFO @ Sun, 03 Jun 2018 13:34:18: 12000000 INFO @ Sun, 03 Jun 2018 13:34:19: 12000000 INFO @ Sun, 03 Jun 2018 13:34:19: 12000000 INFO @ Sun, 03 Jun 2018 13:34:23: 13000000 INFO @ Sun, 03 Jun 2018 13:34:24: 13000000 INFO @ Sun, 03 Jun 2018 13:34:24: 13000000 INFO @ Sun, 03 Jun 2018 13:34:29: 14000000 INFO @ Sun, 03 Jun 2018 13:34:30: 14000000 INFO @ Sun, 03 Jun 2018 13:34:30: 14000000 INFO @ Sun, 03 Jun 2018 13:34:34: 15000000 INFO @ Sun, 03 Jun 2018 13:34:36: 15000000 INFO @ Sun, 03 Jun 2018 13:34:36: 15000000 INFO @ Sun, 03 Jun 2018 13:34:40: 16000000 INFO @ Sun, 03 Jun 2018 13:34:41: 16000000 INFO @ Sun, 03 Jun 2018 13:34:42: 16000000 INFO @ Sun, 03 Jun 2018 13:34:45: 17000000 INFO @ Sun, 03 Jun 2018 13:34:47: 17000000 INFO @ Sun, 03 Jun 2018 13:34:47: 17000000 INFO @ Sun, 03 Jun 2018 13:34:51: 18000000 INFO @ Sun, 03 Jun 2018 13:34:53: 18000000 INFO @ Sun, 03 Jun 2018 13:34:53: 18000000 INFO @ Sun, 03 Jun 2018 13:34:56: 19000000 INFO @ Sun, 03 Jun 2018 13:34:59: 19000000 INFO @ Sun, 03 Jun 2018 13:34:59: 19000000 INFO @ Sun, 03 Jun 2018 13:35:02: 20000000 INFO @ Sun, 03 Jun 2018 13:35:04: 20000000 INFO @ Sun, 03 Jun 2018 13:35:05: 20000000 INFO @ Sun, 03 Jun 2018 13:35:07: 21000000 INFO @ Sun, 03 Jun 2018 13:35:10: 21000000 INFO @ Sun, 03 Jun 2018 13:35:11: 21000000 INFO @ Sun, 03 Jun 2018 13:35:12: 22000000 INFO @ Sun, 03 Jun 2018 13:35:16: 22000000 INFO @ Sun, 03 Jun 2018 13:35:17: 22000000 INFO @ Sun, 03 Jun 2018 13:35:18: 23000000 INFO @ Sun, 03 Jun 2018 13:35:22: 23000000 INFO @ Sun, 03 Jun 2018 13:35:23: 23000000 INFO @ Sun, 03 Jun 2018 13:35:23: 24000000 INFO @ Sun, 03 Jun 2018 13:35:28: 24000000 INFO @ Sun, 03 Jun 2018 13:35:29: 24000000 INFO @ Sun, 03 Jun 2018 13:35:29: 25000000 INFO @ Sun, 03 Jun 2018 13:35:34: 25000000 INFO @ Sun, 03 Jun 2018 13:35:34: 26000000 INFO @ Sun, 03 Jun 2018 13:35:35: 25000000 INFO @ Sun, 03 Jun 2018 13:35:40: 27000000 INFO @ Sun, 03 Jun 2018 13:35:40: 26000000 INFO @ Sun, 03 Jun 2018 13:35:41: 26000000 INFO @ Sun, 03 Jun 2018 13:35:45: 28000000 INFO @ Sun, 03 Jun 2018 13:35:46: 27000000 INFO @ Sun, 03 Jun 2018 13:35:47: 27000000 INFO @ Sun, 03 Jun 2018 13:35:51: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:35:51: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:35:51: #1 total tags in treatment: 14132298 INFO @ Sun, 03 Jun 2018 13:35:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:35:51: #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 13:35:51: #1 tags after filtering in treatment: 11946474 INFO @ Sun, 03 Jun 2018 13:35:51: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:35:51: #1 finished! INFO @ Sun, 03 Jun 2018 13:35:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:35:52: #2 number of paired peaks: 181 WARNING @ Sun, 03 Jun 2018 13:35:52: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sun, 03 Jun 2018 13:35:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:35:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:35:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:35:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:35:52: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 13:35:52: #2 alternative fragment length(s) may be 2,107,124,159 bps INFO @ Sun, 03 Jun 2018 13:35:52: #2.2 Generate R script for model : SRX4085430.20_model.r INFO @ Sun, 03 Jun 2018 13:35:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:35:52: 28000000 INFO @ Sun, 03 Jun 2018 13:35:53: 28000000 INFO @ Sun, 03 Jun 2018 13:35:58: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:35:58: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:35:58: #1 total tags in treatment: 14132298 INFO @ Sun, 03 Jun 2018 13:35:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:35:58: #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 13:35:59: #1 tags after filtering in treatment: 11946474 INFO @ Sun, 03 Jun 2018 13:35:59: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:35:59: #1 finished! INFO @ Sun, 03 Jun 2018 13:35:59: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:35:59: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:35:59: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:35:59: #1 total tags in treatment: 14132298 INFO @ Sun, 03 Jun 2018 13:35:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:35:59: #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 13:36:00: #1 tags after filtering in treatment: 11946474 INFO @ Sun, 03 Jun 2018 13:36:00: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:36:00: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:00: #2 number of paired peaks: 181 WARNING @ Sun, 03 Jun 2018 13:36:00: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sun, 03 Jun 2018 13:36:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:00: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:00: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:00: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:00: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 13:36:00: #2 alternative fragment length(s) may be 2,107,124,159 bps INFO @ Sun, 03 Jun 2018 13:36:00: #2.2 Generate R script for model : SRX4085430.05_model.r INFO @ Sun, 03 Jun 2018 13:36:00: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:00: #2 number of paired peaks: 181 WARNING @ Sun, 03 Jun 2018 13:36:00: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sun, 03 Jun 2018 13:36:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:00: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:00: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:00: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:00: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 13:36:00: #2 alternative fragment length(s) may be 2,107,124,159 bps INFO @ Sun, 03 Jun 2018 13:36:00: #2.2 Generate R script for model : SRX4085430.10_model.r INFO @ Sun, 03 Jun 2018 13:36:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:31: #4 Write output xls file... SRX4085430.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:31: #4 Write peak in narrowPeak format file... SRX4085430.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:31: #4 Write summits bed file... SRX4085430.20_summits.bed INFO @ Sun, 03 Jun 2018 13:36:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:36:40: #4 Write output xls file... SRX4085430.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:40: #4 Write peak in narrowPeak format file... SRX4085430.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:40: #4 Write summits bed file... SRX4085430.10_summits.bed INFO @ Sun, 03 Jun 2018 13:36:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:36:42: #4 Write output xls file... SRX4085430.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:42: #4 Write peak in narrowPeak format file... SRX4085430.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:42: #4 Write summits bed file... SRX4085430.05_summits.bed INFO @ Sun, 03 Jun 2018 13:36:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1312 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。