Job ID = 10714426 sra ファイルのダウンロード中... Completed: 1913964K bytes transferred in 48 seconds (321027K 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 26880650 spots for /home/okishinya/chipatlas/results/ce10/SRX4085342/SRR7167371.sra Written 26880650 spots for /home/okishinya/chipatlas/results/ce10/SRX4085342/SRR7167371.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: 00:27:10 26880650 reads; of these: 26880650 (100.00%) were paired; of these: 2024389 (7.53%) aligned concordantly 0 times 21727234 (80.83%) aligned concordantly exactly 1 time 3129027 (11.64%) aligned concordantly >1 times ---- 2024389 pairs aligned concordantly 0 times; of these: 188883 (9.33%) aligned discordantly 1 time ---- 1835506 pairs aligned 0 times concordantly or discordantly; of these: 3671012 mates make up the pairs; of these: 2074813 (56.52%) aligned 0 times 1316899 (35.87%) aligned exactly 1 time 279300 (7.61%) aligned >1 times 96.14% overall alignment rate Time searching: 00:27:10 Overall time: 00:27:10 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 24 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] 4637954 / 24986431 = 0.1856 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 13:14:11: # Command line: callpeak -t SRX4085342.bam -f BAM -g ce -n SRX4085342.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085342.05 # format = BAM # ChIP-seq file = ['SRX4085342.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 13:14:11: # Command line: callpeak -t SRX4085342.bam -f BAM -g ce -n SRX4085342.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085342.10 # format = BAM # ChIP-seq file = ['SRX4085342.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 13:14:11: # Command line: callpeak -t SRX4085342.bam -f BAM -g ce -n SRX4085342.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085342.20 # format = BAM # ChIP-seq file = ['SRX4085342.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 13:14:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:14:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:14:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:14:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:14:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:14:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:14:18: 1000000 INFO @ Sun, 03 Jun 2018 13:14:18: 1000000 INFO @ Sun, 03 Jun 2018 13:14:18: 1000000 INFO @ Sun, 03 Jun 2018 13:14:24: 2000000 INFO @ Sun, 03 Jun 2018 13:14:25: 2000000 INFO @ Sun, 03 Jun 2018 13:14:25: 2000000 INFO @ Sun, 03 Jun 2018 13:14:31: 3000000 INFO @ Sun, 03 Jun 2018 13:14:31: 3000000 INFO @ Sun, 03 Jun 2018 13:14:32: 3000000 INFO @ Sun, 03 Jun 2018 13:14:37: 4000000 INFO @ Sun, 03 Jun 2018 13:14:38: 4000000 INFO @ Sun, 03 Jun 2018 13:14:39: 4000000 INFO @ Sun, 03 Jun 2018 13:14:43: 5000000 INFO @ Sun, 03 Jun 2018 13:14:45: 5000000 INFO @ Sun, 03 Jun 2018 13:14:46: 5000000 INFO @ Sun, 03 Jun 2018 13:14:50: 6000000 INFO @ Sun, 03 Jun 2018 13:14:52: 6000000 INFO @ Sun, 03 Jun 2018 13:14:52: 6000000 INFO @ Sun, 03 Jun 2018 13:14:57: 7000000 INFO @ Sun, 03 Jun 2018 13:14:59: 7000000 INFO @ Sun, 03 Jun 2018 13:14:59: 7000000 INFO @ Sun, 03 Jun 2018 13:15:04: 8000000 INFO @ Sun, 03 Jun 2018 13:15:05: 8000000 INFO @ Sun, 03 Jun 2018 13:15:06: 8000000 INFO @ Sun, 03 Jun 2018 13:15:11: 9000000 INFO @ Sun, 03 Jun 2018 13:15:12: 9000000 INFO @ Sun, 03 Jun 2018 13:15:12: 9000000 INFO @ Sun, 03 Jun 2018 13:15:17: 10000000 INFO @ Sun, 03 Jun 2018 13:15:18: 10000000 INFO @ Sun, 03 Jun 2018 13:15:19: 10000000 INFO @ Sun, 03 Jun 2018 13:15:24: 11000000 INFO @ Sun, 03 Jun 2018 13:15:25: 11000000 INFO @ Sun, 03 Jun 2018 13:15:26: 11000000 INFO @ Sun, 03 Jun 2018 13:15:30: 12000000 INFO @ Sun, 03 Jun 2018 13:15:31: 12000000 INFO @ Sun, 03 Jun 2018 13:15:33: 12000000 INFO @ Sun, 03 Jun 2018 13:15:37: 13000000 INFO @ Sun, 03 Jun 2018 13:15:38: 13000000 INFO @ Sun, 03 Jun 2018 13:15:40: 13000000 INFO @ Sun, 03 Jun 2018 13:15:43: 14000000 INFO @ Sun, 03 Jun 2018 13:15:45: 14000000 INFO @ Sun, 03 Jun 2018 13:15:47: 14000000 INFO @ Sun, 03 Jun 2018 13:15:50: 15000000 INFO @ Sun, 03 Jun 2018 13:15:51: 15000000 INFO @ Sun, 03 Jun 2018 13:15:54: 15000000 INFO @ Sun, 03 Jun 2018 13:15:56: 16000000 INFO @ Sun, 03 Jun 2018 13:15:58: 16000000 INFO @ Sun, 03 Jun 2018 13:16:01: 16000000 INFO @ Sun, 03 Jun 2018 13:16:03: 17000000 INFO @ Sun, 03 Jun 2018 13:16:04: 17000000 INFO @ Sun, 03 Jun 2018 13:16:08: 17000000 INFO @ Sun, 03 Jun 2018 13:16:10: 18000000 INFO @ Sun, 03 Jun 2018 13:16:10: 18000000 INFO @ Sun, 03 Jun 2018 13:16:15: 18000000 INFO @ Sun, 03 Jun 2018 13:16:17: 19000000 INFO @ Sun, 03 Jun 2018 13:16:17: 19000000 INFO @ Sun, 03 Jun 2018 13:16:22: 19000000 INFO @ Sun, 03 Jun 2018 13:16:23: 20000000 INFO @ Sun, 03 Jun 2018 13:16:24: 20000000 INFO @ Sun, 03 Jun 2018 13:16:28: 20000000 INFO @ Sun, 03 Jun 2018 13:16:30: 21000000 INFO @ Sun, 03 Jun 2018 13:16:30: 21000000 INFO @ Sun, 03 Jun 2018 13:16:35: 21000000 INFO @ Sun, 03 Jun 2018 13:16:36: 22000000 INFO @ Sun, 03 Jun 2018 13:16:37: 22000000 INFO @ Sun, 03 Jun 2018 13:16:42: 22000000 INFO @ Sun, 03 Jun 2018 13:16:43: 23000000 INFO @ Sun, 03 Jun 2018 13:16:44: 23000000 INFO @ Sun, 03 Jun 2018 13:16:49: 23000000 INFO @ Sun, 03 Jun 2018 13:16:49: 24000000 INFO @ Sun, 03 Jun 2018 13:16:51: 24000000 INFO @ Sun, 03 Jun 2018 13:16:55: 25000000 INFO @ Sun, 03 Jun 2018 13:16:55: 24000000 INFO @ Sun, 03 Jun 2018 13:16:57: 25000000 INFO @ Sun, 03 Jun 2018 13:17:02: 26000000 INFO @ Sun, 03 Jun 2018 13:17:02: 25000000 INFO @ Sun, 03 Jun 2018 13:17:04: 26000000 INFO @ Sun, 03 Jun 2018 13:17:08: 27000000 INFO @ Sun, 03 Jun 2018 13:17:09: 26000000 INFO @ Sun, 03 Jun 2018 13:17:10: 27000000 INFO @ Sun, 03 Jun 2018 13:17:15: 28000000 INFO @ Sun, 03 Jun 2018 13:17:16: 27000000 INFO @ Sun, 03 Jun 2018 13:17:17: 28000000 INFO @ Sun, 03 Jun 2018 13:17:22: 29000000 INFO @ Sun, 03 Jun 2018 13:17:23: 29000000 INFO @ Sun, 03 Jun 2018 13:17:23: 28000000 INFO @ Sun, 03 Jun 2018 13:17:28: 30000000 INFO @ Sun, 03 Jun 2018 13:17:29: 30000000 INFO @ Sun, 03 Jun 2018 13:17:30: 29000000 INFO @ Sun, 03 Jun 2018 13:17:35: 31000000 INFO @ Sun, 03 Jun 2018 13:17:36: 31000000 INFO @ Sun, 03 Jun 2018 13:17:37: 30000000 INFO @ Sun, 03 Jun 2018 13:17:42: 32000000 INFO @ Sun, 03 Jun 2018 13:17:43: 32000000 INFO @ Sun, 03 Jun 2018 13:17:43: 31000000 INFO @ Sun, 03 Jun 2018 13:17:48: 33000000 INFO @ Sun, 03 Jun 2018 13:17:50: 33000000 INFO @ Sun, 03 Jun 2018 13:17:50: 32000000 INFO @ Sun, 03 Jun 2018 13:17:55: 34000000 INFO @ Sun, 03 Jun 2018 13:17:56: 33000000 INFO @ Sun, 03 Jun 2018 13:17:56: 34000000 INFO @ Sun, 03 Jun 2018 13:18:02: 35000000 INFO @ Sun, 03 Jun 2018 13:18:03: 34000000 INFO @ Sun, 03 Jun 2018 13:18:03: 35000000 INFO @ Sun, 03 Jun 2018 13:18:09: 36000000 INFO @ Sun, 03 Jun 2018 13:18:09: 35000000 INFO @ Sun, 03 Jun 2018 13:18:11: 36000000 INFO @ Sun, 03 Jun 2018 13:18:16: 36000000 INFO @ Sun, 03 Jun 2018 13:18:16: 37000000 INFO @ Sun, 03 Jun 2018 13:18:17: 37000000 INFO @ Sun, 03 Jun 2018 13:18:22: 37000000 INFO @ Sun, 03 Jun 2018 13:18:23: 38000000 INFO @ Sun, 03 Jun 2018 13:18:24: 38000000 INFO @ Sun, 03 Jun 2018 13:18:29: 38000000 INFO @ Sun, 03 Jun 2018 13:18:30: 39000000 INFO @ Sun, 03 Jun 2018 13:18:31: 39000000 INFO @ Sun, 03 Jun 2018 13:18:35: 39000000 INFO @ Sun, 03 Jun 2018 13:18:37: 40000000 INFO @ Sun, 03 Jun 2018 13:18:38: 40000000 INFO @ Sun, 03 Jun 2018 13:18:42: 40000000 INFO @ Sun, 03 Jun 2018 13:18:44: 41000000 INFO @ Sun, 03 Jun 2018 13:18:45: 41000000 INFO @ Sun, 03 Jun 2018 13:18:48: 41000000 INFO @ Sun, 03 Jun 2018 13:18:50: 42000000 INFO @ Sun, 03 Jun 2018 13:18:52: 42000000 INFO @ Sun, 03 Jun 2018 13:18:53: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:53: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:53: #1 total tags in treatment: 20233059 INFO @ Sun, 03 Jun 2018 13:18:53: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:53: #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 13:18:54: #1 tags after filtering in treatment: 17101362 INFO @ Sun, 03 Jun 2018 13:18:54: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:18:54: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:54: 42000000 INFO @ Sun, 03 Jun 2018 13:18:55: #2 number of paired peaks: 172 WARNING @ Sun, 03 Jun 2018 13:18:55: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:55: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:55: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:55: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:55: #1 total tags in treatment: 20233059 INFO @ Sun, 03 Jun 2018 13:18:55: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:55: #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 13:18:55: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:55: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:55: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:55: #2 predicted fragment length is 117 bps INFO @ Sun, 03 Jun 2018 13:18:55: #2 alternative fragment length(s) may be 2,86,117,138 bps INFO @ Sun, 03 Jun 2018 13:18:55: #2.2 Generate R script for model : SRX4085342.20_model.r INFO @ Sun, 03 Jun 2018 13:18:55: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:18:55: #1 tags after filtering in treatment: 17101362 INFO @ Sun, 03 Jun 2018 13:18:55: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:18:55: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:55: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:56: #2 number of paired peaks: 172 WARNING @ Sun, 03 Jun 2018 13:18:56: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:56: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:57: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:57: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:57: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:57: #2 predicted fragment length is 117 bps INFO @ Sun, 03 Jun 2018 13:18:57: #2 alternative fragment length(s) may be 2,86,117,138 bps INFO @ Sun, 03 Jun 2018 13:18:57: #2.2 Generate R script for model : SRX4085342.05_model.r INFO @ Sun, 03 Jun 2018 13:18:57: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:18:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:57: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:57: #1 total tags in treatment: 20233059 INFO @ Sun, 03 Jun 2018 13:18:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:57: #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 13:18:58: #1 tags after filtering in treatment: 17101362 INFO @ Sun, 03 Jun 2018 13:18:58: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:18:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:59: #2 number of paired peaks: 172 WARNING @ Sun, 03 Jun 2018 13:18:59: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:59: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:59: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:59: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:59: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:59: #2 predicted fragment length is 117 bps INFO @ Sun, 03 Jun 2018 13:18:59: #2 alternative fragment length(s) may be 2,86,117,138 bps INFO @ Sun, 03 Jun 2018 13:18:59: #2.2 Generate R script for model : SRX4085342.10_model.r INFO @ Sun, 03 Jun 2018 13:18:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:31: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:32: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:43: #4 Write output xls file... SRX4085342.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:43: #4 Write peak in narrowPeak format file... SRX4085342.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:44: #4 Write summits bed file... SRX4085342.20_summits.bed INFO @ Sun, 03 Jun 2018 13:19:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (538 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:49: #4 Write output xls file... SRX4085342.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:49: #4 Write peak in narrowPeak format file... SRX4085342.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:49: #4 Write summits bed file... SRX4085342.05_summits.bed INFO @ Sun, 03 Jun 2018 13:19:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2114 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:49: #4 Write output xls file... SRX4085342.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:49: #4 Write peak in narrowPeak format file... SRX4085342.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:49: #4 Write summits bed file... SRX4085342.10_summits.bed INFO @ Sun, 03 Jun 2018 13:19:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1133 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。