Job ID = 10714489 sra ファイルのダウンロード中... Completed: 2944231K bytes transferred in 51 seconds (465177K 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 41433735 spots for /home/okishinya/chipatlas/results/ce10/SRX4085406/SRR7167435.sra Written 41433735 spots for /home/okishinya/chipatlas/results/ce10/SRX4085406/SRR7167435.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:40:24 41433735 reads; of these: 41433735 (100.00%) were paired; of these: 2698501 (6.51%) aligned concordantly 0 times 34258133 (82.68%) aligned concordantly exactly 1 time 4477101 (10.81%) aligned concordantly >1 times ---- 2698501 pairs aligned concordantly 0 times; of these: 636187 (23.58%) aligned discordantly 1 time ---- 2062314 pairs aligned 0 times concordantly or discordantly; of these: 4124628 mates make up the pairs; of these: 2418190 (58.63%) aligned 0 times 1340527 (32.50%) aligned exactly 1 time 365911 (8.87%) aligned >1 times 97.08% overall alignment rate Time searching: 00:40:25 Overall time: 00:40:25 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 36 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] 28146709 / 39110813 = 0.7197 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 13:47:55: # Command line: callpeak -t SRX4085406.bam -f BAM -g ce -n SRX4085406.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085406.10 # format = BAM # ChIP-seq file = ['SRX4085406.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 13:47:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:47:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:47:55: # Command line: callpeak -t SRX4085406.bam -f BAM -g ce -n SRX4085406.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085406.20 # format = BAM # ChIP-seq file = ['SRX4085406.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 13:47:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:47:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:47:55: # Command line: callpeak -t SRX4085406.bam -f BAM -g ce -n SRX4085406.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085406.05 # format = BAM # ChIP-seq file = ['SRX4085406.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 13:47:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:47:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:48:02: 1000000 INFO @ Sun, 03 Jun 2018 13:48:02: 1000000 INFO @ Sun, 03 Jun 2018 13:48:02: 1000000 INFO @ Sun, 03 Jun 2018 13:48:08: 2000000 INFO @ Sun, 03 Jun 2018 13:48:08: 2000000 INFO @ Sun, 03 Jun 2018 13:48:08: 2000000 INFO @ Sun, 03 Jun 2018 13:48:14: 3000000 INFO @ Sun, 03 Jun 2018 13:48:14: 3000000 INFO @ Sun, 03 Jun 2018 13:48:15: 3000000 INFO @ Sun, 03 Jun 2018 13:48:20: 4000000 INFO @ Sun, 03 Jun 2018 13:48:20: 4000000 INFO @ Sun, 03 Jun 2018 13:48:21: 4000000 INFO @ Sun, 03 Jun 2018 13:48:26: 5000000 INFO @ Sun, 03 Jun 2018 13:48:26: 5000000 INFO @ Sun, 03 Jun 2018 13:48:28: 5000000 INFO @ Sun, 03 Jun 2018 13:48:32: 6000000 INFO @ Sun, 03 Jun 2018 13:48:32: 6000000 INFO @ Sun, 03 Jun 2018 13:48:34: 6000000 INFO @ Sun, 03 Jun 2018 13:48:39: 7000000 INFO @ Sun, 03 Jun 2018 13:48:39: 7000000 INFO @ Sun, 03 Jun 2018 13:48:41: 7000000 INFO @ Sun, 03 Jun 2018 13:48:45: 8000000 INFO @ Sun, 03 Jun 2018 13:48:45: 8000000 INFO @ Sun, 03 Jun 2018 13:48:47: 8000000 INFO @ Sun, 03 Jun 2018 13:48:51: 9000000 INFO @ Sun, 03 Jun 2018 13:48:51: 9000000 INFO @ Sun, 03 Jun 2018 13:48:53: 9000000 INFO @ Sun, 03 Jun 2018 13:48:57: 10000000 INFO @ Sun, 03 Jun 2018 13:48:57: 10000000 INFO @ Sun, 03 Jun 2018 13:49:00: 10000000 INFO @ Sun, 03 Jun 2018 13:49:03: 11000000 INFO @ Sun, 03 Jun 2018 13:49:03: 11000000 INFO @ Sun, 03 Jun 2018 13:49:06: 11000000 INFO @ Sun, 03 Jun 2018 13:49:10: 12000000 INFO @ Sun, 03 Jun 2018 13:49:10: 12000000 INFO @ Sun, 03 Jun 2018 13:49:13: 12000000 INFO @ Sun, 03 Jun 2018 13:49:16: 13000000 INFO @ Sun, 03 Jun 2018 13:49:16: 13000000 INFO @ Sun, 03 Jun 2018 13:49:19: 13000000 INFO @ Sun, 03 Jun 2018 13:49:22: 14000000 INFO @ Sun, 03 Jun 2018 13:49:22: 14000000 INFO @ Sun, 03 Jun 2018 13:49:26: 14000000 INFO @ Sun, 03 Jun 2018 13:49:28: 15000000 INFO @ Sun, 03 Jun 2018 13:49:28: 15000000 INFO @ Sun, 03 Jun 2018 13:49:32: 15000000 INFO @ Sun, 03 Jun 2018 13:49:35: 16000000 INFO @ Sun, 03 Jun 2018 13:49:35: 16000000 INFO @ Sun, 03 Jun 2018 13:49:39: 16000000 INFO @ Sun, 03 Jun 2018 13:49:41: 17000000 INFO @ Sun, 03 Jun 2018 13:49:41: 17000000 INFO @ Sun, 03 Jun 2018 13:49:45: 17000000 INFO @ Sun, 03 Jun 2018 13:49:47: 18000000 INFO @ Sun, 03 Jun 2018 13:49:47: 18000000 INFO @ Sun, 03 Jun 2018 13:49:51: 18000000 INFO @ Sun, 03 Jun 2018 13:49:54: 19000000 INFO @ Sun, 03 Jun 2018 13:49:54: 19000000 INFO @ Sun, 03 Jun 2018 13:49:58: 19000000 INFO @ Sun, 03 Jun 2018 13:50:00: 20000000 INFO @ Sun, 03 Jun 2018 13:50:00: 20000000 INFO @ Sun, 03 Jun 2018 13:50:04: 20000000 INFO @ Sun, 03 Jun 2018 13:50:06: 21000000 INFO @ Sun, 03 Jun 2018 13:50:06: 21000000 INFO @ Sun, 03 Jun 2018 13:50:11: 21000000 INFO @ Sun, 03 Jun 2018 13:50:12: 22000000 INFO @ Sun, 03 Jun 2018 13:50:12: 22000000 INFO @ Sun, 03 Jun 2018 13:50:17: 22000000 INFO @ Sun, 03 Jun 2018 13:50:18: 23000000 INFO @ Sun, 03 Jun 2018 13:50:18: 23000000 INFO @ Sun, 03 Jun 2018 13:50:24: 23000000 INFO @ Sun, 03 Jun 2018 13:50:24: 24000000 INFO @ Sun, 03 Jun 2018 13:50:24: 24000000 INFO @ Sun, 03 Jun 2018 13:50:25: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:50:25: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:50:25: #1 total tags in treatment: 10800706 INFO @ Sun, 03 Jun 2018 13:50:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:50:25: #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 13:50:25: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:50:25: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:50:25: #1 total tags in treatment: 10800706 INFO @ Sun, 03 Jun 2018 13:50:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:50:25: #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 13:50:25: #1 tags after filtering in treatment: 9498165 INFO @ Sun, 03 Jun 2018 13:50:25: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:50:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:50:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:50:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:50:25: #1 tags after filtering in treatment: 9498165 INFO @ Sun, 03 Jun 2018 13:50:25: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:50:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:50:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:50:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:50:26: #2 number of paired peaks: 350 WARNING @ Sun, 03 Jun 2018 13:50:26: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sun, 03 Jun 2018 13:50:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:50:26: #2 number of paired peaks: 350 WARNING @ Sun, 03 Jun 2018 13:50:26: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sun, 03 Jun 2018 13:50:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:50:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:50:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:50:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:50:26: #2 predicted fragment length is 115 bps INFO @ Sun, 03 Jun 2018 13:50:26: #2 alternative fragment length(s) may be 3,89,115 bps INFO @ Sun, 03 Jun 2018 13:50:26: #2.2 Generate R script for model : SRX4085406.20_model.r INFO @ Sun, 03 Jun 2018 13:50:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:50:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:50:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:50:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:50:26: #2 predicted fragment length is 115 bps INFO @ Sun, 03 Jun 2018 13:50:26: #2 alternative fragment length(s) may be 3,89,115 bps INFO @ Sun, 03 Jun 2018 13:50:26: #2.2 Generate R script for model : SRX4085406.10_model.r INFO @ Sun, 03 Jun 2018 13:50:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:50:31: 24000000 INFO @ Sun, 03 Jun 2018 13:50:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:50:32: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:50:32: #1 total tags in treatment: 10800706 INFO @ Sun, 03 Jun 2018 13:50:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:50:32: #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 13:50:32: #1 tags after filtering in treatment: 9498165 INFO @ Sun, 03 Jun 2018 13:50:32: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:50:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:50:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:50:32: #2 number of paired peaks: 350 WARNING @ Sun, 03 Jun 2018 13:50:32: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Sun, 03 Jun 2018 13:50:32: start model_add_line... INFO @ Sun, 03 Jun 2018 13:50:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:50:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:50:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:50:33: #2 predicted fragment length is 115 bps INFO @ Sun, 03 Jun 2018 13:50:33: #2 alternative fragment length(s) may be 3,89,115 bps INFO @ Sun, 03 Jun 2018 13:50:33: #2.2 Generate R script for model : SRX4085406.05_model.r INFO @ Sun, 03 Jun 2018 13:50:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:50:47: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:50:48: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:50:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:50:59: #4 Write output xls file... SRX4085406.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:50:59: #4 Write output xls file... SRX4085406.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:50:59: #4 Write peak in narrowPeak format file... SRX4085406.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:50:59: #4 Write summits bed file... SRX4085406.20_summits.bed INFO @ Sun, 03 Jun 2018 13:50:59: #4 Write peak in narrowPeak format file... SRX4085406.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:50:59: Done! INFO @ Sun, 03 Jun 2018 13:50:59: #4 Write summits bed file... SRX4085406.10_summits.bed INFO @ Sun, 03 Jun 2018 13:50:59: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:51:07: #4 Write output xls file... SRX4085406.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:51:07: #4 Write peak in narrowPeak format file... SRX4085406.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:51:07: #4 Write summits bed file... SRX4085406.05_summits.bed INFO @ Sun, 03 Jun 2018 13:51:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (500 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。