Job ID = 10714471 sra ファイルのダウンロード中... Completed: 1025499K bytes transferred in 21 seconds (386862K 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 16752074 spots for /home/okishinya/chipatlas/results/ce10/SRX4085387/SRR7167416.sra Written 16752074 spots for /home/okishinya/chipatlas/results/ce10/SRX4085387/SRR7167416.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:38 16752074 reads; of these: 16752074 (100.00%) were paired; of these: 6045301 (36.09%) aligned concordantly 0 times 9236228 (55.13%) aligned concordantly exactly 1 time 1470545 (8.78%) aligned concordantly >1 times ---- 6045301 pairs aligned concordantly 0 times; of these: 366524 (6.06%) aligned discordantly 1 time ---- 5678777 pairs aligned 0 times concordantly or discordantly; of these: 11357554 mates make up the pairs; of these: 7901789 (69.57%) aligned 0 times 3007749 (26.48%) aligned exactly 1 time 448016 (3.94%) aligned >1 times 76.42% overall alignment rate Time searching: 00:14:39 Overall time: 00:14:39 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 12 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] 734707 / 10914409 = 0.0673 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 13:04:52: # Command line: callpeak -t SRX4085387.bam -f BAM -g ce -n SRX4085387.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085387.05 # format = BAM # ChIP-seq file = ['SRX4085387.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 13:04:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:04:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:04:52: # Command line: callpeak -t SRX4085387.bam -f BAM -g ce -n SRX4085387.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085387.10 # format = BAM # ChIP-seq file = ['SRX4085387.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 13:04:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:04:52: # Command line: callpeak -t SRX4085387.bam -f BAM -g ce -n SRX4085387.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085387.20 # format = BAM # ChIP-seq file = ['SRX4085387.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 13:04:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:04:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:04:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:04:58: 1000000 INFO @ Sun, 03 Jun 2018 13:04:58: 1000000 INFO @ Sun, 03 Jun 2018 13:04:59: 1000000 INFO @ Sun, 03 Jun 2018 13:05:03: 2000000 INFO @ Sun, 03 Jun 2018 13:05:05: 2000000 INFO @ Sun, 03 Jun 2018 13:05:06: 2000000 INFO @ Sun, 03 Jun 2018 13:05:09: 3000000 INFO @ Sun, 03 Jun 2018 13:05:11: 3000000 INFO @ Sun, 03 Jun 2018 13:05:13: 3000000 INFO @ Sun, 03 Jun 2018 13:05:14: 4000000 INFO @ Sun, 03 Jun 2018 13:05:17: 4000000 INFO @ Sun, 03 Jun 2018 13:05:20: 5000000 INFO @ Sun, 03 Jun 2018 13:05:20: 4000000 INFO @ Sun, 03 Jun 2018 13:05:24: 5000000 INFO @ Sun, 03 Jun 2018 13:05:26: 6000000 INFO @ Sun, 03 Jun 2018 13:05:27: 5000000 INFO @ Sun, 03 Jun 2018 13:05:30: 6000000 INFO @ Sun, 03 Jun 2018 13:05:32: 7000000 INFO @ Sun, 03 Jun 2018 13:05:34: 6000000 INFO @ Sun, 03 Jun 2018 13:05:36: 7000000 INFO @ Sun, 03 Jun 2018 13:05:38: 8000000 INFO @ Sun, 03 Jun 2018 13:05:40: 7000000 INFO @ Sun, 03 Jun 2018 13:05:42: 8000000 INFO @ Sun, 03 Jun 2018 13:05:44: 9000000 INFO @ Sun, 03 Jun 2018 13:05:47: 8000000 INFO @ Sun, 03 Jun 2018 13:05:48: 9000000 INFO @ Sun, 03 Jun 2018 13:05:49: 10000000 INFO @ Sun, 03 Jun 2018 13:05:54: 9000000 INFO @ Sun, 03 Jun 2018 13:05:54: 10000000 INFO @ Sun, 03 Jun 2018 13:05:55: 11000000 INFO @ Sun, 03 Jun 2018 13:06:00: 11000000 INFO @ Sun, 03 Jun 2018 13:06:01: 10000000 INFO @ Sun, 03 Jun 2018 13:06:01: 12000000 INFO @ Sun, 03 Jun 2018 13:06:06: 12000000 INFO @ Sun, 03 Jun 2018 13:06:06: 13000000 INFO @ Sun, 03 Jun 2018 13:06:08: 11000000 INFO @ Sun, 03 Jun 2018 13:06:12: 14000000 INFO @ Sun, 03 Jun 2018 13:06:13: 13000000 INFO @ Sun, 03 Jun 2018 13:06:15: 12000000 INFO @ Sun, 03 Jun 2018 13:06:17: 15000000 INFO @ Sun, 03 Jun 2018 13:06:19: 14000000 INFO @ Sun, 03 Jun 2018 13:06:22: 13000000 INFO @ Sun, 03 Jun 2018 13:06:23: 16000000 INFO @ Sun, 03 Jun 2018 13:06:26: 15000000 INFO @ Sun, 03 Jun 2018 13:06:28: 17000000 INFO @ Sun, 03 Jun 2018 13:06:29: 14000000 INFO @ Sun, 03 Jun 2018 13:06:33: 16000000 INFO @ Sun, 03 Jun 2018 13:06:34: 18000000 INFO @ Sun, 03 Jun 2018 13:06:37: 15000000 INFO @ Sun, 03 Jun 2018 13:06:39: 17000000 INFO @ Sun, 03 Jun 2018 13:06:39: 19000000 INFO @ Sun, 03 Jun 2018 13:06:44: 16000000 INFO @ Sun, 03 Jun 2018 13:06:45: 20000000 INFO @ Sun, 03 Jun 2018 13:06:46: 18000000 INFO @ Sun, 03 Jun 2018 13:06:51: 21000000 INFO @ Sun, 03 Jun 2018 13:06:52: 17000000 INFO @ Sun, 03 Jun 2018 13:06:53: 19000000 INFO @ Sun, 03 Jun 2018 13:06:56: 22000000 INFO @ Sun, 03 Jun 2018 13:06:59: 20000000 INFO @ Sun, 03 Jun 2018 13:07:00: 18000000 INFO @ Sun, 03 Jun 2018 13:07:01: 23000000 INFO @ Sun, 03 Jun 2018 13:07:06: 21000000 INFO @ Sun, 03 Jun 2018 13:07:06: 24000000 INFO @ Sun, 03 Jun 2018 13:07:07: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:07:07: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:07:07: #1 total tags in treatment: 9984920 INFO @ Sun, 03 Jun 2018 13:07:07: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:07:07: #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 13:07:07: #1 tags after filtering in treatment: 8754844 INFO @ Sun, 03 Jun 2018 13:07:07: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:07:07: #1 finished! INFO @ Sun, 03 Jun 2018 13:07:07: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:07:07: 19000000 INFO @ Sun, 03 Jun 2018 13:07:08: #2 number of paired peaks: 267 WARNING @ Sun, 03 Jun 2018 13:07:08: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sun, 03 Jun 2018 13:07:08: start model_add_line... INFO @ Sun, 03 Jun 2018 13:07:08: start X-correlation... INFO @ Sun, 03 Jun 2018 13:07:08: end of X-cor INFO @ Sun, 03 Jun 2018 13:07:08: #2 finished! INFO @ Sun, 03 Jun 2018 13:07:08: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 13:07:08: #2 alternative fragment length(s) may be 4,103 bps INFO @ Sun, 03 Jun 2018 13:07:08: #2.2 Generate R script for model : SRX4085387.10_model.r INFO @ Sun, 03 Jun 2018 13:07:08: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:07:13: 22000000 INFO @ Sun, 03 Jun 2018 13:07:15: 20000000 INFO @ Sun, 03 Jun 2018 13:07:20: 23000000 INFO @ Sun, 03 Jun 2018 13:07:22: 21000000 INFO @ Sun, 03 Jun 2018 13:07:26: 24000000 INFO @ Sun, 03 Jun 2018 13:07:27: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:07:27: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:07:27: #1 total tags in treatment: 9984920 INFO @ Sun, 03 Jun 2018 13:07:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:07:27: #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 13:07:27: #1 tags after filtering in treatment: 8754844 INFO @ Sun, 03 Jun 2018 13:07:27: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:07:27: #1 finished! INFO @ Sun, 03 Jun 2018 13:07:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:07:28: #2 number of paired peaks: 267 WARNING @ Sun, 03 Jun 2018 13:07:28: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sun, 03 Jun 2018 13:07:28: start model_add_line... INFO @ Sun, 03 Jun 2018 13:07:28: start X-correlation... INFO @ Sun, 03 Jun 2018 13:07:28: end of X-cor INFO @ Sun, 03 Jun 2018 13:07:28: #2 finished! INFO @ Sun, 03 Jun 2018 13:07:28: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 13:07:28: #2 alternative fragment length(s) may be 4,103 bps INFO @ Sun, 03 Jun 2018 13:07:28: #2.2 Generate R script for model : SRX4085387.05_model.r INFO @ Sun, 03 Jun 2018 13:07:28: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:07:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:07:29: 22000000 INFO @ Sun, 03 Jun 2018 13:07:35: 23000000 INFO @ Sun, 03 Jun 2018 13:07:40: #4 Write output xls file... SRX4085387.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:07:40: #4 Write peak in narrowPeak format file... SRX4085387.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:07:40: #4 Write summits bed file... SRX4085387.10_summits.bed INFO @ Sun, 03 Jun 2018 13:07:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1156 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:07:41: 24000000 INFO @ Sun, 03 Jun 2018 13:07:41: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:07:41: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:07:41: #1 total tags in treatment: 9984920 INFO @ Sun, 03 Jun 2018 13:07:41: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:07:41: #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 13:07:42: #1 tags after filtering in treatment: 8754844 INFO @ Sun, 03 Jun 2018 13:07:42: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:07:42: #1 finished! INFO @ Sun, 03 Jun 2018 13:07:42: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:07:42: #2 number of paired peaks: 267 WARNING @ Sun, 03 Jun 2018 13:07:42: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sun, 03 Jun 2018 13:07:42: start model_add_line... INFO @ Sun, 03 Jun 2018 13:07:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:07:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:07:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:07:42: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 13:07:42: #2 alternative fragment length(s) may be 4,103 bps INFO @ Sun, 03 Jun 2018 13:07:42: #2.2 Generate R script for model : SRX4085387.20_model.r INFO @ Sun, 03 Jun 2018 13:07:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:07:49: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:08:01: #4 Write output xls file... SRX4085387.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:08:01: #4 Write peak in narrowPeak format file... SRX4085387.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:08:01: #4 Write summits bed file... SRX4085387.05_summits.bed INFO @ Sun, 03 Jun 2018 13:08:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2294 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:08:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:08:13: #4 Write output xls file... SRX4085387.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:08:13: #4 Write peak in narrowPeak format file... SRX4085387.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:08:13: #4 Write summits bed file... SRX4085387.20_summits.bed INFO @ Sun, 03 Jun 2018 13:08:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (364 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。