Job ID = 10714456 sra ファイルのダウンロード中... Completed: 925965K bytes transferred in 11 seconds (654148K 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 14357347 spots for /home/okishinya/chipatlas/results/ce10/SRX4085372/SRR7167401.sra Written 14357347 spots for /home/okishinya/chipatlas/results/ce10/SRX4085372/SRR7167401.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: 00:09:59 14357347 reads; of these: 14357347 (100.00%) were paired; of these: 7394137 (51.50%) aligned concordantly 0 times 6124528 (42.66%) aligned concordantly exactly 1 time 838682 (5.84%) aligned concordantly >1 times ---- 7394137 pairs aligned concordantly 0 times; of these: 259455 (3.51%) aligned discordantly 1 time ---- 7134682 pairs aligned 0 times concordantly or discordantly; of these: 14269364 mates make up the pairs; of these: 11326295 (79.37%) aligned 0 times 2569245 (18.01%) aligned exactly 1 time 373824 (2.62%) aligned >1 times 60.56% overall alignment rate Time searching: 00:09:59 Overall time: 00:09:59 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 8 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] 528825 / 7114328 = 0.0743 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 12:55:38: # Command line: callpeak -t SRX4085372.bam -f BAM -g ce -n SRX4085372.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085372.20 # format = BAM # ChIP-seq file = ['SRX4085372.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 12:55:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:55:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:55:38: # Command line: callpeak -t SRX4085372.bam -f BAM -g ce -n SRX4085372.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085372.05 # format = BAM # ChIP-seq file = ['SRX4085372.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 12:55:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:55:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:55:38: # Command line: callpeak -t SRX4085372.bam -f BAM -g ce -n SRX4085372.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085372.10 # format = BAM # ChIP-seq file = ['SRX4085372.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 12:55:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:55:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:55:44: 1000000 INFO @ Sun, 03 Jun 2018 12:55:44: 1000000 INFO @ Sun, 03 Jun 2018 12:55:44: 1000000 INFO @ Sun, 03 Jun 2018 12:55:50: 2000000 INFO @ Sun, 03 Jun 2018 12:55:50: 2000000 INFO @ Sun, 03 Jun 2018 12:55:50: 2000000 INFO @ Sun, 03 Jun 2018 12:55:56: 3000000 INFO @ Sun, 03 Jun 2018 12:55:56: 3000000 INFO @ Sun, 03 Jun 2018 12:55:57: 3000000 INFO @ Sun, 03 Jun 2018 12:56:03: 4000000 INFO @ Sun, 03 Jun 2018 12:56:03: 4000000 INFO @ Sun, 03 Jun 2018 12:56:04: 4000000 INFO @ Sun, 03 Jun 2018 12:56:09: 5000000 INFO @ Sun, 03 Jun 2018 12:56:09: 5000000 INFO @ Sun, 03 Jun 2018 12:56:11: 5000000 INFO @ Sun, 03 Jun 2018 12:56:16: 6000000 INFO @ Sun, 03 Jun 2018 12:56:16: 6000000 INFO @ Sun, 03 Jun 2018 12:56:18: 6000000 INFO @ Sun, 03 Jun 2018 12:56:23: 7000000 INFO @ Sun, 03 Jun 2018 12:56:24: 7000000 INFO @ Sun, 03 Jun 2018 12:56:27: 7000000 INFO @ Sun, 03 Jun 2018 12:56:31: 8000000 INFO @ Sun, 03 Jun 2018 12:56:32: 8000000 INFO @ Sun, 03 Jun 2018 12:56:36: 8000000 INFO @ Sun, 03 Jun 2018 12:56:38: 9000000 INFO @ Sun, 03 Jun 2018 12:56:39: 9000000 INFO @ Sun, 03 Jun 2018 12:56:44: 9000000 INFO @ Sun, 03 Jun 2018 12:56:45: 10000000 INFO @ Sun, 03 Jun 2018 12:56:47: 10000000 INFO @ Sun, 03 Jun 2018 12:56:51: 11000000 INFO @ Sun, 03 Jun 2018 12:56:53: 10000000 INFO @ Sun, 03 Jun 2018 12:56:55: 11000000 INFO @ Sun, 03 Jun 2018 12:56:58: 12000000 INFO @ Sun, 03 Jun 2018 12:57:01: 11000000 INFO @ Sun, 03 Jun 2018 12:57:02: 12000000 INFO @ Sun, 03 Jun 2018 12:57:05: 13000000 INFO @ Sun, 03 Jun 2018 12:57:10: 12000000 INFO @ Sun, 03 Jun 2018 12:57:10: 13000000 INFO @ Sun, 03 Jun 2018 12:57:12: 14000000 INFO @ Sun, 03 Jun 2018 12:57:18: 14000000 INFO @ Sun, 03 Jun 2018 12:57:18: 13000000 INFO @ Sun, 03 Jun 2018 12:57:19: 15000000 INFO @ Sun, 03 Jun 2018 12:57:25: 15000000 INFO @ Sun, 03 Jun 2018 12:57:26: 16000000 INFO @ Sun, 03 Jun 2018 12:57:27: 14000000 INFO @ Sun, 03 Jun 2018 12:57:28: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:28: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:28: #1 total tags in treatment: 6444969 INFO @ Sun, 03 Jun 2018 12:57:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:28: #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 12:57:28: #1 tags after filtering in treatment: 6014294 INFO @ Sun, 03 Jun 2018 12:57:28: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 12:57:28: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:29: #2 number of paired peaks: 197 WARNING @ Sun, 03 Jun 2018 12:57:29: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:29: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:29: #2 predicted fragment length is 160 bps INFO @ Sun, 03 Jun 2018 12:57:29: #2 alternative fragment length(s) may be 4,79,88,105,113,135,145,160,586 bps INFO @ Sun, 03 Jun 2018 12:57:29: #2.2 Generate R script for model : SRX4085372.20_model.r INFO @ Sun, 03 Jun 2018 12:57:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:33: 16000000 INFO @ Sun, 03 Jun 2018 12:57:35: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:35: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:35: #1 total tags in treatment: 6444969 INFO @ Sun, 03 Jun 2018 12:57:35: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:35: #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 12:57:36: 15000000 INFO @ Sun, 03 Jun 2018 12:57:36: #1 tags after filtering in treatment: 6014294 INFO @ Sun, 03 Jun 2018 12:57:36: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 12:57:36: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:36: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:36: #2 number of paired peaks: 197 WARNING @ Sun, 03 Jun 2018 12:57:36: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:36: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:36: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:36: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:36: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:36: #2 predicted fragment length is 160 bps INFO @ Sun, 03 Jun 2018 12:57:36: #2 alternative fragment length(s) may be 4,79,88,105,113,135,145,160,586 bps INFO @ Sun, 03 Jun 2018 12:57:36: #2.2 Generate R script for model : SRX4085372.10_model.r INFO @ Sun, 03 Jun 2018 12:57:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:43: 16000000 INFO @ Sun, 03 Jun 2018 12:57:43: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:57:45: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:45: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:45: #1 total tags in treatment: 6444969 INFO @ Sun, 03 Jun 2018 12:57:45: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:45: #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 12:57:45: #1 tags after filtering in treatment: 6014294 INFO @ Sun, 03 Jun 2018 12:57:45: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 12:57:45: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:45: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:46: #2 number of paired peaks: 197 WARNING @ Sun, 03 Jun 2018 12:57:46: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:46: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:46: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:46: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:46: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:46: #2 predicted fragment length is 160 bps INFO @ Sun, 03 Jun 2018 12:57:46: #2 alternative fragment length(s) may be 4,79,88,105,113,135,145,160,586 bps INFO @ Sun, 03 Jun 2018 12:57:46: #2.2 Generate R script for model : SRX4085372.05_model.r INFO @ Sun, 03 Jun 2018 12:57:46: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:50: #4 Write output xls file... SRX4085372.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:57:50: #4 Write peak in narrowPeak format file... SRX4085372.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:57:50: #4 Write summits bed file... SRX4085372.20_summits.bed INFO @ Sun, 03 Jun 2018 12:57:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:57:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:00: #4 Write output xls file... SRX4085372.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:00: #4 Write peak in narrowPeak format file... SRX4085372.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:00: #4 Write summits bed file... SRX4085372.10_summits.bed INFO @ Sun, 03 Jun 2018 12:58:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:01: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:08: #4 Write output xls file... SRX4085372.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:08: #4 Write peak in narrowPeak format file... SRX4085372.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:08: #4 Write summits bed file... SRX4085372.05_summits.bed INFO @ Sun, 03 Jun 2018 12:58:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (217 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。