Job ID = 10714526 sra ファイルのダウンロード中... Completed: 910748K bytes transferred in 10 seconds (719424K 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 14155206 spots for /home/okishinya/chipatlas/results/ce10/SRX4085441/SRR7167470.sra Written 14155206 spots for /home/okishinya/chipatlas/results/ce10/SRX4085441/SRR7167470.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: 00:10:02 14155206 reads; of these: 14155206 (100.00%) were paired; of these: 8228273 (58.13%) aligned concordantly 0 times 5084466 (35.92%) aligned concordantly exactly 1 time 842467 (5.95%) aligned concordantly >1 times ---- 8228273 pairs aligned concordantly 0 times; of these: 150782 (1.83%) aligned discordantly 1 time ---- 8077491 pairs aligned 0 times concordantly or discordantly; of these: 16154982 mates make up the pairs; of these: 12355149 (76.48%) aligned 0 times 3364969 (20.83%) aligned exactly 1 time 434864 (2.69%) aligned >1 times 56.36% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 537124 / 6012480 = 0.0893 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 13:24:09: # Command line: callpeak -t SRX4085441.bam -f BAM -g ce -n SRX4085441.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085441.05 # format = BAM # ChIP-seq file = ['SRX4085441.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 13:24:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:24:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:24:09: # Command line: callpeak -t SRX4085441.bam -f BAM -g ce -n SRX4085441.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085441.10 # format = BAM # ChIP-seq file = ['SRX4085441.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 13:24:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:24:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:24:09: # Command line: callpeak -t SRX4085441.bam -f BAM -g ce -n SRX4085441.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085441.20 # format = BAM # ChIP-seq file = ['SRX4085441.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 13:24:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:24:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:24:15: 1000000 INFO @ Sun, 03 Jun 2018 13:24:15: 1000000 INFO @ Sun, 03 Jun 2018 13:24:16: 1000000 INFO @ Sun, 03 Jun 2018 13:24:21: 2000000 INFO @ Sun, 03 Jun 2018 13:24:22: 2000000 INFO @ Sun, 03 Jun 2018 13:24:22: 2000000 INFO @ Sun, 03 Jun 2018 13:24:27: 3000000 INFO @ Sun, 03 Jun 2018 13:24:28: 3000000 INFO @ Sun, 03 Jun 2018 13:24:29: 3000000 INFO @ Sun, 03 Jun 2018 13:24:32: 4000000 INFO @ Sun, 03 Jun 2018 13:24:34: 4000000 INFO @ Sun, 03 Jun 2018 13:24:35: 4000000 INFO @ Sun, 03 Jun 2018 13:24:38: 5000000 INFO @ Sun, 03 Jun 2018 13:24:40: 5000000 INFO @ Sun, 03 Jun 2018 13:24:41: 5000000 INFO @ Sun, 03 Jun 2018 13:24:43: 6000000 INFO @ Sun, 03 Jun 2018 13:24:46: 6000000 INFO @ Sun, 03 Jun 2018 13:24:47: 6000000 INFO @ Sun, 03 Jun 2018 13:24:49: 7000000 INFO @ Sun, 03 Jun 2018 13:24:52: 7000000 INFO @ Sun, 03 Jun 2018 13:24:53: 7000000 INFO @ Sun, 03 Jun 2018 13:24:54: 8000000 INFO @ Sun, 03 Jun 2018 13:24:59: 8000000 INFO @ Sun, 03 Jun 2018 13:24:59: 8000000 INFO @ Sun, 03 Jun 2018 13:25:00: 9000000 INFO @ Sun, 03 Jun 2018 13:25:05: 9000000 INFO @ Sun, 03 Jun 2018 13:25:05: 9000000 INFO @ Sun, 03 Jun 2018 13:25:06: 10000000 INFO @ Sun, 03 Jun 2018 13:25:11: 10000000 INFO @ Sun, 03 Jun 2018 13:25:11: 11000000 INFO @ Sun, 03 Jun 2018 13:25:12: 10000000 INFO @ Sun, 03 Jun 2018 13:25:17: 12000000 INFO @ Sun, 03 Jun 2018 13:25:17: 11000000 INFO @ Sun, 03 Jun 2018 13:25:18: 11000000 INFO @ Sun, 03 Jun 2018 13:25:22: 13000000 INFO @ Sun, 03 Jun 2018 13:25:23: 12000000 INFO @ Sun, 03 Jun 2018 13:25:24: 12000000 INFO @ Sun, 03 Jun 2018 13:25:28: 14000000 INFO @ Sun, 03 Jun 2018 13:25:29: 13000000 INFO @ Sun, 03 Jun 2018 13:25:30: 13000000 INFO @ Sun, 03 Jun 2018 13:25:33: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:25:33: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:25:33: #1 total tags in treatment: 5395207 INFO @ Sun, 03 Jun 2018 13:25:33: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:25:33: #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 13:25:33: #1 tags after filtering in treatment: 4897856 INFO @ Sun, 03 Jun 2018 13:25:33: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:25:33: #1 finished! INFO @ Sun, 03 Jun 2018 13:25:33: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:25:33: #2 number of paired peaks: 258 WARNING @ Sun, 03 Jun 2018 13:25:33: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 03 Jun 2018 13:25:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:25:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:25:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:25:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:25:33: #2 predicted fragment length is 106 bps INFO @ Sun, 03 Jun 2018 13:25:33: #2 alternative fragment length(s) may be 106,126 bps INFO @ Sun, 03 Jun 2018 13:25:33: #2.2 Generate R script for model : SRX4085441.20_model.r INFO @ Sun, 03 Jun 2018 13:25:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:25:35: 14000000 INFO @ Sun, 03 Jun 2018 13:25:36: 14000000 INFO @ Sun, 03 Jun 2018 13:25:40: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:25:40: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:25:40: #1 total tags in treatment: 5395207 INFO @ Sun, 03 Jun 2018 13:25:40: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:25:40: #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 13:25:41: #1 tags after filtering in treatment: 4897856 INFO @ Sun, 03 Jun 2018 13:25:41: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:25:41: #1 finished! INFO @ Sun, 03 Jun 2018 13:25:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:25:41: #2 number of paired peaks: 258 WARNING @ Sun, 03 Jun 2018 13:25:41: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 03 Jun 2018 13:25:41: start model_add_line... INFO @ Sun, 03 Jun 2018 13:25:41: start X-correlation... INFO @ Sun, 03 Jun 2018 13:25:41: end of X-cor INFO @ Sun, 03 Jun 2018 13:25:41: #2 finished! INFO @ Sun, 03 Jun 2018 13:25:41: #2 predicted fragment length is 106 bps INFO @ Sun, 03 Jun 2018 13:25:41: #2 alternative fragment length(s) may be 106,126 bps INFO @ Sun, 03 Jun 2018 13:25:41: #2.2 Generate R script for model : SRX4085441.05_model.r INFO @ Sun, 03 Jun 2018 13:25:41: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:25:41: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:25:41: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:25:41: #1 total tags in treatment: 5395207 INFO @ Sun, 03 Jun 2018 13:25:41: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:25:41: #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 13:25:41: #1 tags after filtering in treatment: 4897856 INFO @ Sun, 03 Jun 2018 13:25:41: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:25:41: #1 finished! INFO @ Sun, 03 Jun 2018 13:25:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:25:42: #2 number of paired peaks: 258 WARNING @ Sun, 03 Jun 2018 13:25:42: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 03 Jun 2018 13:25:42: start model_add_line... INFO @ Sun, 03 Jun 2018 13:25:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:25:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:25:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:25:42: #2 predicted fragment length is 106 bps INFO @ Sun, 03 Jun 2018 13:25:42: #2 alternative fragment length(s) may be 106,126 bps INFO @ Sun, 03 Jun 2018 13:25:42: #2.2 Generate R script for model : SRX4085441.10_model.r INFO @ Sun, 03 Jun 2018 13:25:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:25:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:25:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:52: #4 Write output xls file... SRX4085441.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:52: #4 Write peak in narrowPeak format file... SRX4085441.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:52: #4 Write summits bed file... SRX4085441.20_summits.bed INFO @ Sun, 03 Jun 2018 13:25:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:25:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:59: #4 Write output xls file... SRX4085441.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:59: #4 Write peak in narrowPeak format file... SRX4085441.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:59: #4 Write summits bed file... SRX4085441.10_summits.bed INFO @ Sun, 03 Jun 2018 13:25:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (428 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:26:00: #4 Write output xls file... SRX4085441.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:26:00: #4 Write peak in narrowPeak format file... SRX4085441.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:26:00: #4 Write summits bed file... SRX4085441.05_summits.bed INFO @ Sun, 03 Jun 2018 13:26:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1217 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。