Job ID = 10201967 sra ファイルのダウンロード中... Completed: 457020K bytes transferred in 14 seconds (264497K 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: SINGLE fastq に変換中... Written 19947557 spots for /home/okishinya/chipatlas/results/ce10/SRX2576636/SRR5272593.sra Written 19947557 spots total 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: 00:00:01 Multiseed full-index search: 00:03:34 19947557 reads; of these: 19947557 (100.00%) were unpaired; of these: 717958 (3.60%) aligned 0 times 15849176 (79.45%) aligned exactly 1 time 3380423 (16.95%) aligned >1 times 96.40% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_rmdupse_core] 3301306 / 19229599 = 0.1717 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 @ Mon, 13 Nov 2017 13:16:42: # Command line: callpeak -t SRX2576636.bam -f BAM -g ce -n SRX2576636.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576636.05 # format = BAM # ChIP-seq file = ['SRX2576636.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 @ Mon, 13 Nov 2017 13:16:42: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:42: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:42: # Command line: callpeak -t SRX2576636.bam -f BAM -g ce -n SRX2576636.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576636.10 # format = BAM # ChIP-seq file = ['SRX2576636.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 @ Mon, 13 Nov 2017 13:16:42: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:42: # Command line: callpeak -t SRX2576636.bam -f BAM -g ce -n SRX2576636.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576636.20 # format = BAM # ChIP-seq file = ['SRX2576636.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 @ Mon, 13 Nov 2017 13:16:42: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:42: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:42: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:50: 1000000 INFO @ Mon, 13 Nov 2017 13:16:50: 1000000 INFO @ Mon, 13 Nov 2017 13:16:50: 1000000 INFO @ Mon, 13 Nov 2017 13:16:58: 2000000 INFO @ Mon, 13 Nov 2017 13:16:58: 2000000 INFO @ Mon, 13 Nov 2017 13:16:58: 2000000 INFO @ Mon, 13 Nov 2017 13:17:06: 3000000 INFO @ Mon, 13 Nov 2017 13:17:06: 3000000 INFO @ Mon, 13 Nov 2017 13:17:06: 3000000 INFO @ Mon, 13 Nov 2017 13:17:13: 4000000 INFO @ Mon, 13 Nov 2017 13:17:13: 4000000 INFO @ Mon, 13 Nov 2017 13:17:13: 4000000 INFO @ Mon, 13 Nov 2017 13:17:19: 5000000 INFO @ Mon, 13 Nov 2017 13:17:20: 5000000 INFO @ Mon, 13 Nov 2017 13:17:20: 5000000 INFO @ Mon, 13 Nov 2017 13:17:26: 6000000 INFO @ Mon, 13 Nov 2017 13:17:27: 6000000 INFO @ Mon, 13 Nov 2017 13:17:27: 6000000 INFO @ Mon, 13 Nov 2017 13:17:32: 7000000 INFO @ Mon, 13 Nov 2017 13:17:34: 7000000 INFO @ Mon, 13 Nov 2017 13:17:34: 7000000 INFO @ Mon, 13 Nov 2017 13:17:39: 8000000 INFO @ Mon, 13 Nov 2017 13:17:41: 8000000 INFO @ Mon, 13 Nov 2017 13:17:41: 8000000 INFO @ Mon, 13 Nov 2017 13:17:46: 9000000 INFO @ Mon, 13 Nov 2017 13:17:48: 9000000 INFO @ Mon, 13 Nov 2017 13:17:48: 9000000 INFO @ Mon, 13 Nov 2017 13:17:53: 10000000 INFO @ Mon, 13 Nov 2017 13:17:55: 10000000 INFO @ Mon, 13 Nov 2017 13:17:55: 10000000 INFO @ Mon, 13 Nov 2017 13:17:59: 11000000 INFO @ Mon, 13 Nov 2017 13:18:01: 11000000 INFO @ Mon, 13 Nov 2017 13:18:01: 11000000 INFO @ Mon, 13 Nov 2017 13:18:06: 12000000 INFO @ Mon, 13 Nov 2017 13:18:08: 12000000 INFO @ Mon, 13 Nov 2017 13:18:08: 12000000 INFO @ Mon, 13 Nov 2017 13:18:12: 13000000 INFO @ Mon, 13 Nov 2017 13:18:15: 13000000 INFO @ Mon, 13 Nov 2017 13:18:15: 13000000 INFO @ Mon, 13 Nov 2017 13:18:19: 14000000 INFO @ Mon, 13 Nov 2017 13:18:21: 14000000 INFO @ Mon, 13 Nov 2017 13:18:21: 14000000 INFO @ Mon, 13 Nov 2017 13:18:25: 15000000 INFO @ Mon, 13 Nov 2017 13:18:28: 15000000 INFO @ Mon, 13 Nov 2017 13:18:28: 15000000 INFO @ Mon, 13 Nov 2017 13:18:31: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:18:31: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:18:31: #1 total tags in treatment: 15928293 INFO @ Mon, 13 Nov 2017 13:18:31: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:31: #1 tags after filtering in treatment: 15928293 INFO @ Mon, 13 Nov 2017 13:18:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:31: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:31: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:33: #2 number of paired peaks: 530 WARNING @ Mon, 13 Nov 2017 13:18:33: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:33: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:33: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:33: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:33: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:33: #2 predicted fragment length is 127 bps INFO @ Mon, 13 Nov 2017 13:18:33: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 13 Nov 2017 13:18:33: #2.2 Generate R script for model : SRX2576636.05_model.r INFO @ Mon, 13 Nov 2017 13:18:33: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:34: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:18:34: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:18:34: #1 total tags in treatment: 15928293 INFO @ Mon, 13 Nov 2017 13:18:34: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:34: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:18:34: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:18:34: #1 total tags in treatment: 15928293 INFO @ Mon, 13 Nov 2017 13:18:34: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:35: #1 tags after filtering in treatment: 15928293 INFO @ Mon, 13 Nov 2017 13:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:35: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:35: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:35: #1 tags after filtering in treatment: 15928293 INFO @ Mon, 13 Nov 2017 13:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:35: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:35: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:36: #2 number of paired peaks: 530 WARNING @ Mon, 13 Nov 2017 13:18:36: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:36: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:36: #2 number of paired peaks: 530 WARNING @ Mon, 13 Nov 2017 13:18:36: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:36: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:36: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:36: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:36: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:36: #2 predicted fragment length is 127 bps INFO @ Mon, 13 Nov 2017 13:18:36: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 13 Nov 2017 13:18:36: #2.2 Generate R script for model : SRX2576636.10_model.r INFO @ Mon, 13 Nov 2017 13:18:36: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:36: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:36: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:36: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:36: #2 predicted fragment length is 127 bps INFO @ Mon, 13 Nov 2017 13:18:36: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 13 Nov 2017 13:18:36: #2.2 Generate R script for model : SRX2576636.20_model.r INFO @ Mon, 13 Nov 2017 13:18:36: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:07: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:11: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:11: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:23: #4 Write output xls file... SRX2576636.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:23: #4 Write peak in narrowPeak format file... SRX2576636.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:23: #4 Write summits bed file... SRX2576636.05_summits.bed INFO @ Mon, 13 Nov 2017 13:19:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2799 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:27: #4 Write output xls file... SRX2576636.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:27: #4 Write peak in narrowPeak format file... SRX2576636.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:27: #4 Write summits bed file... SRX2576636.20_summits.bed INFO @ Mon, 13 Nov 2017 13:19:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1366 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:27: #4 Write output xls file... SRX2576636.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:27: #4 Write peak in narrowPeak format file... SRX2576636.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:27: #4 Write summits bed file... SRX2576636.10_summits.bed INFO @ Mon, 13 Nov 2017 13:19:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1996 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。