Job ID = 10201980 sra ファイルのダウンロード中... Completed: 651587K bytes transferred in 18 seconds (295137K 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 19310034 spots for /home/okishinya/chipatlas/results/ce10/SRX2576649/SRR5272606.sra Written 19310034 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: 00:13:10 19310034 reads; of these: 19310034 (100.00%) were unpaired; of these: 872235 (4.52%) aligned 0 times 15153463 (78.47%) aligned exactly 1 time 3284336 (17.01%) aligned >1 times 95.48% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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] 4048624 / 18437799 = 0.2196 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 13:30:24: # Command line: callpeak -t SRX2576649.bam -f BAM -g ce -n SRX2576649.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576649.20 # format = BAM # ChIP-seq file = ['SRX2576649.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 13:30:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:30:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:30:24: # Command line: callpeak -t SRX2576649.bam -f BAM -g ce -n SRX2576649.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576649.10 # format = BAM # ChIP-seq file = ['SRX2576649.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 13:30:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:30:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:30:24: # Command line: callpeak -t SRX2576649.bam -f BAM -g ce -n SRX2576649.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576649.05 # format = BAM # ChIP-seq file = ['SRX2576649.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 13:30:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:30:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:30:40: 1000000 INFO @ Mon, 13 Nov 2017 13:30:45: 1000000 INFO @ Mon, 13 Nov 2017 13:30:48: 1000000 INFO @ Mon, 13 Nov 2017 13:30:58: 2000000 INFO @ Mon, 13 Nov 2017 13:31:07: 2000000 INFO @ Mon, 13 Nov 2017 13:31:11: 2000000 INFO @ Mon, 13 Nov 2017 13:31:15: 3000000 INFO @ Mon, 13 Nov 2017 13:31:24: 3000000 INFO @ Mon, 13 Nov 2017 13:31:35: 3000000 INFO @ Mon, 13 Nov 2017 13:31:36: 4000000 INFO @ Mon, 13 Nov 2017 13:31:42: 4000000 INFO @ Mon, 13 Nov 2017 13:31:57: 4000000 INFO @ Mon, 13 Nov 2017 13:32:01: 5000000 INFO @ Mon, 13 Nov 2017 13:32:03: 5000000 INFO @ Mon, 13 Nov 2017 13:32:19: 6000000 INFO @ Mon, 13 Nov 2017 13:32:20: 5000000 INFO @ Mon, 13 Nov 2017 13:32:30: 6000000 INFO @ Mon, 13 Nov 2017 13:32:36: 7000000 INFO @ Mon, 13 Nov 2017 13:32:43: 6000000 INFO @ Mon, 13 Nov 2017 13:32:53: 8000000 INFO @ Mon, 13 Nov 2017 13:32:56: 7000000 INFO @ Mon, 13 Nov 2017 13:33:06: 7000000 INFO @ Mon, 13 Nov 2017 13:33:10: 9000000 INFO @ Mon, 13 Nov 2017 13:33:24: 8000000 INFO @ Mon, 13 Nov 2017 13:33:26: 10000000 INFO @ Mon, 13 Nov 2017 13:33:29: 8000000 INFO @ Mon, 13 Nov 2017 13:33:42: 11000000 INFO @ Mon, 13 Nov 2017 13:33:48: 9000000 INFO @ Mon, 13 Nov 2017 13:33:52: 9000000 INFO @ Mon, 13 Nov 2017 13:33:59: 12000000 INFO @ Mon, 13 Nov 2017 13:34:05: 10000000 INFO @ Mon, 13 Nov 2017 13:34:14: 10000000 INFO @ Mon, 13 Nov 2017 13:34:17: 13000000 INFO @ Mon, 13 Nov 2017 13:34:25: 11000000 INFO @ Mon, 13 Nov 2017 13:34:32: 14000000 INFO @ Mon, 13 Nov 2017 13:34:36: 11000000 INFO @ Mon, 13 Nov 2017 13:34:38: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:34:38: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:34:38: #1 total tags in treatment: 14389175 INFO @ Mon, 13 Nov 2017 13:34:38: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:34:38: #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 13:34:39: #1 tags after filtering in treatment: 14389175 INFO @ Mon, 13 Nov 2017 13:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:34:39: #1 finished! INFO @ Mon, 13 Nov 2017 13:34:39: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:34:40: #2 number of paired peaks: 353 WARNING @ Mon, 13 Nov 2017 13:34:40: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 13 Nov 2017 13:34:40: start model_add_line... INFO @ Mon, 13 Nov 2017 13:34:40: start X-correlation... INFO @ Mon, 13 Nov 2017 13:34:40: end of X-cor INFO @ Mon, 13 Nov 2017 13:34:40: #2 finished! INFO @ Mon, 13 Nov 2017 13:34:40: #2 predicted fragment length is 133 bps INFO @ Mon, 13 Nov 2017 13:34:40: #2 alternative fragment length(s) may be 4,133 bps INFO @ Mon, 13 Nov 2017 13:34:40: #2.2 Generate R script for model : SRX2576649.05_model.r INFO @ Mon, 13 Nov 2017 13:34:40: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:34:50: 12000000 INFO @ Mon, 13 Nov 2017 13:34:59: 12000000 INFO @ Mon, 13 Nov 2017 13:35:14: 13000000 INFO @ Mon, 13 Nov 2017 13:35:19: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:35:21: 13000000 INFO @ Mon, 13 Nov 2017 13:35:39: 14000000 INFO @ Mon, 13 Nov 2017 13:35:40: #4 Write output xls file... SRX2576649.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:35:40: #4 Write peak in narrowPeak format file... SRX2576649.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:35:40: #4 Write summits bed file... SRX2576649.05_summits.bed INFO @ Mon, 13 Nov 2017 13:35:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1889 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:35:45: 14000000 INFO @ Mon, 13 Nov 2017 13:35:48: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:35:48: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:35:48: #1 total tags in treatment: 14389175 INFO @ Mon, 13 Nov 2017 13:35:48: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:35:48: #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 13:35:49: #1 tags after filtering in treatment: 14389175 INFO @ Mon, 13 Nov 2017 13:35:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:35:49: #1 finished! INFO @ Mon, 13 Nov 2017 13:35:49: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:35:50: #2 number of paired peaks: 353 WARNING @ Mon, 13 Nov 2017 13:35:50: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 13 Nov 2017 13:35:50: start model_add_line... INFO @ Mon, 13 Nov 2017 13:35:50: start X-correlation... INFO @ Mon, 13 Nov 2017 13:35:50: end of X-cor INFO @ Mon, 13 Nov 2017 13:35:50: #2 finished! INFO @ Mon, 13 Nov 2017 13:35:50: #2 predicted fragment length is 133 bps INFO @ Mon, 13 Nov 2017 13:35:50: #2 alternative fragment length(s) may be 4,133 bps INFO @ Mon, 13 Nov 2017 13:35:50: #2.2 Generate R script for model : SRX2576649.20_model.r INFO @ Mon, 13 Nov 2017 13:35:50: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:35:53: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:35:53: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:35:53: #1 total tags in treatment: 14389175 INFO @ Mon, 13 Nov 2017 13:35:53: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:35:53: #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 13:35:53: #1 tags after filtering in treatment: 14389175 INFO @ Mon, 13 Nov 2017 13:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:35:53: #1 finished! INFO @ Mon, 13 Nov 2017 13:35:53: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:35:55: #2 number of paired peaks: 353 WARNING @ Mon, 13 Nov 2017 13:35:55: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 13 Nov 2017 13:35:55: start model_add_line... INFO @ Mon, 13 Nov 2017 13:35:55: start X-correlation... INFO @ Mon, 13 Nov 2017 13:35:55: end of X-cor INFO @ Mon, 13 Nov 2017 13:35:55: #2 finished! INFO @ Mon, 13 Nov 2017 13:35:55: #2 predicted fragment length is 133 bps INFO @ Mon, 13 Nov 2017 13:35:55: #2 alternative fragment length(s) may be 4,133 bps INFO @ Mon, 13 Nov 2017 13:35:55: #2.2 Generate R script for model : SRX2576649.10_model.r INFO @ Mon, 13 Nov 2017 13:35:55: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:36:29: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:36:35: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:36:50: #4 Write output xls file... SRX2576649.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:36:50: #4 Write peak in narrowPeak format file... SRX2576649.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:36:50: #4 Write summits bed file... SRX2576649.20_summits.bed INFO @ Mon, 13 Nov 2017 13:36:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:36:56: #4 Write output xls file... SRX2576649.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:36:56: #4 Write peak in narrowPeak format file... SRX2576649.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:36:56: #4 Write summits bed file... SRX2576649.10_summits.bed INFO @ Mon, 13 Nov 2017 13:36:56: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (1320 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。