Job ID = 9157168 sra ファイルのダウンロード中... Completed: 294043K bytes transferred in 5 seconds (433778K bits/sec), in 1 file, 2 directories. 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 13966004 spots for /home/okishinya/chipatlas/results/ce10/SRX2228890/SRR4380346.sra Written 13966004 spots total 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: 00:03:16 13966004 reads; of these: 13966004 (100.00%) were unpaired; of these: 1700098 (12.17%) aligned 0 times 10321786 (73.91%) aligned exactly 1 time 1944120 (13.92%) aligned >1 times 87.83% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 2060402 / 12265906 = 0.1680 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 @ Tue, 27 Jun 2017 10:56:21: # Command line: callpeak -t SRX2228890.bam -f BAM -g ce -n SRX2228890.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228890.05 # format = BAM # ChIP-seq file = ['SRX2228890.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 @ Tue, 27 Jun 2017 10:56:21: # Command line: callpeak -t SRX2228890.bam -f BAM -g ce -n SRX2228890.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228890.20 # format = BAM # ChIP-seq file = ['SRX2228890.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 @ Tue, 27 Jun 2017 10:56:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:56:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:56:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:56:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:56:21: # Command line: callpeak -t SRX2228890.bam -f BAM -g ce -n SRX2228890.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228890.10 # format = BAM # ChIP-seq file = ['SRX2228890.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 @ Tue, 27 Jun 2017 10:56:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:56:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:56:28: 1000000 INFO @ Tue, 27 Jun 2017 10:56:28: 1000000 INFO @ Tue, 27 Jun 2017 10:56:28: 1000000 INFO @ Tue, 27 Jun 2017 10:56:35: 2000000 INFO @ Tue, 27 Jun 2017 10:56:35: 2000000 INFO @ Tue, 27 Jun 2017 10:56:35: 2000000 INFO @ Tue, 27 Jun 2017 10:56:42: 3000000 INFO @ Tue, 27 Jun 2017 10:56:42: 3000000 INFO @ Tue, 27 Jun 2017 10:56:42: 3000000 INFO @ Tue, 27 Jun 2017 10:56:49: 4000000 INFO @ Tue, 27 Jun 2017 10:56:49: 4000000 INFO @ Tue, 27 Jun 2017 10:56:49: 4000000 INFO @ Tue, 27 Jun 2017 10:56:55: 5000000 INFO @ Tue, 27 Jun 2017 10:56:56: 5000000 INFO @ Tue, 27 Jun 2017 10:56:56: 5000000 INFO @ Tue, 27 Jun 2017 10:57:02: 6000000 INFO @ Tue, 27 Jun 2017 10:57:03: 6000000 INFO @ Tue, 27 Jun 2017 10:57:03: 6000000 INFO @ Tue, 27 Jun 2017 10:57:09: 7000000 INFO @ Tue, 27 Jun 2017 10:57:10: 7000000 INFO @ Tue, 27 Jun 2017 10:57:10: 7000000 INFO @ Tue, 27 Jun 2017 10:57:16: 8000000 INFO @ Tue, 27 Jun 2017 10:57:17: 8000000 INFO @ Tue, 27 Jun 2017 10:57:17: 8000000 INFO @ Tue, 27 Jun 2017 10:57:23: 9000000 INFO @ Tue, 27 Jun 2017 10:57:24: 9000000 INFO @ Tue, 27 Jun 2017 10:57:24: 9000000 INFO @ Tue, 27 Jun 2017 10:57:30: 10000000 INFO @ Tue, 27 Jun 2017 10:57:31: 10000000 INFO @ Tue, 27 Jun 2017 10:57:31: 10000000 INFO @ Tue, 27 Jun 2017 10:57:32: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:57:32: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:57:32: #1 total tags in treatment: 10205504 INFO @ Tue, 27 Jun 2017 10:57:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:57:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 10:57:32: #1 tags after filtering in treatment: 10205504 INFO @ Tue, 27 Jun 2017 10:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:57:32: #1 finished! INFO @ Tue, 27 Jun 2017 10:57:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:57:32: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:57:32: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:57:32: #1 total tags in treatment: 10205504 INFO @ Tue, 27 Jun 2017 10:57:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:57:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 10:57:33: #1 tags after filtering in treatment: 10205504 INFO @ Tue, 27 Jun 2017 10:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:57:33: #1 finished! INFO @ Tue, 27 Jun 2017 10:57:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:57:33: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:57:33: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:57:33: #1 total tags in treatment: 10205504 INFO @ Tue, 27 Jun 2017 10:57:33: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:57:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 10:57:33: #1 tags after filtering in treatment: 10205504 INFO @ Tue, 27 Jun 2017 10:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:57:33: #1 finished! INFO @ Tue, 27 Jun 2017 10:57:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:57:33: #2 number of paired peaks: 849 WARNING @ Tue, 27 Jun 2017 10:57:33: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Tue, 27 Jun 2017 10:57:33: start model_add_line... INFO @ Tue, 27 Jun 2017 10:57:33: start X-correlation... INFO @ Tue, 27 Jun 2017 10:57:33: end of X-cor INFO @ Tue, 27 Jun 2017 10:57:33: #2 finished! INFO @ Tue, 27 Jun 2017 10:57:33: #2 predicted fragment length is 183 bps INFO @ Tue, 27 Jun 2017 10:57:33: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 27 Jun 2017 10:57:33: #2.2 Generate R script for model : SRX2228890.20_model.r INFO @ Tue, 27 Jun 2017 10:57:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:57:33: #2 number of paired peaks: 849 WARNING @ Tue, 27 Jun 2017 10:57:33: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Tue, 27 Jun 2017 10:57:33: start model_add_line... INFO @ Tue, 27 Jun 2017 10:57:34: start X-correlation... INFO @ Tue, 27 Jun 2017 10:57:34: end of X-cor INFO @ Tue, 27 Jun 2017 10:57:34: #2 finished! INFO @ Tue, 27 Jun 2017 10:57:34: #2 predicted fragment length is 183 bps INFO @ Tue, 27 Jun 2017 10:57:34: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 27 Jun 2017 10:57:34: #2.2 Generate R script for model : SRX2228890.05_model.r INFO @ Tue, 27 Jun 2017 10:57:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:57:34: #2 number of paired peaks: 849 WARNING @ Tue, 27 Jun 2017 10:57:34: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Tue, 27 Jun 2017 10:57:34: start model_add_line... INFO @ Tue, 27 Jun 2017 10:57:34: start X-correlation... INFO @ Tue, 27 Jun 2017 10:57:34: end of X-cor INFO @ Tue, 27 Jun 2017 10:57:34: #2 finished! INFO @ Tue, 27 Jun 2017 10:57:34: #2 predicted fragment length is 183 bps INFO @ Tue, 27 Jun 2017 10:57:34: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 27 Jun 2017 10:57:34: #2.2 Generate R script for model : SRX2228890.10_model.r INFO @ Tue, 27 Jun 2017 10:57:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:57:59: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:00: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:01: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:11: #4 Write output xls file... SRX2228890.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:11: #4 Write peak in narrowPeak format file... SRX2228890.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:11: #4 Write summits bed file... SRX2228890.05_summits.bed INFO @ Tue, 27 Jun 2017 10:58:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2575 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:58:11: #4 Write output xls file... SRX2228890.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:11: #4 Write peak in narrowPeak format file... SRX2228890.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:11: #4 Write summits bed file... SRX2228890.20_summits.bed INFO @ Tue, 27 Jun 2017 10:58:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (931 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:58:12: #4 Write output xls file... SRX2228890.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:12: #4 Write peak in narrowPeak format file... SRX2228890.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:12: #4 Write summits bed file... SRX2228890.10_summits.bed INFO @ Tue, 27 Jun 2017 10:58:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1561 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。