Job ID = 9156967 sra ファイルのダウンロード中... Completed: 534155K bytes transferred in 7 seconds (554917K 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 15555360 spots for /home/okishinya/chipatlas/results/ce10/SRX2228860/SRR4380316.sra Written 15555360 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: 00:03:58 15555360 reads; of these: 15555360 (100.00%) were unpaired; of these: 2142098 (13.77%) aligned 0 times 11142819 (71.63%) aligned exactly 1 time 2270443 (14.60%) aligned >1 times 86.23% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 2258694 / 13413262 = 0.1684 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 10:41:06: # Command line: callpeak -t SRX2228860.bam -f BAM -g ce -n SRX2228860.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228860.20 # format = BAM # ChIP-seq file = ['SRX2228860.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 10:41:06: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:41:06: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:41:06: # Command line: callpeak -t SRX2228860.bam -f BAM -g ce -n SRX2228860.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228860.05 # format = BAM # ChIP-seq file = ['SRX2228860.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 10:41:06: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:41:06: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:41:06: # Command line: callpeak -t SRX2228860.bam -f BAM -g ce -n SRX2228860.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228860.10 # format = BAM # ChIP-seq file = ['SRX2228860.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 10:41:06: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:41:06: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:41:12: 1000000 INFO @ Tue, 27 Jun 2017 10:41:12: 1000000 INFO @ Tue, 27 Jun 2017 10:41:13: 1000000 INFO @ Tue, 27 Jun 2017 10:41:19: 2000000 INFO @ Tue, 27 Jun 2017 10:41:19: 2000000 INFO @ Tue, 27 Jun 2017 10:41:19: 2000000 INFO @ Tue, 27 Jun 2017 10:41:25: 3000000 INFO @ Tue, 27 Jun 2017 10:41:25: 3000000 INFO @ Tue, 27 Jun 2017 10:41:25: 3000000 INFO @ Tue, 27 Jun 2017 10:41:31: 4000000 INFO @ Tue, 27 Jun 2017 10:41:31: 4000000 INFO @ Tue, 27 Jun 2017 10:41:31: 4000000 INFO @ Tue, 27 Jun 2017 10:41:37: 5000000 INFO @ Tue, 27 Jun 2017 10:41:37: 5000000 INFO @ Tue, 27 Jun 2017 10:41:37: 5000000 INFO @ Tue, 27 Jun 2017 10:41:43: 6000000 INFO @ Tue, 27 Jun 2017 10:41:43: 6000000 INFO @ Tue, 27 Jun 2017 10:41:43: 6000000 INFO @ Tue, 27 Jun 2017 10:41:49: 7000000 INFO @ Tue, 27 Jun 2017 10:41:49: 7000000 INFO @ Tue, 27 Jun 2017 10:41:50: 7000000 INFO @ Tue, 27 Jun 2017 10:41:55: 8000000 INFO @ Tue, 27 Jun 2017 10:41:56: 8000000 INFO @ Tue, 27 Jun 2017 10:41:56: 8000000 INFO @ Tue, 27 Jun 2017 10:42:02: 9000000 INFO @ Tue, 27 Jun 2017 10:42:02: 9000000 INFO @ Tue, 27 Jun 2017 10:42:02: 9000000 INFO @ Tue, 27 Jun 2017 10:42:08: 10000000 INFO @ Tue, 27 Jun 2017 10:42:08: 10000000 INFO @ Tue, 27 Jun 2017 10:42:08: 10000000 INFO @ Tue, 27 Jun 2017 10:42:14: 11000000 INFO @ Tue, 27 Jun 2017 10:42:14: 11000000 INFO @ Tue, 27 Jun 2017 10:42:15: 11000000 INFO @ Tue, 27 Jun 2017 10:42:15: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:42:15: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:42:15: #1 total tags in treatment: 11154568 INFO @ Tue, 27 Jun 2017 10:42:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:42:15: #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 10:42:15: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:42:15: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:42:15: #1 total tags in treatment: 11154568 INFO @ Tue, 27 Jun 2017 10:42:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:42:15: #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 10:42:16: #1 tags after filtering in treatment: 11154568 INFO @ Tue, 27 Jun 2017 10:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:42:16: #1 finished! INFO @ Tue, 27 Jun 2017 10:42:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:42:16: #1 tags after filtering in treatment: 11154568 INFO @ Tue, 27 Jun 2017 10:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:42:16: #1 finished! INFO @ Tue, 27 Jun 2017 10:42:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:42:16: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:42:16: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:42:16: #1 total tags in treatment: 11154568 INFO @ Tue, 27 Jun 2017 10:42:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:42:16: #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 10:42:16: #1 tags after filtering in treatment: 11154568 INFO @ Tue, 27 Jun 2017 10:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:42:16: #1 finished! INFO @ Tue, 27 Jun 2017 10:42:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:42:16: #2 number of paired peaks: 377 WARNING @ Tue, 27 Jun 2017 10:42:16: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 27 Jun 2017 10:42:16: start model_add_line... INFO @ Tue, 27 Jun 2017 10:42:16: #2 number of paired peaks: 377 WARNING @ Tue, 27 Jun 2017 10:42:16: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 27 Jun 2017 10:42:16: start model_add_line... INFO @ Tue, 27 Jun 2017 10:42:17: start X-correlation... INFO @ Tue, 27 Jun 2017 10:42:17: end of X-cor INFO @ Tue, 27 Jun 2017 10:42:17: #2 finished! INFO @ Tue, 27 Jun 2017 10:42:17: #2 predicted fragment length is 114 bps INFO @ Tue, 27 Jun 2017 10:42:17: #2 alternative fragment length(s) may be 4,90,114,598 bps INFO @ Tue, 27 Jun 2017 10:42:17: #2.2 Generate R script for model : SRX2228860.10_model.r INFO @ Tue, 27 Jun 2017 10:42:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:42:17: start X-correlation... INFO @ Tue, 27 Jun 2017 10:42:17: end of X-cor INFO @ Tue, 27 Jun 2017 10:42:17: #2 finished! INFO @ Tue, 27 Jun 2017 10:42:17: #2 predicted fragment length is 114 bps INFO @ Tue, 27 Jun 2017 10:42:17: #2 alternative fragment length(s) may be 4,90,114,598 bps INFO @ Tue, 27 Jun 2017 10:42:17: #2.2 Generate R script for model : SRX2228860.20_model.r INFO @ Tue, 27 Jun 2017 10:42:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:42:17: #2 number of paired peaks: 377 WARNING @ Tue, 27 Jun 2017 10:42:17: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Tue, 27 Jun 2017 10:42:17: start model_add_line... INFO @ Tue, 27 Jun 2017 10:42:17: start X-correlation... INFO @ Tue, 27 Jun 2017 10:42:17: end of X-cor INFO @ Tue, 27 Jun 2017 10:42:17: #2 finished! INFO @ Tue, 27 Jun 2017 10:42:17: #2 predicted fragment length is 114 bps INFO @ Tue, 27 Jun 2017 10:42:17: #2 alternative fragment length(s) may be 4,90,114,598 bps INFO @ Tue, 27 Jun 2017 10:42:17: #2.2 Generate R script for model : SRX2228860.05_model.r INFO @ Tue, 27 Jun 2017 10:42:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:42:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:42:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:42:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:42:54: #4 Write output xls file... SRX2228860.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:42:54: #4 Write peak in narrowPeak format file... SRX2228860.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:42:54: #4 Write summits bed file... SRX2228860.05_summits.bed INFO @ Tue, 27 Jun 2017 10:42:54: Done! INFO @ Tue, 27 Jun 2017 10:42:54: #4 Write output xls file... SRX2228860.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:42:54: #4 Write peak in narrowPeak format file... SRX2228860.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:42:54: #4 Write summits bed file... SRX2228860.20_summits.bed INFO @ Tue, 27 Jun 2017 10:42:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1841 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:42:56: #4 Write output xls file... SRX2228860.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:42:56: #4 Write peak in narrowPeak format file... SRX2228860.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:42:56: #4 Write summits bed file... SRX2228860.10_summits.bed INFO @ Tue, 27 Jun 2017 10:42:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (979 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。