Job ID = 9156884 sra ファイルのダウンロード中... Completed: 260389K bytes transferred in 5 seconds (393502K 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 8154140 spots for /home/okishinya/chipatlas/results/ce10/SRX2228849/SRR4380305.sra Written 8154140 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:02 8154140 reads; of these: 8154140 (100.00%) were unpaired; of these: 1505912 (18.47%) aligned 0 times 5616380 (68.88%) aligned exactly 1 time 1031848 (12.65%) aligned >1 times 81.53% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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_rmdupse_core] 1478006 / 6648228 = 0.2223 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 10:24:11: # Command line: callpeak -t SRX2228849.bam -f BAM -g ce -n SRX2228849.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228849.05 # format = BAM # ChIP-seq file = ['SRX2228849.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 10:24:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:24:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:24:11: # Command line: callpeak -t SRX2228849.bam -f BAM -g ce -n SRX2228849.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228849.20 # format = BAM # ChIP-seq file = ['SRX2228849.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 10:24:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:24:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:24:11: # Command line: callpeak -t SRX2228849.bam -f BAM -g ce -n SRX2228849.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228849.10 # format = BAM # ChIP-seq file = ['SRX2228849.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 10:24:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:24:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:24:20: 1000000 INFO @ Tue, 27 Jun 2017 10:24:20: 1000000 INFO @ Tue, 27 Jun 2017 10:24:20: 1000000 INFO @ Tue, 27 Jun 2017 10:24:29: 2000000 INFO @ Tue, 27 Jun 2017 10:24:29: 2000000 INFO @ Tue, 27 Jun 2017 10:24:29: 2000000 INFO @ Tue, 27 Jun 2017 10:24:37: 3000000 INFO @ Tue, 27 Jun 2017 10:24:38: 3000000 INFO @ Tue, 27 Jun 2017 10:24:38: 3000000 INFO @ Tue, 27 Jun 2017 10:24:46: 4000000 INFO @ Tue, 27 Jun 2017 10:24:47: 4000000 INFO @ Tue, 27 Jun 2017 10:24:47: 4000000 INFO @ Tue, 27 Jun 2017 10:24:54: 5000000 INFO @ Tue, 27 Jun 2017 10:24:56: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:24:56: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:24:56: #1 total tags in treatment: 5170222 INFO @ Tue, 27 Jun 2017 10:24:56: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:24:56: #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 10:24:56: #1 tags after filtering in treatment: 5170222 INFO @ Tue, 27 Jun 2017 10:24:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:24:56: #1 finished! INFO @ Tue, 27 Jun 2017 10:24:56: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:24:56: 5000000 INFO @ Tue, 27 Jun 2017 10:24:56: 5000000 INFO @ Tue, 27 Jun 2017 10:24:56: #2 number of paired peaks: 582 WARNING @ Tue, 27 Jun 2017 10:24:56: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Tue, 27 Jun 2017 10:24:56: start model_add_line... INFO @ Tue, 27 Jun 2017 10:24:56: start X-correlation... INFO @ Tue, 27 Jun 2017 10:24:56: end of X-cor INFO @ Tue, 27 Jun 2017 10:24:56: #2 finished! INFO @ Tue, 27 Jun 2017 10:24:56: #2 predicted fragment length is 177 bps INFO @ Tue, 27 Jun 2017 10:24:56: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 27 Jun 2017 10:24:56: #2.2 Generate R script for model : SRX2228849.10_model.r INFO @ Tue, 27 Jun 2017 10:24:56: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:24:57: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:24:57: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:24:57: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:24:57: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:24:57: #1 total tags in treatment: 5170222 INFO @ Tue, 27 Jun 2017 10:24:57: #1 total tags in treatment: 5170222 INFO @ Tue, 27 Jun 2017 10:24:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:24:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:24:57: #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 10:24:57: #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 10:24:58: #1 tags after filtering in treatment: 5170222 INFO @ Tue, 27 Jun 2017 10:24:58: #1 tags after filtering in treatment: 5170222 INFO @ Tue, 27 Jun 2017 10:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:24:58: #1 finished! INFO @ Tue, 27 Jun 2017 10:24:58: #1 finished! INFO @ Tue, 27 Jun 2017 10:24:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:24:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:24:58: #2 number of paired peaks: 582 WARNING @ Tue, 27 Jun 2017 10:24:58: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Tue, 27 Jun 2017 10:24:58: start model_add_line... INFO @ Tue, 27 Jun 2017 10:24:58: #2 number of paired peaks: 582 WARNING @ Tue, 27 Jun 2017 10:24:58: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Tue, 27 Jun 2017 10:24:58: start model_add_line... INFO @ Tue, 27 Jun 2017 10:24:58: start X-correlation... INFO @ Tue, 27 Jun 2017 10:24:58: start X-correlation... INFO @ Tue, 27 Jun 2017 10:24:58: end of X-cor INFO @ Tue, 27 Jun 2017 10:24:58: #2 finished! INFO @ Tue, 27 Jun 2017 10:24:58: #2 predicted fragment length is 177 bps INFO @ Tue, 27 Jun 2017 10:24:58: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 27 Jun 2017 10:24:58: #2.2 Generate R script for model : SRX2228849.20_model.r INFO @ Tue, 27 Jun 2017 10:24:58: end of X-cor INFO @ Tue, 27 Jun 2017 10:24:58: #2 finished! INFO @ Tue, 27 Jun 2017 10:24:58: #2 predicted fragment length is 177 bps INFO @ Tue, 27 Jun 2017 10:24:58: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 27 Jun 2017 10:24:58: #2.2 Generate R script for model : SRX2228849.05_model.r INFO @ Tue, 27 Jun 2017 10:24:58: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:24:58: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:25:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:25:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:25:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write output xls file... SRX2228849.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write peak in narrowPeak format file... SRX2228849.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write summits bed file... SRX2228849.05_summits.bed INFO @ Tue, 27 Jun 2017 10:25:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (642 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write output xls file... SRX2228849.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write peak in narrowPeak format file... SRX2228849.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write summits bed file... SRX2228849.10_summits.bed INFO @ Tue, 27 Jun 2017 10:25:19: Done! INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write output xls file... SRX2228849.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write peak in narrowPeak format file... SRX2228849.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:25:19: #4 Write summits bed file... SRX2228849.20_summits.bed INFO @ Tue, 27 Jun 2017 10:25:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。