Job ID = 9157147 sra ファイルのダウンロード中... Completed: 474967K bytes transferred in 5 seconds (655405K 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 14851943 spots for /home/okishinya/chipatlas/results/ce10/SRX2228876/SRR4380332.sra Written 14851943 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: 00:03:11 14851943 reads; of these: 14851943 (100.00%) were unpaired; of these: 5473427 (36.85%) aligned 0 times 7679656 (51.71%) aligned exactly 1 time 1698860 (11.44%) aligned >1 times 63.15% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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_rmdupse_core] 3805442 / 9378516 = 0.4058 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 10:49:44: # Command line: callpeak -t SRX2228876.bam -f BAM -g ce -n SRX2228876.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228876.05 # format = BAM # ChIP-seq file = ['SRX2228876.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 10:49:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:44: # Command line: callpeak -t SRX2228876.bam -f BAM -g ce -n SRX2228876.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228876.20 # format = BAM # ChIP-seq file = ['SRX2228876.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 10:49:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:44: # Command line: callpeak -t SRX2228876.bam -f BAM -g ce -n SRX2228876.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228876.10 # format = BAM # ChIP-seq file = ['SRX2228876.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 10:49:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:51: 1000000 INFO @ Tue, 27 Jun 2017 10:49:51: 1000000 INFO @ Tue, 27 Jun 2017 10:49:51: 1000000 INFO @ Tue, 27 Jun 2017 10:49:57: 2000000 INFO @ Tue, 27 Jun 2017 10:49:57: 2000000 INFO @ Tue, 27 Jun 2017 10:49:58: 2000000 INFO @ Tue, 27 Jun 2017 10:50:04: 3000000 INFO @ Tue, 27 Jun 2017 10:50:04: 3000000 INFO @ Tue, 27 Jun 2017 10:50:05: 3000000 INFO @ Tue, 27 Jun 2017 10:50:10: 4000000 INFO @ Tue, 27 Jun 2017 10:50:11: 4000000 INFO @ Tue, 27 Jun 2017 10:50:11: 4000000 INFO @ Tue, 27 Jun 2017 10:50:16: 5000000 INFO @ Tue, 27 Jun 2017 10:50:18: 5000000 INFO @ Tue, 27 Jun 2017 10:50:19: 5000000 INFO @ Tue, 27 Jun 2017 10:50:20: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:50:20: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:50:20: #1 total tags in treatment: 5573074 INFO @ Tue, 27 Jun 2017 10:50:20: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:50:20: #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 10:50:20: #1 tags after filtering in treatment: 5573074 INFO @ Tue, 27 Jun 2017 10:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:50:20: #1 finished! INFO @ Tue, 27 Jun 2017 10:50:20: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:50:21: #2 number of paired peaks: 501 WARNING @ Tue, 27 Jun 2017 10:50:21: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Tue, 27 Jun 2017 10:50:21: start model_add_line... INFO @ Tue, 27 Jun 2017 10:50:21: start X-correlation... INFO @ Tue, 27 Jun 2017 10:50:21: end of X-cor INFO @ Tue, 27 Jun 2017 10:50:21: #2 finished! INFO @ Tue, 27 Jun 2017 10:50:21: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 10:50:21: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 27 Jun 2017 10:50:21: #2.2 Generate R script for model : SRX2228876.10_model.r WARNING @ Tue, 27 Jun 2017 10:50:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:50:21: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 27 Jun 2017 10:50:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 10:50:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:50:22: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:50:22: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:50:22: #1 total tags in treatment: 5573074 INFO @ Tue, 27 Jun 2017 10:50:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:50:22: #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 10:50:22: #1 tags after filtering in treatment: 5573074 INFO @ Tue, 27 Jun 2017 10:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:50:22: #1 finished! INFO @ Tue, 27 Jun 2017 10:50:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:50:22: #2 number of paired peaks: 501 WARNING @ Tue, 27 Jun 2017 10:50:22: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Tue, 27 Jun 2017 10:50:22: start model_add_line... INFO @ Tue, 27 Jun 2017 10:50:22: start X-correlation... INFO @ Tue, 27 Jun 2017 10:50:22: end of X-cor INFO @ Tue, 27 Jun 2017 10:50:22: #2 finished! INFO @ Tue, 27 Jun 2017 10:50:22: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 10:50:22: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 27 Jun 2017 10:50:22: #2.2 Generate R script for model : SRX2228876.20_model.r WARNING @ Tue, 27 Jun 2017 10:50:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:50:22: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 27 Jun 2017 10:50:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 10:50:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:50:23: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:50:23: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:50:23: #1 total tags in treatment: 5573074 INFO @ Tue, 27 Jun 2017 10:50:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:50:23: #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 10:50:23: #1 tags after filtering in treatment: 5573074 INFO @ Tue, 27 Jun 2017 10:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:50:23: #1 finished! INFO @ Tue, 27 Jun 2017 10:50:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:50:23: #2 number of paired peaks: 501 WARNING @ Tue, 27 Jun 2017 10:50:23: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Tue, 27 Jun 2017 10:50:23: start model_add_line... INFO @ Tue, 27 Jun 2017 10:50:23: start X-correlation... INFO @ Tue, 27 Jun 2017 10:50:23: end of X-cor INFO @ Tue, 27 Jun 2017 10:50:23: #2 finished! INFO @ Tue, 27 Jun 2017 10:50:23: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 10:50:23: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 27 Jun 2017 10:50:23: #2.2 Generate R script for model : SRX2228876.05_model.r WARNING @ Tue, 27 Jun 2017 10:50:23: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:50:23: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 27 Jun 2017 10:50:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 10:50:23: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:50:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:50:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:50:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:50:41: #4 Write output xls file... SRX2228876.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:50:41: #4 Write peak in narrowPeak format file... SRX2228876.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:50:41: #4 Write summits bed file... SRX2228876.10_summits.bed INFO @ Tue, 27 Jun 2017 10:50:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (470 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:50:43: #4 Write output xls file... SRX2228876.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:50:43: #4 Write peak in narrowPeak format file... SRX2228876.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:50:43: #4 Write summits bed file... SRX2228876.20_summits.bed INFO @ Tue, 27 Jun 2017 10:50:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:50:45: #4 Write output xls file... SRX2228876.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:50:45: #4 Write peak in narrowPeak format file... SRX2228876.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:50:45: #4 Write summits bed file... SRX2228876.05_summits.bed INFO @ Tue, 27 Jun 2017 10:50:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (646 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。