Job ID = 10043490 sra ファイルのダウンロード中... Completed: 665515K bytes transferred in 16 seconds (336306K bits/sec), in 2 files, 3 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 8454590 spots for /home/okishinya/chipatlas/results/dm3/SRX2165273/SRR4244775.sra Written 8454590 spots total Written 9663745 spots for /home/okishinya/chipatlas/results/dm3/SRX2165273/SRR4244776.sra Written 9663745 spots total 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: 00:07:16 18118335 reads; of these: 18118335 (100.00%) were unpaired; of these: 4967310 (27.42%) aligned 0 times 9234207 (50.97%) aligned exactly 1 time 3916818 (21.62%) aligned >1 times 72.58% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4282432 / 13151025 = 0.3256 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, 02 Oct 2017 03:39:04: # Command line: callpeak -t SRX2165273.bam -f BAM -g dm -n SRX2165273.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165273.05 # format = BAM # ChIP-seq file = ['SRX2165273.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Oct 2017 03:39:04: # Command line: callpeak -t SRX2165273.bam -f BAM -g dm -n SRX2165273.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165273.10 # format = BAM # ChIP-seq file = ['SRX2165273.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Oct 2017 03:39:04: # Command line: callpeak -t SRX2165273.bam -f BAM -g dm -n SRX2165273.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165273.20 # format = BAM # ChIP-seq file = ['SRX2165273.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Oct 2017 03:39:04: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:39:04: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:39:04: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:39:04: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:39:04: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:39:04: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:39:11: 1000000 INFO @ Mon, 02 Oct 2017 03:39:11: 1000000 INFO @ Mon, 02 Oct 2017 03:39:11: 1000000 INFO @ Mon, 02 Oct 2017 03:39:18: 2000000 INFO @ Mon, 02 Oct 2017 03:39:18: 2000000 INFO @ Mon, 02 Oct 2017 03:39:18: 2000000 INFO @ Mon, 02 Oct 2017 03:39:24: 3000000 INFO @ Mon, 02 Oct 2017 03:39:24: 3000000 INFO @ Mon, 02 Oct 2017 03:39:25: 3000000 INFO @ Mon, 02 Oct 2017 03:39:31: 4000000 INFO @ Mon, 02 Oct 2017 03:39:31: 4000000 INFO @ Mon, 02 Oct 2017 03:39:31: 4000000 INFO @ Mon, 02 Oct 2017 03:39:38: 5000000 INFO @ Mon, 02 Oct 2017 03:39:38: 5000000 INFO @ Mon, 02 Oct 2017 03:39:38: 5000000 INFO @ Mon, 02 Oct 2017 03:39:44: 6000000 INFO @ Mon, 02 Oct 2017 03:39:44: 6000000 INFO @ Mon, 02 Oct 2017 03:39:45: 6000000 INFO @ Mon, 02 Oct 2017 03:39:51: 7000000 INFO @ Mon, 02 Oct 2017 03:39:51: 7000000 INFO @ Mon, 02 Oct 2017 03:39:51: 7000000 INFO @ Mon, 02 Oct 2017 03:39:57: 8000000 INFO @ Mon, 02 Oct 2017 03:39:57: 8000000 INFO @ Mon, 02 Oct 2017 03:39:58: 8000000 INFO @ Mon, 02 Oct 2017 03:40:03: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:40:03: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:40:03: #1 total tags in treatment: 8868593 INFO @ Mon, 02 Oct 2017 03:40:03: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:40:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:40:03: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:40:03: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:40:03: #1 total tags in treatment: 8868593 INFO @ Mon, 02 Oct 2017 03:40:03: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:40:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:40:03: #1 tags after filtering in treatment: 8868593 INFO @ Mon, 02 Oct 2017 03:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:40:03: #1 finished! INFO @ Mon, 02 Oct 2017 03:40:03: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:40:03: #1 tags after filtering in treatment: 8868593 INFO @ Mon, 02 Oct 2017 03:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:40:03: #1 finished! INFO @ Mon, 02 Oct 2017 03:40:03: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:40:04: #2 number of paired peaks: 396 WARNING @ Mon, 02 Oct 2017 03:40:04: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Mon, 02 Oct 2017 03:40:04: start model_add_line... INFO @ Mon, 02 Oct 2017 03:40:04: #2 number of paired peaks: 396 WARNING @ Mon, 02 Oct 2017 03:40:04: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Mon, 02 Oct 2017 03:40:04: start model_add_line... INFO @ Mon, 02 Oct 2017 03:40:04: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:40:04: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:40:04: #1 total tags in treatment: 8868593 INFO @ Mon, 02 Oct 2017 03:40:04: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:40:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:40:04: start X-correlation... INFO @ Mon, 02 Oct 2017 03:40:04: start X-correlation... INFO @ Mon, 02 Oct 2017 03:40:04: #1 tags after filtering in treatment: 8868593 INFO @ Mon, 02 Oct 2017 03:40:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:40:04: #1 finished! INFO @ Mon, 02 Oct 2017 03:40:04: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:40:04: end of X-cor INFO @ Mon, 02 Oct 2017 03:40:04: #2 finished! INFO @ Mon, 02 Oct 2017 03:40:04: end of X-cor INFO @ Mon, 02 Oct 2017 03:40:04: #2 predicted fragment length is 66 bps INFO @ Mon, 02 Oct 2017 03:40:04: #2 finished! INFO @ Mon, 02 Oct 2017 03:40:04: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 02 Oct 2017 03:40:04: #2.2 Generate R script for model : SRX2165273.05_model.r INFO @ Mon, 02 Oct 2017 03:40:04: #2 predicted fragment length is 66 bps INFO @ Mon, 02 Oct 2017 03:40:04: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 02 Oct 2017 03:40:04: #2.2 Generate R script for model : SRX2165273.10_model.r WARNING @ Mon, 02 Oct 2017 03:40:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:40:04: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 02 Oct 2017 03:40:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:40:04: #3 Call peaks... WARNING @ Mon, 02 Oct 2017 03:40:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:40:04: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 02 Oct 2017 03:40:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:40:04: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:40:05: #2 number of paired peaks: 396 WARNING @ Mon, 02 Oct 2017 03:40:05: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Mon, 02 Oct 2017 03:40:05: start model_add_line... INFO @ Mon, 02 Oct 2017 03:40:05: start X-correlation... INFO @ Mon, 02 Oct 2017 03:40:05: end of X-cor INFO @ Mon, 02 Oct 2017 03:40:05: #2 finished! INFO @ Mon, 02 Oct 2017 03:40:05: #2 predicted fragment length is 66 bps INFO @ Mon, 02 Oct 2017 03:40:05: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 02 Oct 2017 03:40:05: #2.2 Generate R script for model : SRX2165273.20_model.r WARNING @ Mon, 02 Oct 2017 03:40:05: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:40:05: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 02 Oct 2017 03:40:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:40:05: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:40:23: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:40:24: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:40:26: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:40:34: #4 Write output xls file... SRX2165273.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:40:34: #4 Write peak in narrowPeak format file... SRX2165273.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:40:34: #4 Write summits bed file... SRX2165273.10_summits.bed INFO @ Mon, 02 Oct 2017 03:40:34: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1411 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:40:34: #4 Write output xls file... SRX2165273.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:40:34: #4 Write peak in narrowPeak format file... SRX2165273.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:40:34: #4 Write summits bed file... SRX2165273.05_summits.bed INFO @ Mon, 02 Oct 2017 03:40:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2105 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:40:38: #4 Write output xls file... SRX2165273.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:40:38: #4 Write peak in narrowPeak format file... SRX2165273.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:40:38: #4 Write summits bed file... SRX2165273.20_summits.bed INFO @ Mon, 02 Oct 2017 03:40:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (899 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。