Job ID = 10043484 sra ファイルのダウンロード中... Completed: 952456K bytes transferred in 13 seconds (599611K 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 11516541 spots for /home/okishinya/chipatlas/results/dm3/SRX2165268/SRR4244765.sra Written 11516541 spots total Written 14754328 spots for /home/okishinya/chipatlas/results/dm3/SRX2165268/SRR4244766.sra Written 14754328 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: 00:00:00 Multiseed full-index search: 00:11:18 26270869 reads; of these: 26270869 (100.00%) were unpaired; of these: 5835127 (22.21%) aligned 0 times 14156883 (53.89%) aligned exactly 1 time 6278859 (23.90%) aligned >1 times 77.79% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 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 12 files... [bam_rmdupse_core] 7543110 / 20435742 = 0.3691 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 03:44:57: # Command line: callpeak -t SRX2165268.bam -f BAM -g dm -n SRX2165268.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165268.10 # format = BAM # ChIP-seq file = ['SRX2165268.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 03:44:57: # Command line: callpeak -t SRX2165268.bam -f BAM -g dm -n SRX2165268.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165268.20 # format = BAM # ChIP-seq file = ['SRX2165268.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 03:44:57: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:44:57: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:44:57: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:44:57: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:44:57: # Command line: callpeak -t SRX2165268.bam -f BAM -g dm -n SRX2165268.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165268.05 # format = BAM # ChIP-seq file = ['SRX2165268.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 03:44:57: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:44:57: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:45:03: 1000000 INFO @ Mon, 02 Oct 2017 03:45:04: 1000000 INFO @ Mon, 02 Oct 2017 03:45:04: 1000000 INFO @ Mon, 02 Oct 2017 03:45:10: 2000000 INFO @ Mon, 02 Oct 2017 03:45:10: 2000000 INFO @ Mon, 02 Oct 2017 03:45:10: 2000000 INFO @ Mon, 02 Oct 2017 03:45:17: 3000000 INFO @ Mon, 02 Oct 2017 03:45:17: 3000000 INFO @ Mon, 02 Oct 2017 03:45:17: 3000000 INFO @ Mon, 02 Oct 2017 03:45:24: 4000000 INFO @ Mon, 02 Oct 2017 03:45:24: 4000000 INFO @ Mon, 02 Oct 2017 03:45:25: 4000000 INFO @ Mon, 02 Oct 2017 03:45:31: 5000000 INFO @ Mon, 02 Oct 2017 03:45:31: 5000000 INFO @ Mon, 02 Oct 2017 03:45:32: 5000000 INFO @ Mon, 02 Oct 2017 03:45:38: 6000000 INFO @ Mon, 02 Oct 2017 03:45:39: 6000000 INFO @ Mon, 02 Oct 2017 03:45:39: 6000000 INFO @ Mon, 02 Oct 2017 03:45:45: 7000000 INFO @ Mon, 02 Oct 2017 03:45:46: 7000000 INFO @ Mon, 02 Oct 2017 03:45:47: 7000000 INFO @ Mon, 02 Oct 2017 03:45:53: 8000000 INFO @ Mon, 02 Oct 2017 03:45:53: 8000000 INFO @ Mon, 02 Oct 2017 03:45:54: 8000000 INFO @ Mon, 02 Oct 2017 03:46:00: 9000000 INFO @ Mon, 02 Oct 2017 03:46:01: 9000000 INFO @ Mon, 02 Oct 2017 03:46:02: 9000000 INFO @ Mon, 02 Oct 2017 03:46:08: 10000000 INFO @ Mon, 02 Oct 2017 03:46:09: 10000000 INFO @ Mon, 02 Oct 2017 03:46:10: 10000000 INFO @ Mon, 02 Oct 2017 03:46:15: 11000000 INFO @ Mon, 02 Oct 2017 03:46:16: 11000000 INFO @ Mon, 02 Oct 2017 03:46:17: 11000000 INFO @ Mon, 02 Oct 2017 03:46:22: 12000000 INFO @ Mon, 02 Oct 2017 03:46:24: 12000000 INFO @ Mon, 02 Oct 2017 03:46:25: 12000000 INFO @ Mon, 02 Oct 2017 03:46:29: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:46:29: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:46:29: #1 total tags in treatment: 12892632 INFO @ Mon, 02 Oct 2017 03:46:29: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:46:29: #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 03:46:29: #1 tags after filtering in treatment: 12892632 INFO @ Mon, 02 Oct 2017 03:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:46:29: #1 finished! INFO @ Mon, 02 Oct 2017 03:46:29: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:46:30: #2 number of paired peaks: 358 WARNING @ Mon, 02 Oct 2017 03:46:30: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 02 Oct 2017 03:46:30: start model_add_line... INFO @ Mon, 02 Oct 2017 03:46:30: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:46:30: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:46:30: #1 total tags in treatment: 12892632 INFO @ Mon, 02 Oct 2017 03:46:30: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:46:30: #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 03:46:30: start X-correlation... INFO @ Mon, 02 Oct 2017 03:46:31: #1 tags after filtering in treatment: 12892632 INFO @ Mon, 02 Oct 2017 03:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:46:31: #1 finished! INFO @ Mon, 02 Oct 2017 03:46:31: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:46:31: end of X-cor INFO @ Mon, 02 Oct 2017 03:46:31: #2 finished! INFO @ Mon, 02 Oct 2017 03:46:31: #2 predicted fragment length is 62 bps INFO @ Mon, 02 Oct 2017 03:46:31: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 02 Oct 2017 03:46:31: #2.2 Generate R script for model : SRX2165268.10_model.r WARNING @ Mon, 02 Oct 2017 03:46:31: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:46:31: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 02 Oct 2017 03:46:31: #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 03:46:31: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:46:32: #2 number of paired peaks: 358 WARNING @ Mon, 02 Oct 2017 03:46:32: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 02 Oct 2017 03:46:32: start model_add_line... INFO @ Mon, 02 Oct 2017 03:46:32: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:46:32: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:46:32: #1 total tags in treatment: 12892632 INFO @ Mon, 02 Oct 2017 03:46:32: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:46:32: #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 03:46:32: start X-correlation... INFO @ Mon, 02 Oct 2017 03:46:32: end of X-cor INFO @ Mon, 02 Oct 2017 03:46:32: #2 finished! INFO @ Mon, 02 Oct 2017 03:46:32: #2 predicted fragment length is 62 bps INFO @ Mon, 02 Oct 2017 03:46:32: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 02 Oct 2017 03:46:32: #2.2 Generate R script for model : SRX2165268.05_model.r WARNING @ Mon, 02 Oct 2017 03:46:32: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:46:32: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 02 Oct 2017 03:46:32: #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 03:46:32: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:46:32: #1 tags after filtering in treatment: 12892632 INFO @ Mon, 02 Oct 2017 03:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:46:32: #1 finished! INFO @ Mon, 02 Oct 2017 03:46:32: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:46:33: #2 number of paired peaks: 358 WARNING @ Mon, 02 Oct 2017 03:46:33: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 02 Oct 2017 03:46:33: start model_add_line... INFO @ Mon, 02 Oct 2017 03:46:33: start X-correlation... INFO @ Mon, 02 Oct 2017 03:46:33: end of X-cor INFO @ Mon, 02 Oct 2017 03:46:33: #2 finished! INFO @ Mon, 02 Oct 2017 03:46:33: #2 predicted fragment length is 62 bps INFO @ Mon, 02 Oct 2017 03:46:33: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 02 Oct 2017 03:46:33: #2.2 Generate R script for model : SRX2165268.20_model.r WARNING @ Mon, 02 Oct 2017 03:46:33: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:46:33: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 02 Oct 2017 03:46:33: #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 03:46:33: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:46:58: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:46:58: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:46:59: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:47:14: #4 Write output xls file... SRX2165268.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:47:14: #4 Write peak in narrowPeak format file... SRX2165268.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:47:14: #4 Write summits bed file... SRX2165268.10_summits.bed INFO @ Mon, 02 Oct 2017 03:47:14: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1372 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:47:14: #4 Write output xls file... SRX2165268.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:47:14: #4 Write peak in narrowPeak format file... SRX2165268.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:47:14: #4 Write summits bed file... SRX2165268.05_summits.bed INFO @ Mon, 02 Oct 2017 03:47:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2041 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:47:15: #4 Write output xls file... SRX2165268.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:47:15: #4 Write peak in narrowPeak format file... SRX2165268.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:47:15: #4 Write summits bed file... SRX2165268.20_summits.bed INFO @ Mon, 02 Oct 2017 03:47:15: Done! pass1 - making usageList (9 chroms): 3 millis pass2 - checking and writing primary data (962 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。