Job ID = 9033133 sra ファイルのダウンロード中... Completed: 491351K bytes transferred in 8 seconds (470903K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 20110 0 20110 0 0 2508 0 --:--:-- 0:00:08 --:--:-- 13442 100 61840 0 61840 0 0 6860 0 --:--:-- 0:00:09 --:--:-- 24825 100 61840 0 61840 0 0 6860 0 --:--:-- 0:00:09 --:--:-- 24815 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 19174550 spots for /home/okishinya/chipatlas/results/dm3/SRX914957/SRR1873267.sra Written 19174550 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: 00:05:09 19174550 reads; of these: 19174550 (100.00%) were unpaired; of these: 2672007 (13.94%) aligned 0 times 13721254 (71.56%) aligned exactly 1 time 2781289 (14.51%) aligned >1 times 86.06% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 4952429 / 16502543 = 0.3001 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 @ Sun, 04 Jun 2017 00:12:50: # Command line: callpeak -t SRX914957.bam -f BAM -g dm -n SRX914957.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914957.20 # format = BAM # ChIP-seq file = ['SRX914957.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 INFO @ Sun, 04 Jun 2017 00:12:50: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:50: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:50: # Command line: callpeak -t SRX914957.bam -f BAM -g dm -n SRX914957.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914957.05 # format = BAM # ChIP-seq file = ['SRX914957.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 INFO @ Sun, 04 Jun 2017 00:12:50: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:50: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:50: # Command line: callpeak -t SRX914957.bam -f BAM -g dm -n SRX914957.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914957.10 # format = BAM # ChIP-seq file = ['SRX914957.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 INFO @ Sun, 04 Jun 2017 00:12:50: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:50: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:56: 1000000 INFO @ Sun, 04 Jun 2017 00:12:56: 1000000 INFO @ Sun, 04 Jun 2017 00:12:56: 1000000 INFO @ Sun, 04 Jun 2017 00:13:02: 2000000 INFO @ Sun, 04 Jun 2017 00:13:02: 2000000 INFO @ Sun, 04 Jun 2017 00:13:02: 2000000 INFO @ Sun, 04 Jun 2017 00:13:07: 3000000 INFO @ Sun, 04 Jun 2017 00:13:07: 3000000 INFO @ Sun, 04 Jun 2017 00:13:08: 3000000 INFO @ Sun, 04 Jun 2017 00:13:12: 4000000 INFO @ Sun, 04 Jun 2017 00:13:13: 4000000 INFO @ Sun, 04 Jun 2017 00:13:13: 4000000 INFO @ Sun, 04 Jun 2017 00:13:17: 5000000 INFO @ Sun, 04 Jun 2017 00:13:19: 5000000 INFO @ Sun, 04 Jun 2017 00:13:19: 5000000 INFO @ Sun, 04 Jun 2017 00:13:22: 6000000 INFO @ Sun, 04 Jun 2017 00:13:24: 6000000 INFO @ Sun, 04 Jun 2017 00:13:25: 6000000 INFO @ Sun, 04 Jun 2017 00:13:27: 7000000 INFO @ Sun, 04 Jun 2017 00:13:30: 7000000 INFO @ Sun, 04 Jun 2017 00:13:31: 7000000 INFO @ Sun, 04 Jun 2017 00:13:33: 8000000 INFO @ Sun, 04 Jun 2017 00:13:36: 8000000 INFO @ Sun, 04 Jun 2017 00:13:37: 8000000 INFO @ Sun, 04 Jun 2017 00:13:38: 9000000 INFO @ Sun, 04 Jun 2017 00:13:41: 9000000 INFO @ Sun, 04 Jun 2017 00:13:42: 9000000 INFO @ Sun, 04 Jun 2017 00:13:43: 10000000 INFO @ Sun, 04 Jun 2017 00:13:47: 10000000 INFO @ Sun, 04 Jun 2017 00:13:48: 11000000 INFO @ Sun, 04 Jun 2017 00:13:48: 10000000 INFO @ Sun, 04 Jun 2017 00:13:51: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:13:51: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:13:51: #1 total tags in treatment: 11550114 INFO @ Sun, 04 Jun 2017 00:13:51: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:13:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:13:53: 11000000 INFO @ Sun, 04 Jun 2017 00:13:53: #1 tags after filtering in treatment: 11548195 INFO @ Sun, 04 Jun 2017 00:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:13:53: #1 finished! INFO @ Sun, 04 Jun 2017 00:13:53: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:13:54: 11000000 INFO @ Sun, 04 Jun 2017 00:13:56: #2 number of paired peaks: 129 WARNING @ Sun, 04 Jun 2017 00:13:56: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 04 Jun 2017 00:13:56: start model_add_line... INFO @ Sun, 04 Jun 2017 00:13:56: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:13:56: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:13:56: #1 total tags in treatment: 11550114 INFO @ Sun, 04 Jun 2017 00:13:56: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:13:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:13:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:13:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:13:57: #1 total tags in treatment: 11550114 INFO @ Sun, 04 Jun 2017 00:13:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:13:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:13:58: start X-correlation... INFO @ Sun, 04 Jun 2017 00:13:58: end of X-cor INFO @ Sun, 04 Jun 2017 00:13:58: #2 finished! INFO @ Sun, 04 Jun 2017 00:13:58: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 00:13:58: #2 alternative fragment length(s) may be 2,37,96,123,447,473,533,547,576 bps INFO @ Sun, 04 Jun 2017 00:13:58: #2.2 Generate R script for model : SRX914957.10_model.r WARNING @ Sun, 04 Jun 2017 00:13:58: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:13:58: #2 You may need to consider one of the other alternative d(s): 2,37,96,123,447,473,533,547,576 WARNING @ Sun, 04 Jun 2017 00:13:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:13:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:13:58: #1 tags after filtering in treatment: 11548195 INFO @ Sun, 04 Jun 2017 00:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:13:58: #1 finished! INFO @ Sun, 04 Jun 2017 00:13:58: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:13:59: #1 tags after filtering in treatment: 11548195 INFO @ Sun, 04 Jun 2017 00:13:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:13:59: #1 finished! INFO @ Sun, 04 Jun 2017 00:13:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:14:00: #2 number of paired peaks: 129 WARNING @ Sun, 04 Jun 2017 00:14:00: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 04 Jun 2017 00:14:00: start model_add_line... INFO @ Sun, 04 Jun 2017 00:14:01: #2 number of paired peaks: 129 WARNING @ Sun, 04 Jun 2017 00:14:01: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 04 Jun 2017 00:14:01: start model_add_line... INFO @ Sun, 04 Jun 2017 00:14:02: start X-correlation... INFO @ Sun, 04 Jun 2017 00:14:02: end of X-cor INFO @ Sun, 04 Jun 2017 00:14:02: #2 finished! INFO @ Sun, 04 Jun 2017 00:14:02: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 00:14:02: #2 alternative fragment length(s) may be 2,37,96,123,447,473,533,547,576 bps INFO @ Sun, 04 Jun 2017 00:14:02: #2.2 Generate R script for model : SRX914957.20_model.r WARNING @ Sun, 04 Jun 2017 00:14:02: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:14:02: #2 You may need to consider one of the other alternative d(s): 2,37,96,123,447,473,533,547,576 WARNING @ Sun, 04 Jun 2017 00:14:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:14:02: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:14:04: start X-correlation... INFO @ Sun, 04 Jun 2017 00:14:04: end of X-cor INFO @ Sun, 04 Jun 2017 00:14:04: #2 finished! INFO @ Sun, 04 Jun 2017 00:14:04: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 00:14:04: #2 alternative fragment length(s) may be 2,37,96,123,447,473,533,547,576 bps INFO @ Sun, 04 Jun 2017 00:14:04: #2.2 Generate R script for model : SRX914957.05_model.r WARNING @ Sun, 04 Jun 2017 00:14:04: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:14:04: #2 You may need to consider one of the other alternative d(s): 2,37,96,123,447,473,533,547,576 WARNING @ Sun, 04 Jun 2017 00:14:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:14:04: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:15:00: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:15:05: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:15:08: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:15:46: #4 Write output xls file... SRX914957.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:15:46: #4 Write peak in narrowPeak format file... SRX914957.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:15:46: #4 Write summits bed file... SRX914957.10_summits.bed INFO @ Sun, 04 Jun 2017 00:15:46: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:15:51: #4 Write output xls file... SRX914957.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:15:51: #4 Write peak in narrowPeak format file... SRX914957.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:15:51: #4 Write summits bed file... SRX914957.05_summits.bed INFO @ Sun, 04 Jun 2017 00:15:51: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:15:54: #4 Write output xls file... SRX914957.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:15:54: #4 Write peak in narrowPeak format file... SRX914957.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:15:54: #4 Write summits bed file... SRX914957.20_summits.bed INFO @ Sun, 04 Jun 2017 00:15:54: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。