Job ID = 9029818 sra ファイルのダウンロード中... Completed: 768307K bytes transferred in 9 seconds (646672K 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 --:--:-- 0 100 14324 0 14324 0 0 1975 0 --:--:-- 0:00:07 --:--:-- 17320 100 29916 0 29916 0 0 3780 0 --:--:-- 0:00:07 --:--:-- 20064 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 25521864 spots for /home/okishinya/chipatlas/results/dm3/SRX2172430/SRR4252441.sra Written 25521864 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: 00:09:57 25521864 reads; of these: 25521864 (100.00%) were unpaired; of these: 1041809 (4.08%) aligned 0 times 16591524 (65.01%) aligned exactly 1 time 7888531 (30.91%) aligned >1 times 95.92% overall alignment rate Time searching: 00:09:57 Overall time: 00:09:57 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] 3095232 / 24480055 = 0.1264 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 @ Sat, 03 Jun 2017 15:40:17: # Command line: callpeak -t SRX2172430.bam -f BAM -g dm -n SRX2172430.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2172430.10 # format = BAM # ChIP-seq file = ['SRX2172430.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 @ Sat, 03 Jun 2017 15:40:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:40:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:40:17: # Command line: callpeak -t SRX2172430.bam -f BAM -g dm -n SRX2172430.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2172430.20 # format = BAM # ChIP-seq file = ['SRX2172430.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 @ Sat, 03 Jun 2017 15:40:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:40:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:40:17: # Command line: callpeak -t SRX2172430.bam -f BAM -g dm -n SRX2172430.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2172430.05 # format = BAM # ChIP-seq file = ['SRX2172430.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 @ Sat, 03 Jun 2017 15:40:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:40:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:40:24: 1000000 INFO @ Sat, 03 Jun 2017 15:40:24: 1000000 INFO @ Sat, 03 Jun 2017 15:40:24: 1000000 INFO @ Sat, 03 Jun 2017 15:40:31: 2000000 INFO @ Sat, 03 Jun 2017 15:40:31: 2000000 INFO @ Sat, 03 Jun 2017 15:40:31: 2000000 INFO @ Sat, 03 Jun 2017 15:40:38: 3000000 INFO @ Sat, 03 Jun 2017 15:40:38: 3000000 INFO @ Sat, 03 Jun 2017 15:40:38: 3000000 INFO @ Sat, 03 Jun 2017 15:40:45: 4000000 INFO @ Sat, 03 Jun 2017 15:40:45: 4000000 INFO @ Sat, 03 Jun 2017 15:40:45: 4000000 INFO @ Sat, 03 Jun 2017 15:40:52: 5000000 INFO @ Sat, 03 Jun 2017 15:40:52: 5000000 INFO @ Sat, 03 Jun 2017 15:40:52: 5000000 INFO @ Sat, 03 Jun 2017 15:40:58: 6000000 INFO @ Sat, 03 Jun 2017 15:40:59: 6000000 INFO @ Sat, 03 Jun 2017 15:40:59: 6000000 INFO @ Sat, 03 Jun 2017 15:41:05: 7000000 INFO @ Sat, 03 Jun 2017 15:41:06: 7000000 INFO @ Sat, 03 Jun 2017 15:41:06: 7000000 INFO @ Sat, 03 Jun 2017 15:41:12: 8000000 INFO @ Sat, 03 Jun 2017 15:41:13: 8000000 INFO @ Sat, 03 Jun 2017 15:41:13: 8000000 INFO @ Sat, 03 Jun 2017 15:41:20: 9000000 INFO @ Sat, 03 Jun 2017 15:41:20: 9000000 INFO @ Sat, 03 Jun 2017 15:41:21: 9000000 INFO @ Sat, 03 Jun 2017 15:41:28: 10000000 INFO @ Sat, 03 Jun 2017 15:41:28: 10000000 INFO @ Sat, 03 Jun 2017 15:41:28: 10000000 INFO @ Sat, 03 Jun 2017 15:41:35: 11000000 INFO @ Sat, 03 Jun 2017 15:41:35: 11000000 INFO @ Sat, 03 Jun 2017 15:41:37: 11000000 INFO @ Sat, 03 Jun 2017 15:41:42: 12000000 INFO @ Sat, 03 Jun 2017 15:41:43: 12000000 INFO @ Sat, 03 Jun 2017 15:41:45: 12000000 INFO @ Sat, 03 Jun 2017 15:41:50: 13000000 INFO @ Sat, 03 Jun 2017 15:41:50: 13000000 INFO @ Sat, 03 Jun 2017 15:41:53: 13000000 INFO @ Sat, 03 Jun 2017 15:41:57: 14000000 INFO @ Sat, 03 Jun 2017 15:41:58: 14000000 INFO @ Sat, 03 Jun 2017 15:42:02: 14000000 INFO @ Sat, 03 Jun 2017 15:42:05: 15000000 INFO @ Sat, 03 Jun 2017 15:42:05: 15000000 INFO @ Sat, 03 Jun 2017 15:42:10: 15000000 INFO @ Sat, 03 Jun 2017 15:42:12: 16000000 INFO @ Sat, 03 Jun 2017 15:42:13: 16000000 INFO @ Sat, 03 Jun 2017 15:42:18: 16000000 INFO @ Sat, 03 Jun 2017 15:42:20: 17000000 INFO @ Sat, 03 Jun 2017 15:42:20: 17000000 INFO @ Sat, 03 Jun 2017 15:42:26: 17000000 INFO @ Sat, 03 Jun 2017 15:42:27: 18000000 INFO @ Sat, 03 Jun 2017 15:42:28: 18000000 INFO @ Sat, 03 Jun 2017 15:42:34: 19000000 INFO @ Sat, 03 Jun 2017 15:42:35: 18000000 INFO @ Sat, 03 Jun 2017 15:42:35: 19000000 INFO @ Sat, 03 Jun 2017 15:42:42: 20000000 INFO @ Sat, 03 Jun 2017 15:42:42: 20000000 INFO @ Sat, 03 Jun 2017 15:42:43: 19000000 INFO @ Sat, 03 Jun 2017 15:42:49: 21000000 INFO @ Sat, 03 Jun 2017 15:42:49: 21000000 INFO @ Sat, 03 Jun 2017 15:42:51: 20000000 INFO @ Sat, 03 Jun 2017 15:42:52: #1 tag size is determined as 45 bps INFO @ Sat, 03 Jun 2017 15:42:52: #1 tag size = 45 INFO @ Sat, 03 Jun 2017 15:42:52: #1 total tags in treatment: 21384823 INFO @ Sat, 03 Jun 2017 15:42:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:42:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:42:52: #1 tag size is determined as 45 bps INFO @ Sat, 03 Jun 2017 15:42:52: #1 tag size = 45 INFO @ Sat, 03 Jun 2017 15:42:52: #1 total tags in treatment: 21384823 INFO @ Sat, 03 Jun 2017 15:42:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:42:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:42:56: #1 tags after filtering in treatment: 21377911 INFO @ Sat, 03 Jun 2017 15:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:42:56: #1 finished! INFO @ Sat, 03 Jun 2017 15:42:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:42:56: #1 tags after filtering in treatment: 21377911 INFO @ Sat, 03 Jun 2017 15:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:42:56: #1 finished! INFO @ Sat, 03 Jun 2017 15:42:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:42:57: 21000000 INFO @ Sat, 03 Jun 2017 15:42:59: #2 number of paired peaks: 495 WARNING @ Sat, 03 Jun 2017 15:42:59: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 03 Jun 2017 15:42:59: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:00: #1 tag size is determined as 45 bps INFO @ Sat, 03 Jun 2017 15:43:00: #1 tag size = 45 INFO @ Sat, 03 Jun 2017 15:43:00: #1 total tags in treatment: 21384823 INFO @ Sat, 03 Jun 2017 15:43:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:43:00: #2 number of paired peaks: 495 WARNING @ Sat, 03 Jun 2017 15:43:00: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 03 Jun 2017 15:43:00: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:04: #1 tags after filtering in treatment: 21377911 INFO @ Sat, 03 Jun 2017 15:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:04: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:07: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:07: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:07: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:07: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 15:43:07: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sat, 03 Jun 2017 15:43:07: #2.2 Generate R script for model : SRX2172430.05_model.r WARNING @ Sat, 03 Jun 2017 15:43:07: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:07: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sat, 03 Jun 2017 15:43:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:43:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:08: #2 number of paired peaks: 495 WARNING @ Sat, 03 Jun 2017 15:43:08: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 03 Jun 2017 15:43:08: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:08: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:08: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:08: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:08: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 15:43:08: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sat, 03 Jun 2017 15:43:08: #2.2 Generate R script for model : SRX2172430.20_model.r WARNING @ Sat, 03 Jun 2017 15:43:08: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:08: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sat, 03 Jun 2017 15:43:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:43:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:16: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:16: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:16: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:16: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 15:43:16: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sat, 03 Jun 2017 15:43:16: #2.2 Generate R script for model : SRX2172430.10_model.r WARNING @ Sat, 03 Jun 2017 15:43:16: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:16: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sat, 03 Jun 2017 15:43:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:43:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:44:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:45:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:45:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:46:04: #4 Write output xls file... SRX2172430.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:46:04: #4 Write peak in narrowPeak format file... SRX2172430.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:46:04: #4 Write summits bed file... SRX2172430.05_summits.bed INFO @ Sat, 03 Jun 2017 15:46:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3728 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:46:22: #4 Write output xls file... SRX2172430.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:46:22: #4 Write peak in narrowPeak format file... SRX2172430.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:46:22: #4 Write summits bed file... SRX2172430.20_summits.bed INFO @ Sat, 03 Jun 2017 15:46:22: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1411 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:46:28: #4 Write output xls file... SRX2172430.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:46:28: #4 Write peak in narrowPeak format file... SRX2172430.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:46:28: #4 Write summits bed file... SRX2172430.10_summits.bed INFO @ Sat, 03 Jun 2017 15:46:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2451 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。