Job ID = 10194826 sra ファイルのダウンロード中... Completed: 696175K bytes transferred in 14 seconds (386206K bits/sec), in 1 file. 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 36286006 spots for /home/okishinya/chipatlas/results/rn6/SRX1977116/SRR3952248.sra Written 36286006 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:04:10 36286006 reads; of these: 36286006 (100.00%) were unpaired; of these: 16483843 (45.43%) aligned 0 times 11170717 (30.79%) aligned exactly 1 time 8631446 (23.79%) aligned >1 times 54.57% overall alignment rate Time searching: 01:04:14 Overall time: 01:04:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1478611 / 19802163 = 0.0747 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, 11 Nov 2017 02:11:36: # Command line: callpeak -t SRX1977116.bam -f BAM -g 2.15e9 -n SRX1977116.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977116.10 # format = BAM # ChIP-seq file = ['SRX1977116.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 02:11:36: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:11:36: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:11:36: # Command line: callpeak -t SRX1977116.bam -f BAM -g 2.15e9 -n SRX1977116.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977116.20 # format = BAM # ChIP-seq file = ['SRX1977116.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 02:11:36: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:11:36: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:11:36: # Command line: callpeak -t SRX1977116.bam -f BAM -g 2.15e9 -n SRX1977116.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977116.05 # format = BAM # ChIP-seq file = ['SRX1977116.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 02:11:36: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:11:36: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:11:42: 1000000 INFO @ Sat, 11 Nov 2017 02:11:43: 1000000 INFO @ Sat, 11 Nov 2017 02:11:44: 1000000 INFO @ Sat, 11 Nov 2017 02:11:50: 2000000 INFO @ Sat, 11 Nov 2017 02:11:51: 2000000 INFO @ Sat, 11 Nov 2017 02:11:51: 2000000 INFO @ Sat, 11 Nov 2017 02:11:57: 3000000 INFO @ Sat, 11 Nov 2017 02:11:58: 3000000 INFO @ Sat, 11 Nov 2017 02:11:58: 3000000 INFO @ Sat, 11 Nov 2017 02:12:05: 4000000 INFO @ Sat, 11 Nov 2017 02:12:06: 4000000 INFO @ Sat, 11 Nov 2017 02:12:07: 4000000 INFO @ Sat, 11 Nov 2017 02:12:13: 5000000 INFO @ Sat, 11 Nov 2017 02:12:15: 5000000 INFO @ Sat, 11 Nov 2017 02:12:16: 5000000 INFO @ Sat, 11 Nov 2017 02:12:21: 6000000 INFO @ Sat, 11 Nov 2017 02:12:23: 6000000 INFO @ Sat, 11 Nov 2017 02:12:23: 6000000 INFO @ Sat, 11 Nov 2017 02:12:28: 7000000 INFO @ Sat, 11 Nov 2017 02:12:30: 7000000 INFO @ Sat, 11 Nov 2017 02:12:31: 7000000 INFO @ Sat, 11 Nov 2017 02:12:37: 8000000 INFO @ Sat, 11 Nov 2017 02:12:38: 8000000 INFO @ Sat, 11 Nov 2017 02:12:39: 8000000 INFO @ Sat, 11 Nov 2017 02:12:45: 9000000 INFO @ Sat, 11 Nov 2017 02:12:46: 9000000 INFO @ Sat, 11 Nov 2017 02:12:47: 9000000 INFO @ Sat, 11 Nov 2017 02:12:53: 10000000 INFO @ Sat, 11 Nov 2017 02:12:54: 10000000 INFO @ Sat, 11 Nov 2017 02:12:54: 10000000 INFO @ Sat, 11 Nov 2017 02:13:00: 11000000 INFO @ Sat, 11 Nov 2017 02:13:01: 11000000 INFO @ Sat, 11 Nov 2017 02:13:02: 11000000 INFO @ Sat, 11 Nov 2017 02:13:08: 12000000 INFO @ Sat, 11 Nov 2017 02:13:08: 12000000 INFO @ Sat, 11 Nov 2017 02:13:10: 12000000 INFO @ Sat, 11 Nov 2017 02:13:15: 13000000 INFO @ Sat, 11 Nov 2017 02:13:15: 13000000 INFO @ Sat, 11 Nov 2017 02:13:17: 13000000 INFO @ Sat, 11 Nov 2017 02:13:22: 14000000 INFO @ Sat, 11 Nov 2017 02:13:22: 14000000 INFO @ Sat, 11 Nov 2017 02:13:24: 14000000 INFO @ Sat, 11 Nov 2017 02:13:29: 15000000 INFO @ Sat, 11 Nov 2017 02:13:29: 15000000 INFO @ Sat, 11 Nov 2017 02:13:31: 15000000 INFO @ Sat, 11 Nov 2017 02:13:36: 16000000 INFO @ Sat, 11 Nov 2017 02:13:36: 16000000 INFO @ Sat, 11 Nov 2017 02:13:38: 16000000 INFO @ Sat, 11 Nov 2017 02:13:43: 17000000 INFO @ Sat, 11 Nov 2017 02:13:43: 17000000 INFO @ Sat, 11 Nov 2017 02:13:45: 17000000 INFO @ Sat, 11 Nov 2017 02:13:51: 18000000 INFO @ Sat, 11 Nov 2017 02:13:51: 18000000 INFO @ Sat, 11 Nov 2017 02:13:53: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:13:53: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:13:53: #1 total tags in treatment: 18323552 INFO @ Sat, 11 Nov 2017 02:13:53: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:13:53: 18000000 INFO @ Sat, 11 Nov 2017 02:13:53: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:13:53: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:13:53: #1 total tags in treatment: 18323552 INFO @ Sat, 11 Nov 2017 02:13:53: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:13:54: #1 tags after filtering in treatment: 18323444 INFO @ Sat, 11 Nov 2017 02:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:13:54: #1 finished! INFO @ Sat, 11 Nov 2017 02:13:54: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:13:54: #1 tags after filtering in treatment: 18323444 INFO @ Sat, 11 Nov 2017 02:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:13:54: #1 finished! INFO @ Sat, 11 Nov 2017 02:13:54: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:13:55: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:13:55: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:13:55: #1 total tags in treatment: 18323552 INFO @ Sat, 11 Nov 2017 02:13:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:13:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:13:56: #1 tags after filtering in treatment: 18323444 INFO @ Sat, 11 Nov 2017 02:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:13:56: #1 finished! INFO @ Sat, 11 Nov 2017 02:13:56: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:13:57: #2 number of paired peaks: 30658 INFO @ Sat, 11 Nov 2017 02:13:57: start model_add_line... INFO @ Sat, 11 Nov 2017 02:13:57: start X-correlation... INFO @ Sat, 11 Nov 2017 02:13:57: end of X-cor INFO @ Sat, 11 Nov 2017 02:13:57: #2 finished! INFO @ Sat, 11 Nov 2017 02:13:57: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Nov 2017 02:13:57: #2 alternative fragment length(s) may be 59,115 bps INFO @ Sat, 11 Nov 2017 02:13:57: #2.2 Generate R script for model : SRX1977116.20_model.r INFO @ Sat, 11 Nov 2017 02:13:57: #2 number of paired peaks: 30658 INFO @ Sat, 11 Nov 2017 02:13:57: start model_add_line... WARNING @ Sat, 11 Nov 2017 02:13:57: #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, 11 Nov 2017 02:13:57: #2 You may need to consider one of the other alternative d(s): 59,115 WARNING @ Sat, 11 Nov 2017 02:13:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:13:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:13:57: start X-correlation... INFO @ Sat, 11 Nov 2017 02:13:57: end of X-cor INFO @ Sat, 11 Nov 2017 02:13:57: #2 finished! INFO @ Sat, 11 Nov 2017 02:13:57: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Nov 2017 02:13:57: #2 alternative fragment length(s) may be 59,115 bps INFO @ Sat, 11 Nov 2017 02:13:57: #2.2 Generate R script for model : SRX1977116.05_model.r WARNING @ Sat, 11 Nov 2017 02:13:57: #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, 11 Nov 2017 02:13:57: #2 You may need to consider one of the other alternative d(s): 59,115 WARNING @ Sat, 11 Nov 2017 02:13:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:13:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:13:59: #2 number of paired peaks: 30658 INFO @ Sat, 11 Nov 2017 02:13:59: start model_add_line... INFO @ Sat, 11 Nov 2017 02:13:59: start X-correlation... INFO @ Sat, 11 Nov 2017 02:13:59: end of X-cor INFO @ Sat, 11 Nov 2017 02:13:59: #2 finished! INFO @ Sat, 11 Nov 2017 02:13:59: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Nov 2017 02:13:59: #2 alternative fragment length(s) may be 59,115 bps INFO @ Sat, 11 Nov 2017 02:13:59: #2.2 Generate R script for model : SRX1977116.10_model.r WARNING @ Sat, 11 Nov 2017 02:13:59: #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, 11 Nov 2017 02:13:59: #2 You may need to consider one of the other alternative d(s): 59,115 WARNING @ Sat, 11 Nov 2017 02:13:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:13:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:14:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:14:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:14:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:15:08: #4 Write output xls file... SRX1977116.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:15:08: #4 Write peak in narrowPeak format file... SRX1977116.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:15:08: #4 Write summits bed file... SRX1977116.20_summits.bed INFO @ Sat, 11 Nov 2017 02:15:08: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:15:12: #4 Write output xls file... SRX1977116.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:15:12: #4 Write peak in narrowPeak format file... SRX1977116.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:15:12: #4 Write summits bed file... SRX1977116.10_summits.bed INFO @ Sat, 11 Nov 2017 02:15:12: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (4510 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:15:14: #4 Write output xls file... SRX1977116.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:15:15: #4 Write peak in narrowPeak format file... SRX1977116.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:15:15: #4 Write summits bed file... SRX1977116.05_summits.bed INFO @ Sat, 11 Nov 2017 02:15:15: Done! pass1 - making usageList (155 chroms): 4 millis pass2 - checking and writing primary data (18534 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。