Job ID = 10194747 sra ファイルのダウンロード中... Completed: 1056243K bytes transferred in 12 seconds (669627K 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 33493040 spots for /home/okishinya/chipatlas/results/rn6/SRX1074891/SRR2080218.sra Written 33493040 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:23 33493040 reads; of these: 33493040 (100.00%) were unpaired; of these: 8043735 (24.02%) aligned 0 times 18100425 (54.04%) aligned exactly 1 time 7348880 (21.94%) aligned >1 times 75.98% overall alignment rate Time searching: 00:29:27 Overall time: 00:29:27 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] 2119364 / 25449305 = 0.0833 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 00:09:30: # Command line: callpeak -t SRX1074891.bam -f BAM -g 2.15e9 -n SRX1074891.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1074891.05 # format = BAM # ChIP-seq file = ['SRX1074891.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 00:09:30: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:09:30: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:09:30: # Command line: callpeak -t SRX1074891.bam -f BAM -g 2.15e9 -n SRX1074891.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1074891.20 # format = BAM # ChIP-seq file = ['SRX1074891.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 00:09:30: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:09:30: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:09:30: # Command line: callpeak -t SRX1074891.bam -f BAM -g 2.15e9 -n SRX1074891.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1074891.10 # format = BAM # ChIP-seq file = ['SRX1074891.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 00:09:30: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:09:30: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:09:37: 1000000 INFO @ Sat, 11 Nov 2017 00:09:38: 1000000 INFO @ Sat, 11 Nov 2017 00:09:38: 1000000 INFO @ Sat, 11 Nov 2017 00:09:45: 2000000 INFO @ Sat, 11 Nov 2017 00:09:45: 2000000 INFO @ Sat, 11 Nov 2017 00:09:46: 2000000 INFO @ Sat, 11 Nov 2017 00:09:53: 3000000 INFO @ Sat, 11 Nov 2017 00:09:53: 3000000 INFO @ Sat, 11 Nov 2017 00:09:54: 3000000 INFO @ Sat, 11 Nov 2017 00:10:01: 4000000 INFO @ Sat, 11 Nov 2017 00:10:01: 4000000 INFO @ Sat, 11 Nov 2017 00:10:02: 4000000 INFO @ Sat, 11 Nov 2017 00:10:08: 5000000 INFO @ Sat, 11 Nov 2017 00:10:09: 5000000 INFO @ Sat, 11 Nov 2017 00:10:10: 5000000 INFO @ Sat, 11 Nov 2017 00:10:16: 6000000 INFO @ Sat, 11 Nov 2017 00:10:17: 6000000 INFO @ Sat, 11 Nov 2017 00:10:18: 6000000 INFO @ Sat, 11 Nov 2017 00:10:23: 7000000 INFO @ Sat, 11 Nov 2017 00:10:26: 7000000 INFO @ Sat, 11 Nov 2017 00:10:26: 7000000 INFO @ Sat, 11 Nov 2017 00:10:31: 8000000 INFO @ Sat, 11 Nov 2017 00:10:34: 8000000 INFO @ Sat, 11 Nov 2017 00:10:34: 8000000 INFO @ Sat, 11 Nov 2017 00:10:39: 9000000 INFO @ Sat, 11 Nov 2017 00:10:42: 9000000 INFO @ Sat, 11 Nov 2017 00:10:42: 9000000 INFO @ Sat, 11 Nov 2017 00:10:46: 10000000 INFO @ Sat, 11 Nov 2017 00:10:50: 10000000 INFO @ Sat, 11 Nov 2017 00:10:51: 10000000 INFO @ Sat, 11 Nov 2017 00:10:55: 11000000 INFO @ Sat, 11 Nov 2017 00:10:57: 11000000 INFO @ Sat, 11 Nov 2017 00:10:59: 11000000 INFO @ Sat, 11 Nov 2017 00:11:03: 12000000 INFO @ Sat, 11 Nov 2017 00:11:05: 12000000 INFO @ Sat, 11 Nov 2017 00:11:07: 12000000 INFO @ Sat, 11 Nov 2017 00:11:11: 13000000 INFO @ Sat, 11 Nov 2017 00:11:12: 13000000 INFO @ Sat, 11 Nov 2017 00:11:16: 13000000 INFO @ Sat, 11 Nov 2017 00:11:19: 14000000 INFO @ Sat, 11 Nov 2017 00:11:19: 14000000 INFO @ Sat, 11 Nov 2017 00:11:24: 14000000 INFO @ Sat, 11 Nov 2017 00:11:27: 15000000 INFO @ Sat, 11 Nov 2017 00:11:28: 15000000 INFO @ Sat, 11 Nov 2017 00:11:32: 15000000 INFO @ Sat, 11 Nov 2017 00:11:34: 16000000 INFO @ Sat, 11 Nov 2017 00:11:36: 16000000 INFO @ Sat, 11 Nov 2017 00:11:41: 16000000 INFO @ Sat, 11 Nov 2017 00:11:42: 17000000 INFO @ Sat, 11 Nov 2017 00:11:44: 17000000 INFO @ Sat, 11 Nov 2017 00:11:49: 17000000 INFO @ Sat, 11 Nov 2017 00:11:50: 18000000 INFO @ Sat, 11 Nov 2017 00:11:53: 18000000 INFO @ Sat, 11 Nov 2017 00:11:57: 18000000 INFO @ Sat, 11 Nov 2017 00:11:57: 19000000 INFO @ Sat, 11 Nov 2017 00:12:01: 19000000 INFO @ Sat, 11 Nov 2017 00:12:05: 20000000 INFO @ Sat, 11 Nov 2017 00:12:05: 19000000 INFO @ Sat, 11 Nov 2017 00:12:09: 20000000 INFO @ Sat, 11 Nov 2017 00:12:12: 21000000 INFO @ Sat, 11 Nov 2017 00:12:13: 20000000 INFO @ Sat, 11 Nov 2017 00:12:17: 21000000 INFO @ Sat, 11 Nov 2017 00:12:20: 22000000 INFO @ Sat, 11 Nov 2017 00:12:21: 21000000 INFO @ Sat, 11 Nov 2017 00:12:25: 22000000 INFO @ Sat, 11 Nov 2017 00:12:27: 23000000 INFO @ Sat, 11 Nov 2017 00:12:29: 22000000 INFO @ Sat, 11 Nov 2017 00:12:30: #1 tag size is determined as 52 bps INFO @ Sat, 11 Nov 2017 00:12:30: #1 tag size = 52 INFO @ Sat, 11 Nov 2017 00:12:30: #1 total tags in treatment: 23329941 INFO @ Sat, 11 Nov 2017 00:12:30: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:12:30: #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 00:12:31: #1 tags after filtering in treatment: 23329821 INFO @ Sat, 11 Nov 2017 00:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:12:31: #1 finished! INFO @ Sat, 11 Nov 2017 00:12:31: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:12:33: #2 number of paired peaks: 5753 INFO @ Sat, 11 Nov 2017 00:12:33: start model_add_line... INFO @ Sat, 11 Nov 2017 00:12:33: start X-correlation... INFO @ Sat, 11 Nov 2017 00:12:33: end of X-cor INFO @ Sat, 11 Nov 2017 00:12:33: #2 finished! INFO @ Sat, 11 Nov 2017 00:12:33: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:12:33: #2 alternative fragment length(s) may be 52,222,392 bps INFO @ Sat, 11 Nov 2017 00:12:33: #2.2 Generate R script for model : SRX1074891.20_model.r WARNING @ Sat, 11 Nov 2017 00:12:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:12:33: #2 You may need to consider one of the other alternative d(s): 52,222,392 WARNING @ Sat, 11 Nov 2017 00:12:33: #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 00:12:33: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:12:34: 23000000 INFO @ Sat, 11 Nov 2017 00:12:36: #1 tag size is determined as 52 bps INFO @ Sat, 11 Nov 2017 00:12:36: #1 tag size = 52 INFO @ Sat, 11 Nov 2017 00:12:36: #1 total tags in treatment: 23329941 INFO @ Sat, 11 Nov 2017 00:12:36: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:12:36: #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 00:12:37: #1 tags after filtering in treatment: 23329821 INFO @ Sat, 11 Nov 2017 00:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:12:37: #1 finished! INFO @ Sat, 11 Nov 2017 00:12:37: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:12:37: 23000000 INFO @ Sat, 11 Nov 2017 00:12:39: #2 number of paired peaks: 5753 INFO @ Sat, 11 Nov 2017 00:12:39: start model_add_line... INFO @ Sat, 11 Nov 2017 00:12:40: start X-correlation... INFO @ Sat, 11 Nov 2017 00:12:40: end of X-cor INFO @ Sat, 11 Nov 2017 00:12:40: #2 finished! INFO @ Sat, 11 Nov 2017 00:12:40: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:12:40: #2 alternative fragment length(s) may be 52,222,392 bps INFO @ Sat, 11 Nov 2017 00:12:40: #2.2 Generate R script for model : SRX1074891.05_model.r WARNING @ Sat, 11 Nov 2017 00:12:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:12:40: #2 You may need to consider one of the other alternative d(s): 52,222,392 WARNING @ Sat, 11 Nov 2017 00:12:40: #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 00:12:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:12:40: #1 tag size is determined as 52 bps INFO @ Sat, 11 Nov 2017 00:12:40: #1 tag size = 52 INFO @ Sat, 11 Nov 2017 00:12:40: #1 total tags in treatment: 23329941 INFO @ Sat, 11 Nov 2017 00:12:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:12:40: #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 00:12:41: #1 tags after filtering in treatment: 23329821 INFO @ Sat, 11 Nov 2017 00:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:12:41: #1 finished! INFO @ Sat, 11 Nov 2017 00:12:41: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:12:43: #2 number of paired peaks: 5753 INFO @ Sat, 11 Nov 2017 00:12:43: start model_add_line... INFO @ Sat, 11 Nov 2017 00:12:44: start X-correlation... INFO @ Sat, 11 Nov 2017 00:12:44: end of X-cor INFO @ Sat, 11 Nov 2017 00:12:44: #2 finished! INFO @ Sat, 11 Nov 2017 00:12:44: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:12:44: #2 alternative fragment length(s) may be 52,222,392 bps INFO @ Sat, 11 Nov 2017 00:12:44: #2.2 Generate R script for model : SRX1074891.10_model.r WARNING @ Sat, 11 Nov 2017 00:12:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:12:44: #2 You may need to consider one of the other alternative d(s): 52,222,392 WARNING @ Sat, 11 Nov 2017 00:12:44: #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 00:12:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:13:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:13:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:13:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:14:06: #4 Write output xls file... SRX1074891.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:14:06: #4 Write peak in narrowPeak format file... SRX1074891.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:14:06: #4 Write summits bed file... SRX1074891.20_summits.bed INFO @ Sat, 11 Nov 2017 00:14:06: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (517 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:14:16: #4 Write output xls file... SRX1074891.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:14:16: #4 Write peak in narrowPeak format file... SRX1074891.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:14:16: #4 Write summits bed file... SRX1074891.05_summits.bed INFO @ Sat, 11 Nov 2017 00:14:16: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1659 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:14:17: #4 Write output xls file... SRX1074891.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:14:17: #4 Write peak in narrowPeak format file... SRX1074891.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:14:17: #4 Write summits bed file... SRX1074891.10_summits.bed INFO @ Sat, 11 Nov 2017 00:14:17: Done! pass1 - making usageList (36 chroms): 0 millis pass2 - checking and writing primary data (1001 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。