Job ID = 10194898 sra ファイルのダウンロード中... Completed: 274774K bytes transferred in 9 seconds (235850K bits/sec), in 1 file. Completed: 276875K bytes transferred in 11 seconds (194302K bits/sec), in 1 file. Completed: 261908K bytes transferred in 15 seconds (140305K bits/sec), in 1 file. Completed: 258363K bytes transferred in 11 seconds (192153K bits/sec), in 1 file. Completed: 301434K bytes transferred in 16 seconds (151983K bits/sec), in 1 file. Completed: 306585K bytes transferred in 18 seconds (133663K 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 6008034 spots for /home/okishinya/chipatlas/results/rn6/SRX2202893/SRR4319904.sra Written 6008034 spots total Written 5936911 spots for /home/okishinya/chipatlas/results/rn6/SRX2202893/SRR4319905.sra Written 5936911 spots total Written 6276450 spots for /home/okishinya/chipatlas/results/rn6/SRX2202893/SRR4319902.sra Written 6276450 spots total Written 6304638 spots for /home/okishinya/chipatlas/results/rn6/SRX2202893/SRR4319903.sra Written 6304638 spots total Written 6741657 spots for /home/okishinya/chipatlas/results/rn6/SRX2202893/SRR4319906.sra Written 6741657 spots total Written 6835237 spots for /home/okishinya/chipatlas/results/rn6/SRX2202893/SRR4319907.sra Written 6835237 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 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: 00:28:41 38102927 reads; of these: 38102927 (100.00%) were unpaired; of these: 1029278 (2.70%) aligned 0 times 26386683 (69.25%) aligned exactly 1 time 10686966 (28.05%) aligned >1 times 97.30% overall alignment rate Time searching: 00:28:45 Overall time: 00:28:45 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 16 files... [bam_rmdupse_core] 1795880 / 37073649 = 0.0484 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 @ Fri, 10 Nov 2017 18:59:33: # Command line: callpeak -t SRX2202893.bam -f BAM -g 2.15e9 -n SRX2202893.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202893.10 # format = BAM # ChIP-seq file = ['SRX2202893.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 @ Fri, 10 Nov 2017 18:59:33: # Command line: callpeak -t SRX2202893.bam -f BAM -g 2.15e9 -n SRX2202893.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202893.05 # format = BAM # ChIP-seq file = ['SRX2202893.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 @ Fri, 10 Nov 2017 18:59:33: # Command line: callpeak -t SRX2202893.bam -f BAM -g 2.15e9 -n SRX2202893.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202893.20 # format = BAM # ChIP-seq file = ['SRX2202893.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 @ Fri, 10 Nov 2017 18:59:33: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:59:33: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:59:33: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:59:33: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:59:33: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:59:33: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:59:42: 1000000 INFO @ Fri, 10 Nov 2017 18:59:42: 1000000 INFO @ Fri, 10 Nov 2017 18:59:42: 1000000 INFO @ Fri, 10 Nov 2017 18:59:51: 2000000 INFO @ Fri, 10 Nov 2017 18:59:51: 2000000 INFO @ Fri, 10 Nov 2017 18:59:51: 2000000 INFO @ Fri, 10 Nov 2017 19:00:00: 3000000 INFO @ Fri, 10 Nov 2017 19:00:00: 3000000 INFO @ Fri, 10 Nov 2017 19:00:00: 3000000 INFO @ Fri, 10 Nov 2017 19:00:09: 4000000 INFO @ Fri, 10 Nov 2017 19:00:09: 4000000 INFO @ Fri, 10 Nov 2017 19:00:09: 4000000 INFO @ Fri, 10 Nov 2017 19:00:18: 5000000 INFO @ Fri, 10 Nov 2017 19:00:18: 5000000 INFO @ Fri, 10 Nov 2017 19:00:18: 5000000 INFO @ Fri, 10 Nov 2017 19:00:27: 6000000 INFO @ Fri, 10 Nov 2017 19:00:27: 6000000 INFO @ Fri, 10 Nov 2017 19:00:27: 6000000 INFO @ Fri, 10 Nov 2017 19:00:36: 7000000 INFO @ Fri, 10 Nov 2017 19:00:36: 7000000 INFO @ Fri, 10 Nov 2017 19:00:36: 7000000 INFO @ Fri, 10 Nov 2017 19:00:43: 8000000 INFO @ Fri, 10 Nov 2017 19:00:45: 8000000 INFO @ Fri, 10 Nov 2017 19:00:45: 8000000 INFO @ Fri, 10 Nov 2017 19:00:51: 9000000 INFO @ Fri, 10 Nov 2017 19:00:54: 9000000 INFO @ Fri, 10 Nov 2017 19:00:54: 9000000 INFO @ Fri, 10 Nov 2017 19:00:58: 10000000 INFO @ Fri, 10 Nov 2017 19:01:02: 10000000 INFO @ Fri, 10 Nov 2017 19:01:02: 10000000 INFO @ Fri, 10 Nov 2017 19:01:06: 11000000 INFO @ Fri, 10 Nov 2017 19:01:11: 11000000 INFO @ Fri, 10 Nov 2017 19:01:11: 11000000 INFO @ Fri, 10 Nov 2017 19:01:14: 12000000 INFO @ Fri, 10 Nov 2017 19:01:19: 12000000 INFO @ Fri, 10 Nov 2017 19:01:19: 12000000 INFO @ Fri, 10 Nov 2017 19:01:21: 13000000 INFO @ Fri, 10 Nov 2017 19:01:28: 13000000 INFO @ Fri, 10 Nov 2017 19:01:28: 13000000 INFO @ Fri, 10 Nov 2017 19:01:29: 14000000 INFO @ Fri, 10 Nov 2017 19:01:36: 15000000 INFO @ Fri, 10 Nov 2017 19:01:37: 14000000 INFO @ Fri, 10 Nov 2017 19:01:37: 14000000 INFO @ Fri, 10 Nov 2017 19:01:44: 16000000 INFO @ Fri, 10 Nov 2017 19:01:45: 15000000 INFO @ Fri, 10 Nov 2017 19:01:45: 15000000 INFO @ Fri, 10 Nov 2017 19:01:52: 17000000 INFO @ Fri, 10 Nov 2017 19:01:54: 16000000 INFO @ Fri, 10 Nov 2017 19:01:54: 16000000 INFO @ Fri, 10 Nov 2017 19:01:59: 18000000 INFO @ Fri, 10 Nov 2017 19:02:02: 17000000 INFO @ Fri, 10 Nov 2017 19:02:02: 17000000 INFO @ Fri, 10 Nov 2017 19:02:07: 19000000 INFO @ Fri, 10 Nov 2017 19:02:11: 18000000 INFO @ Fri, 10 Nov 2017 19:02:11: 18000000 INFO @ Fri, 10 Nov 2017 19:02:14: 20000000 INFO @ Fri, 10 Nov 2017 19:02:20: 19000000 INFO @ Fri, 10 Nov 2017 19:02:20: 19000000 INFO @ Fri, 10 Nov 2017 19:02:21: 21000000 INFO @ Fri, 10 Nov 2017 19:02:28: 20000000 INFO @ Fri, 10 Nov 2017 19:02:28: 20000000 INFO @ Fri, 10 Nov 2017 19:02:29: 22000000 INFO @ Fri, 10 Nov 2017 19:02:37: 21000000 INFO @ Fri, 10 Nov 2017 19:02:37: 21000000 INFO @ Fri, 10 Nov 2017 19:02:37: 23000000 INFO @ Fri, 10 Nov 2017 19:02:44: 24000000 INFO @ Fri, 10 Nov 2017 19:02:45: 22000000 INFO @ Fri, 10 Nov 2017 19:02:45: 22000000 INFO @ Fri, 10 Nov 2017 19:02:52: 25000000 INFO @ Fri, 10 Nov 2017 19:02:54: 23000000 INFO @ Fri, 10 Nov 2017 19:02:54: 23000000 INFO @ Fri, 10 Nov 2017 19:02:59: 26000000 INFO @ Fri, 10 Nov 2017 19:03:03: 24000000 INFO @ Fri, 10 Nov 2017 19:03:03: 24000000 INFO @ Fri, 10 Nov 2017 19:03:07: 27000000 INFO @ Fri, 10 Nov 2017 19:03:11: 25000000 INFO @ Fri, 10 Nov 2017 19:03:11: 25000000 INFO @ Fri, 10 Nov 2017 19:03:14: 28000000 INFO @ Fri, 10 Nov 2017 19:03:20: 26000000 INFO @ Fri, 10 Nov 2017 19:03:20: 26000000 INFO @ Fri, 10 Nov 2017 19:03:22: 29000000 INFO @ Fri, 10 Nov 2017 19:03:28: 27000000 INFO @ Fri, 10 Nov 2017 19:03:28: 27000000 INFO @ Fri, 10 Nov 2017 19:03:30: 30000000 INFO @ Fri, 10 Nov 2017 19:03:37: 28000000 INFO @ Fri, 10 Nov 2017 19:03:37: 28000000 INFO @ Fri, 10 Nov 2017 19:03:38: 31000000 INFO @ Fri, 10 Nov 2017 19:03:45: 32000000 INFO @ Fri, 10 Nov 2017 19:03:46: 29000000 INFO @ Fri, 10 Nov 2017 19:03:46: 29000000 INFO @ Fri, 10 Nov 2017 19:03:53: 33000000 INFO @ Fri, 10 Nov 2017 19:03:54: 30000000 INFO @ Fri, 10 Nov 2017 19:03:54: 30000000 INFO @ Fri, 10 Nov 2017 19:04:00: 34000000 INFO @ Fri, 10 Nov 2017 19:04:03: 31000000 INFO @ Fri, 10 Nov 2017 19:04:03: 31000000 INFO @ Fri, 10 Nov 2017 19:04:08: 35000000 INFO @ Fri, 10 Nov 2017 19:04:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:04:10: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:04:10: #1 total tags in treatment: 35277769 INFO @ Fri, 10 Nov 2017 19:04:10: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 19:04:11: #1 tags after filtering in treatment: 35277691 INFO @ Fri, 10 Nov 2017 19:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:04:11: #1 finished! INFO @ Fri, 10 Nov 2017 19:04:11: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:04:11: 32000000 INFO @ Fri, 10 Nov 2017 19:04:11: 32000000 INFO @ Fri, 10 Nov 2017 19:04:14: #2 number of paired peaks: 5381 INFO @ Fri, 10 Nov 2017 19:04:14: start model_add_line... INFO @ Fri, 10 Nov 2017 19:04:15: start X-correlation... INFO @ Fri, 10 Nov 2017 19:04:15: end of X-cor INFO @ Fri, 10 Nov 2017 19:04:15: #2 finished! INFO @ Fri, 10 Nov 2017 19:04:15: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 19:04:15: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 19:04:15: #2.2 Generate R script for model : SRX2202893.05_model.r WARNING @ Fri, 10 Nov 2017 19:04:15: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:04:15: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 19:04:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 19:04:15: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:04:20: 33000000 INFO @ Fri, 10 Nov 2017 19:04:20: 33000000 INFO @ Fri, 10 Nov 2017 19:04:30: 34000000 INFO @ Fri, 10 Nov 2017 19:04:30: 34000000 INFO @ Fri, 10 Nov 2017 19:04:38: 35000000 INFO @ Fri, 10 Nov 2017 19:04:38: 35000000 INFO @ Fri, 10 Nov 2017 19:04:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:04:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:04:41: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:04:41: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:04:41: #1 total tags in treatment: 35277769 INFO @ Fri, 10 Nov 2017 19:04:41: #1 total tags in treatment: 35277769 INFO @ Fri, 10 Nov 2017 19:04:41: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:04:41: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:04:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 19:04:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 19:04:42: #1 tags after filtering in treatment: 35277691 INFO @ Fri, 10 Nov 2017 19:04:42: #1 tags after filtering in treatment: 35277691 INFO @ Fri, 10 Nov 2017 19:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:04:42: #1 finished! INFO @ Fri, 10 Nov 2017 19:04:42: #1 finished! INFO @ Fri, 10 Nov 2017 19:04:42: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:04:42: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:04:45: #2 number of paired peaks: 5381 INFO @ Fri, 10 Nov 2017 19:04:45: start model_add_line... INFO @ Fri, 10 Nov 2017 19:04:45: #2 number of paired peaks: 5381 INFO @ Fri, 10 Nov 2017 19:04:45: start model_add_line... INFO @ Fri, 10 Nov 2017 19:04:46: start X-correlation... INFO @ Fri, 10 Nov 2017 19:04:46: end of X-cor INFO @ Fri, 10 Nov 2017 19:04:46: #2 finished! INFO @ Fri, 10 Nov 2017 19:04:46: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 19:04:46: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 19:04:46: #2.2 Generate R script for model : SRX2202893.20_model.r WARNING @ Fri, 10 Nov 2017 19:04:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:04:46: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 19:04:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 19:04:46: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:04:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:04:46: start X-correlation... INFO @ Fri, 10 Nov 2017 19:04:46: end of X-cor INFO @ Fri, 10 Nov 2017 19:04:46: #2 finished! INFO @ Fri, 10 Nov 2017 19:04:46: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 19:04:46: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 19:04:46: #2.2 Generate R script for model : SRX2202893.10_model.r WARNING @ Fri, 10 Nov 2017 19:04:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 19:04:46: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 19:04:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 19:04:46: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:04:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:05:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:06:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:06:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:06:31: #4 Write output xls file... SRX2202893.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:06:31: #4 Write peak in narrowPeak format file... SRX2202893.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:06:31: #4 Write summits bed file... SRX2202893.05_summits.bed INFO @ Fri, 10 Nov 2017 19:06:31: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2037 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:07:01: #4 Write output xls file... SRX2202893.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:07:01: #4 Write peak in narrowPeak format file... SRX2202893.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:07:01: #4 Write summits bed file... SRX2202893.10_summits.bed INFO @ Fri, 10 Nov 2017 19:07:01: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1181 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:07:04: #4 Write output xls file... SRX2202893.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:07:04: #4 Write peak in narrowPeak format file... SRX2202893.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:07:04: #4 Write summits bed file... SRX2202893.20_summits.bed INFO @ Fri, 10 Nov 2017 19:07:04: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。