Job ID = 10201963 sra ファイルのダウンロード中... Completed: 441219K bytes transferred in 13 seconds (262321K 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 18906900 spots for /home/okishinya/chipatlas/results/ce10/SRX2576632/SRR5272589.sra Written 18906900 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:26 18906900 reads; of these: 18906900 (100.00%) were unpaired; of these: 485443 (2.57%) aligned 0 times 15155799 (80.16%) aligned exactly 1 time 3265658 (17.27%) aligned >1 times 97.43% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2723841 / 18421457 = 0.1479 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 @ Mon, 13 Nov 2017 13:16:20: # Command line: callpeak -t SRX2576632.bam -f BAM -g ce -n SRX2576632.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576632.05 # format = BAM # ChIP-seq file = ['SRX2576632.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 13 Nov 2017 13:16:20: # Command line: callpeak -t SRX2576632.bam -f BAM -g ce -n SRX2576632.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576632.10 # format = BAM # ChIP-seq file = ['SRX2576632.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 13 Nov 2017 13:16:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:20: # Command line: callpeak -t SRX2576632.bam -f BAM -g ce -n SRX2576632.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576632.20 # format = BAM # ChIP-seq file = ['SRX2576632.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 13 Nov 2017 13:16:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:26: 1000000 INFO @ Mon, 13 Nov 2017 13:16:26: 1000000 INFO @ Mon, 13 Nov 2017 13:16:26: 1000000 INFO @ Mon, 13 Nov 2017 13:16:32: 2000000 INFO @ Mon, 13 Nov 2017 13:16:33: 2000000 INFO @ Mon, 13 Nov 2017 13:16:33: 2000000 INFO @ Mon, 13 Nov 2017 13:16:38: 3000000 INFO @ Mon, 13 Nov 2017 13:16:40: 3000000 INFO @ Mon, 13 Nov 2017 13:16:40: 3000000 INFO @ Mon, 13 Nov 2017 13:16:45: 4000000 INFO @ Mon, 13 Nov 2017 13:16:47: 4000000 INFO @ Mon, 13 Nov 2017 13:16:47: 4000000 INFO @ Mon, 13 Nov 2017 13:16:51: 5000000 INFO @ Mon, 13 Nov 2017 13:16:53: 5000000 INFO @ Mon, 13 Nov 2017 13:16:53: 5000000 INFO @ Mon, 13 Nov 2017 13:16:57: 6000000 INFO @ Mon, 13 Nov 2017 13:17:00: 6000000 INFO @ Mon, 13 Nov 2017 13:17:00: 6000000 INFO @ Mon, 13 Nov 2017 13:17:03: 7000000 INFO @ Mon, 13 Nov 2017 13:17:07: 7000000 INFO @ Mon, 13 Nov 2017 13:17:07: 7000000 INFO @ Mon, 13 Nov 2017 13:17:10: 8000000 INFO @ Mon, 13 Nov 2017 13:17:14: 8000000 INFO @ Mon, 13 Nov 2017 13:17:14: 8000000 INFO @ Mon, 13 Nov 2017 13:17:16: 9000000 INFO @ Mon, 13 Nov 2017 13:17:20: 9000000 INFO @ Mon, 13 Nov 2017 13:17:20: 9000000 INFO @ Mon, 13 Nov 2017 13:17:22: 10000000 INFO @ Mon, 13 Nov 2017 13:17:27: 10000000 INFO @ Mon, 13 Nov 2017 13:17:27: 10000000 INFO @ Mon, 13 Nov 2017 13:17:28: 11000000 INFO @ Mon, 13 Nov 2017 13:17:33: 11000000 INFO @ Mon, 13 Nov 2017 13:17:33: 11000000 INFO @ Mon, 13 Nov 2017 13:17:34: 12000000 INFO @ Mon, 13 Nov 2017 13:17:40: 12000000 INFO @ Mon, 13 Nov 2017 13:17:40: 12000000 INFO @ Mon, 13 Nov 2017 13:17:41: 13000000 INFO @ Mon, 13 Nov 2017 13:17:47: 13000000 INFO @ Mon, 13 Nov 2017 13:17:47: 13000000 INFO @ Mon, 13 Nov 2017 13:17:47: 14000000 INFO @ Mon, 13 Nov 2017 13:17:53: 15000000 INFO @ Mon, 13 Nov 2017 13:17:53: 14000000 INFO @ Mon, 13 Nov 2017 13:17:53: 14000000 INFO @ Mon, 13 Nov 2017 13:17:58: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:58: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:58: #1 total tags in treatment: 15697616 INFO @ Mon, 13 Nov 2017 13:17:58: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:58: #1 tags after filtering in treatment: 15697616 INFO @ Mon, 13 Nov 2017 13:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:58: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:58: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:59: #2 number of paired peaks: 369 WARNING @ Mon, 13 Nov 2017 13:17:59: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:59: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:59: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:59: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:59: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:59: #2 predicted fragment length is 126 bps INFO @ Mon, 13 Nov 2017 13:17:59: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 13 Nov 2017 13:17:59: #2.2 Generate R script for model : SRX2576632.05_model.r INFO @ Mon, 13 Nov 2017 13:17:59: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:00: 15000000 INFO @ Mon, 13 Nov 2017 13:18:00: 15000000 INFO @ Mon, 13 Nov 2017 13:18:04: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:18:04: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:18:04: #1 total tags in treatment: 15697616 INFO @ Mon, 13 Nov 2017 13:18:04: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:04: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:18:04: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:18:04: #1 total tags in treatment: 15697616 INFO @ Mon, 13 Nov 2017 13:18:04: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:05: #1 tags after filtering in treatment: 15697616 INFO @ Mon, 13 Nov 2017 13:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:05: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:05: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:05: #1 tags after filtering in treatment: 15697616 INFO @ Mon, 13 Nov 2017 13:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:05: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:05: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:06: #2 number of paired peaks: 369 WARNING @ Mon, 13 Nov 2017 13:18:06: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:06: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:06: #2 number of paired peaks: 369 WARNING @ Mon, 13 Nov 2017 13:18:06: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:06: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:06: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:06: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:06: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:06: #2 predicted fragment length is 126 bps INFO @ Mon, 13 Nov 2017 13:18:06: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 13 Nov 2017 13:18:06: #2.2 Generate R script for model : SRX2576632.10_model.r INFO @ Mon, 13 Nov 2017 13:18:06: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:06: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:06: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:06: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:06: #2 predicted fragment length is 126 bps INFO @ Mon, 13 Nov 2017 13:18:06: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 13 Nov 2017 13:18:06: #2.2 Generate R script for model : SRX2576632.20_model.r INFO @ Mon, 13 Nov 2017 13:18:06: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:34: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:40: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:42: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:54: #4 Write output xls file... SRX2576632.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:54: #4 Write peak in narrowPeak format file... SRX2576632.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:54: #4 Write summits bed file... SRX2576632.05_summits.bed INFO @ Mon, 13 Nov 2017 13:18:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3073 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:59: #4 Write output xls file... SRX2576632.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:59: #4 Write peak in narrowPeak format file... SRX2576632.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:59: #4 Write summits bed file... SRX2576632.10_summits.bed INFO @ Mon, 13 Nov 2017 13:18:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2036 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:00: #4 Write output xls file... SRX2576632.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:00: #4 Write peak in narrowPeak format file... SRX2576632.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:00: #4 Write summits bed file... SRX2576632.20_summits.bed INFO @ Mon, 13 Nov 2017 13:19:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1318 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。