Job ID = 10201954 sra ファイルのダウンロード中... Completed: 673277K bytes transferred in 16 seconds (336343K 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 21385259 spots for /home/okishinya/chipatlas/results/ce10/SRX2576623/SRR5272580.sra Written 21385259 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: 00:00:00 Multiseed full-index search: 00:14:04 21385259 reads; of these: 21385259 (100.00%) were unpaired; of these: 1042113 (4.87%) aligned 0 times 16660760 (77.91%) aligned exactly 1 time 3682386 (17.22%) aligned >1 times 95.13% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 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 12 files... [bam_rmdupse_core] 6046419 / 20343146 = 0.2972 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 13:30:38: # Command line: callpeak -t SRX2576623.bam -f BAM -g ce -n SRX2576623.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576623.10 # format = BAM # ChIP-seq file = ['SRX2576623.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 13:30:38: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:30:38: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:30:38: # Command line: callpeak -t SRX2576623.bam -f BAM -g ce -n SRX2576623.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576623.20 # format = BAM # ChIP-seq file = ['SRX2576623.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 13:30:38: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:30:38: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:30:38: # Command line: callpeak -t SRX2576623.bam -f BAM -g ce -n SRX2576623.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576623.05 # format = BAM # ChIP-seq file = ['SRX2576623.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 13:30:38: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:30:38: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:30:59: 1000000 INFO @ Mon, 13 Nov 2017 13:30:59: 1000000 INFO @ Mon, 13 Nov 2017 13:31:01: 1000000 INFO @ Mon, 13 Nov 2017 13:31:21: 2000000 INFO @ Mon, 13 Nov 2017 13:31:21: 2000000 INFO @ Mon, 13 Nov 2017 13:31:24: 2000000 INFO @ Mon, 13 Nov 2017 13:31:43: 3000000 INFO @ Mon, 13 Nov 2017 13:31:43: 3000000 INFO @ Mon, 13 Nov 2017 13:31:46: 3000000 INFO @ Mon, 13 Nov 2017 13:32:05: 4000000 INFO @ Mon, 13 Nov 2017 13:32:06: 4000000 INFO @ Mon, 13 Nov 2017 13:32:07: 4000000 INFO @ Mon, 13 Nov 2017 13:32:27: 5000000 INFO @ Mon, 13 Nov 2017 13:32:28: 5000000 INFO @ Mon, 13 Nov 2017 13:32:29: 5000000 INFO @ Mon, 13 Nov 2017 13:32:47: 6000000 INFO @ Mon, 13 Nov 2017 13:32:49: 6000000 INFO @ Mon, 13 Nov 2017 13:32:52: 6000000 INFO @ Mon, 13 Nov 2017 13:33:08: 7000000 INFO @ Mon, 13 Nov 2017 13:33:09: 7000000 INFO @ Mon, 13 Nov 2017 13:33:13: 7000000 INFO @ Mon, 13 Nov 2017 13:33:28: 8000000 INFO @ Mon, 13 Nov 2017 13:33:29: 8000000 INFO @ Mon, 13 Nov 2017 13:33:35: 8000000 INFO @ Mon, 13 Nov 2017 13:33:48: 9000000 INFO @ Mon, 13 Nov 2017 13:33:49: 9000000 INFO @ Mon, 13 Nov 2017 13:33:57: 9000000 INFO @ Mon, 13 Nov 2017 13:34:06: 10000000 INFO @ Mon, 13 Nov 2017 13:34:11: 10000000 INFO @ Mon, 13 Nov 2017 13:34:18: 10000000 INFO @ Mon, 13 Nov 2017 13:34:24: 11000000 INFO @ Mon, 13 Nov 2017 13:34:30: 11000000 INFO @ Mon, 13 Nov 2017 13:34:40: 11000000 INFO @ Mon, 13 Nov 2017 13:34:43: 12000000 INFO @ Mon, 13 Nov 2017 13:34:47: 12000000 INFO @ Mon, 13 Nov 2017 13:35:00: 13000000 INFO @ Mon, 13 Nov 2017 13:35:01: 13000000 INFO @ Mon, 13 Nov 2017 13:35:02: 12000000 INFO @ Mon, 13 Nov 2017 13:35:11: 14000000 INFO @ Mon, 13 Nov 2017 13:35:12: 14000000 INFO @ Mon, 13 Nov 2017 13:35:15: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:35:15: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:35:15: #1 total tags in treatment: 14296727 INFO @ Mon, 13 Nov 2017 13:35:15: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:35:15: #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 13:35:15: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:35:15: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:35:15: #1 total tags in treatment: 14296727 INFO @ Mon, 13 Nov 2017 13:35:15: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:35:15: #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 13:35:15: #1 tags after filtering in treatment: 14296727 INFO @ Mon, 13 Nov 2017 13:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:35:15: #1 finished! INFO @ Mon, 13 Nov 2017 13:35:15: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:35:15: #1 tags after filtering in treatment: 14296727 INFO @ Mon, 13 Nov 2017 13:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:35:15: #1 finished! INFO @ Mon, 13 Nov 2017 13:35:15: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:35:16: #2 number of paired peaks: 440 WARNING @ Mon, 13 Nov 2017 13:35:16: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Mon, 13 Nov 2017 13:35:16: start model_add_line... INFO @ Mon, 13 Nov 2017 13:35:16: #2 number of paired peaks: 440 WARNING @ Mon, 13 Nov 2017 13:35:16: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Mon, 13 Nov 2017 13:35:16: start model_add_line... INFO @ Mon, 13 Nov 2017 13:35:17: start X-correlation... INFO @ Mon, 13 Nov 2017 13:35:17: end of X-cor INFO @ Mon, 13 Nov 2017 13:35:17: #2 finished! INFO @ Mon, 13 Nov 2017 13:35:17: #2 predicted fragment length is 150 bps INFO @ Mon, 13 Nov 2017 13:35:17: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 13 Nov 2017 13:35:17: #2.2 Generate R script for model : SRX2576623.10_model.r INFO @ Mon, 13 Nov 2017 13:35:17: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:35:17: start X-correlation... INFO @ Mon, 13 Nov 2017 13:35:17: end of X-cor INFO @ Mon, 13 Nov 2017 13:35:17: #2 finished! INFO @ Mon, 13 Nov 2017 13:35:17: #2 predicted fragment length is 150 bps INFO @ Mon, 13 Nov 2017 13:35:17: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 13 Nov 2017 13:35:17: #2.2 Generate R script for model : SRX2576623.20_model.r INFO @ Mon, 13 Nov 2017 13:35:17: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:35:24: 13000000 INFO @ Mon, 13 Nov 2017 13:35:48: 14000000 INFO @ Mon, 13 Nov 2017 13:35:53: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:35:53: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:35:53: #1 total tags in treatment: 14296727 INFO @ Mon, 13 Nov 2017 13:35:53: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:35:53: #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 13:35:54: #1 tags after filtering in treatment: 14296727 INFO @ Mon, 13 Nov 2017 13:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:35:54: #1 finished! INFO @ Mon, 13 Nov 2017 13:35:54: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:35:55: #2 number of paired peaks: 440 WARNING @ Mon, 13 Nov 2017 13:35:55: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Mon, 13 Nov 2017 13:35:55: start model_add_line... INFO @ Mon, 13 Nov 2017 13:35:55: start X-correlation... INFO @ Mon, 13 Nov 2017 13:35:55: end of X-cor INFO @ Mon, 13 Nov 2017 13:35:55: #2 finished! INFO @ Mon, 13 Nov 2017 13:35:55: #2 predicted fragment length is 150 bps INFO @ Mon, 13 Nov 2017 13:35:55: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 13 Nov 2017 13:35:55: #2.2 Generate R script for model : SRX2576623.05_model.r INFO @ Mon, 13 Nov 2017 13:35:55: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:35:56: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:35:57: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:36:18: #4 Write output xls file... SRX2576623.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:36:18: #4 Write peak in narrowPeak format file... SRX2576623.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:36:18: #4 Write summits bed file... SRX2576623.20_summits.bed INFO @ Mon, 13 Nov 2017 13:36:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:36:23: #4 Write output xls file... SRX2576623.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:36:23: #4 Write peak in narrowPeak format file... SRX2576623.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:36:23: #4 Write summits bed file... SRX2576623.10_summits.bed INFO @ Mon, 13 Nov 2017 13:36:23: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1346 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:36:35: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:36:58: #4 Write output xls file... SRX2576623.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:36:58: #4 Write peak in narrowPeak format file... SRX2576623.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:36:58: #4 Write summits bed file... SRX2576623.05_summits.bed INFO @ Mon, 13 Nov 2017 13:36:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1822 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。