Job ID = 10201970 sra ファイルのダウンロード中... Completed: 707633K bytes transferred in 18 seconds (305973K 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 20938902 spots for /home/okishinya/chipatlas/results/ce10/SRX2576639/SRR5272596.sra Written 20938902 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: 00:05:22 20938902 reads; of these: 20938902 (100.00%) were unpaired; of these: 888893 (4.25%) aligned 0 times 16471521 (78.66%) aligned exactly 1 time 3578488 (17.09%) aligned >1 times 95.75% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 4394535 / 20050009 = 0.2192 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 13:19:57: # Command line: callpeak -t SRX2576639.bam -f BAM -g ce -n SRX2576639.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576639.05 # format = BAM # ChIP-seq file = ['SRX2576639.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 13:19:57: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:57: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:57: # Command line: callpeak -t SRX2576639.bam -f BAM -g ce -n SRX2576639.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576639.20 # format = BAM # ChIP-seq file = ['SRX2576639.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 13:19:57: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:57: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:57: # Command line: callpeak -t SRX2576639.bam -f BAM -g ce -n SRX2576639.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576639.10 # format = BAM # ChIP-seq file = ['SRX2576639.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 13:19:57: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:57: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:20:04: 1000000 INFO @ Mon, 13 Nov 2017 13:20:04: 1000000 INFO @ Mon, 13 Nov 2017 13:20:04: 1000000 INFO @ Mon, 13 Nov 2017 13:20:11: 2000000 INFO @ Mon, 13 Nov 2017 13:20:11: 2000000 INFO @ Mon, 13 Nov 2017 13:20:11: 2000000 INFO @ Mon, 13 Nov 2017 13:20:18: 3000000 INFO @ Mon, 13 Nov 2017 13:20:18: 3000000 INFO @ Mon, 13 Nov 2017 13:20:18: 3000000 INFO @ Mon, 13 Nov 2017 13:20:25: 4000000 INFO @ Mon, 13 Nov 2017 13:20:25: 4000000 INFO @ Mon, 13 Nov 2017 13:20:26: 4000000 INFO @ Mon, 13 Nov 2017 13:20:32: 5000000 INFO @ Mon, 13 Nov 2017 13:20:33: 5000000 INFO @ Mon, 13 Nov 2017 13:20:33: 5000000 INFO @ Mon, 13 Nov 2017 13:20:39: 6000000 INFO @ Mon, 13 Nov 2017 13:20:40: 6000000 INFO @ Mon, 13 Nov 2017 13:20:40: 6000000 INFO @ Mon, 13 Nov 2017 13:20:46: 7000000 INFO @ Mon, 13 Nov 2017 13:20:47: 7000000 INFO @ Mon, 13 Nov 2017 13:20:48: 7000000 INFO @ Mon, 13 Nov 2017 13:20:53: 8000000 INFO @ Mon, 13 Nov 2017 13:20:54: 8000000 INFO @ Mon, 13 Nov 2017 13:20:56: 8000000 INFO @ Mon, 13 Nov 2017 13:21:00: 9000000 INFO @ Mon, 13 Nov 2017 13:21:02: 9000000 INFO @ Mon, 13 Nov 2017 13:21:03: 9000000 INFO @ Mon, 13 Nov 2017 13:21:07: 10000000 INFO @ Mon, 13 Nov 2017 13:21:09: 10000000 INFO @ Mon, 13 Nov 2017 13:21:11: 10000000 INFO @ Mon, 13 Nov 2017 13:21:14: 11000000 INFO @ Mon, 13 Nov 2017 13:21:16: 11000000 INFO @ Mon, 13 Nov 2017 13:21:18: 11000000 INFO @ Mon, 13 Nov 2017 13:21:21: 12000000 INFO @ Mon, 13 Nov 2017 13:21:23: 12000000 INFO @ Mon, 13 Nov 2017 13:21:26: 12000000 INFO @ Mon, 13 Nov 2017 13:21:29: 13000000 INFO @ Mon, 13 Nov 2017 13:21:31: 13000000 INFO @ Mon, 13 Nov 2017 13:21:33: 13000000 INFO @ Mon, 13 Nov 2017 13:21:36: 14000000 INFO @ Mon, 13 Nov 2017 13:21:38: 14000000 INFO @ Mon, 13 Nov 2017 13:21:41: 14000000 INFO @ Mon, 13 Nov 2017 13:21:43: 15000000 INFO @ Mon, 13 Nov 2017 13:21:45: 15000000 INFO @ Mon, 13 Nov 2017 13:21:47: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:21:47: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:21:47: #1 total tags in treatment: 15655474 INFO @ Mon, 13 Nov 2017 13:21:47: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:21:47: #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 13:21:48: #1 tags after filtering in treatment: 15655474 INFO @ Mon, 13 Nov 2017 13:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:21:48: #1 finished! INFO @ Mon, 13 Nov 2017 13:21:48: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:21:48: 15000000 INFO @ Mon, 13 Nov 2017 13:21:49: #2 number of paired peaks: 356 WARNING @ Mon, 13 Nov 2017 13:21:49: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 13 Nov 2017 13:21:49: start model_add_line... INFO @ Mon, 13 Nov 2017 13:21:49: start X-correlation... INFO @ Mon, 13 Nov 2017 13:21:49: end of X-cor INFO @ Mon, 13 Nov 2017 13:21:49: #2 finished! INFO @ Mon, 13 Nov 2017 13:21:49: #2 predicted fragment length is 113 bps INFO @ Mon, 13 Nov 2017 13:21:49: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 13 Nov 2017 13:21:49: #2.2 Generate R script for model : SRX2576639.05_model.r INFO @ Mon, 13 Nov 2017 13:21:49: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:21:50: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:21:50: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:21:50: #1 total tags in treatment: 15655474 INFO @ Mon, 13 Nov 2017 13:21:50: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:21:50: #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 13:21:50: #1 tags after filtering in treatment: 15655474 INFO @ Mon, 13 Nov 2017 13:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:21:50: #1 finished! INFO @ Mon, 13 Nov 2017 13:21:50: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:21:51: #2 number of paired peaks: 356 WARNING @ Mon, 13 Nov 2017 13:21:51: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 13 Nov 2017 13:21:51: start model_add_line... INFO @ Mon, 13 Nov 2017 13:21:51: start X-correlation... INFO @ Mon, 13 Nov 2017 13:21:51: end of X-cor INFO @ Mon, 13 Nov 2017 13:21:51: #2 finished! INFO @ Mon, 13 Nov 2017 13:21:51: #2 predicted fragment length is 113 bps INFO @ Mon, 13 Nov 2017 13:21:51: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 13 Nov 2017 13:21:51: #2.2 Generate R script for model : SRX2576639.20_model.r INFO @ Mon, 13 Nov 2017 13:21:51: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:21:53: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:21:53: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:21:53: #1 total tags in treatment: 15655474 INFO @ Mon, 13 Nov 2017 13:21:53: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:21:53: #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 13:21:53: #1 tags after filtering in treatment: 15655474 INFO @ Mon, 13 Nov 2017 13:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:21:53: #1 finished! INFO @ Mon, 13 Nov 2017 13:21:53: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:21:54: #2 number of paired peaks: 356 WARNING @ Mon, 13 Nov 2017 13:21:54: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 13 Nov 2017 13:21:54: start model_add_line... INFO @ Mon, 13 Nov 2017 13:21:54: start X-correlation... INFO @ Mon, 13 Nov 2017 13:21:54: end of X-cor INFO @ Mon, 13 Nov 2017 13:21:54: #2 finished! INFO @ Mon, 13 Nov 2017 13:21:54: #2 predicted fragment length is 113 bps INFO @ Mon, 13 Nov 2017 13:21:54: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 13 Nov 2017 13:21:54: #2.2 Generate R script for model : SRX2576639.10_model.r INFO @ Mon, 13 Nov 2017 13:21:54: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:21:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:22:21: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:22:25: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:22:27: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:22:38: #4 Write output xls file... SRX2576639.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:22:38: #4 Write peak in narrowPeak format file... SRX2576639.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:22:38: #4 Write summits bed file... SRX2576639.05_summits.bed INFO @ Mon, 13 Nov 2017 13:22:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1890 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:22:41: #4 Write output xls file... SRX2576639.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:22:41: #4 Write peak in narrowPeak format file... SRX2576639.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:22:41: #4 Write summits bed file... SRX2576639.20_summits.bed INFO @ Mon, 13 Nov 2017 13:22:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (805 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:22:44: #4 Write output xls file... SRX2576639.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:22:44: #4 Write peak in narrowPeak format file... SRX2576639.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:22:44: #4 Write summits bed file... SRX2576639.10_summits.bed INFO @ Mon, 13 Nov 2017 13:22:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1337 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。