Job ID = 10480691 sra ファイルのダウンロード中... Completed: 418737K bytes transferred in 12 seconds (285387K 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 13431315 spots for /home/okishinya/chipatlas/results/dm3/SRX3068962/SRR5907438.sra Written 13431315 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: 00:03:39 13431315 reads; of these: 13431315 (100.00%) were unpaired; of these: 3156360 (23.50%) aligned 0 times 8522378 (63.45%) aligned exactly 1 time 1752577 (13.05%) aligned >1 times 76.50% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3775148 / 10274955 = 0.3674 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, 16 Mar 2018 07:43:28: # Command line: callpeak -t SRX3068962.bam -f BAM -g dm -n SRX3068962.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068962.05 # format = BAM # ChIP-seq file = ['SRX3068962.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:28: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:28: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:28: # Command line: callpeak -t SRX3068962.bam -f BAM -g dm -n SRX3068962.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068962.20 # format = BAM # ChIP-seq file = ['SRX3068962.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:28: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:28: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:28: # Command line: callpeak -t SRX3068962.bam -f BAM -g dm -n SRX3068962.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068962.10 # format = BAM # ChIP-seq file = ['SRX3068962.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:43:28: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:28: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:36: 1000000 INFO @ Fri, 16 Mar 2018 07:43:36: 1000000 INFO @ Fri, 16 Mar 2018 07:43:36: 1000000 INFO @ Fri, 16 Mar 2018 07:43:43: 2000000 INFO @ Fri, 16 Mar 2018 07:43:43: 2000000 INFO @ Fri, 16 Mar 2018 07:43:44: 2000000 INFO @ Fri, 16 Mar 2018 07:43:50: 3000000 INFO @ Fri, 16 Mar 2018 07:43:51: 3000000 INFO @ Fri, 16 Mar 2018 07:43:52: 3000000 INFO @ Fri, 16 Mar 2018 07:43:58: 4000000 INFO @ Fri, 16 Mar 2018 07:43:58: 4000000 INFO @ Fri, 16 Mar 2018 07:44:00: 4000000 INFO @ Fri, 16 Mar 2018 07:44:06: 5000000 INFO @ Fri, 16 Mar 2018 07:44:06: 5000000 INFO @ Fri, 16 Mar 2018 07:44:08: 5000000 INFO @ Fri, 16 Mar 2018 07:44:13: 6000000 INFO @ Fri, 16 Mar 2018 07:44:14: 6000000 INFO @ Fri, 16 Mar 2018 07:44:16: 6000000 INFO @ Fri, 16 Mar 2018 07:44:17: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:17: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:17: #1 total tags in treatment: 6499807 INFO @ Fri, 16 Mar 2018 07:44:17: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:17: #1 tags after filtering in treatment: 6499807 INFO @ Fri, 16 Mar 2018 07:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:17: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:17: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:18: #2 number of paired peaks: 864 WARNING @ Fri, 16 Mar 2018 07:44:18: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 16 Mar 2018 07:44:18: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:18: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:18: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:18: #1 total tags in treatment: 6499807 INFO @ Fri, 16 Mar 2018 07:44:18: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:18: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:18: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:18: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:18: #2 predicted fragment length is 141 bps INFO @ Fri, 16 Mar 2018 07:44:18: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 16 Mar 2018 07:44:18: #2.2 Generate R script for model : SRX3068962.05_model.r INFO @ Fri, 16 Mar 2018 07:44:18: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:18: #1 tags after filtering in treatment: 6499807 INFO @ Fri, 16 Mar 2018 07:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:18: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:18: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:18: #2 number of paired peaks: 864 WARNING @ Fri, 16 Mar 2018 07:44:18: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 16 Mar 2018 07:44:18: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:18: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:18: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:18: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:18: #2 predicted fragment length is 141 bps INFO @ Fri, 16 Mar 2018 07:44:18: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 16 Mar 2018 07:44:18: #2.2 Generate R script for model : SRX3068962.10_model.r INFO @ Fri, 16 Mar 2018 07:44:19: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:20: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:44:20: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:44:20: #1 total tags in treatment: 6499807 INFO @ Fri, 16 Mar 2018 07:44:20: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:44:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:44:21: #1 tags after filtering in treatment: 6499807 INFO @ Fri, 16 Mar 2018 07:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:44:21: #1 finished! INFO @ Fri, 16 Mar 2018 07:44:21: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:44:21: #2 number of paired peaks: 864 WARNING @ Fri, 16 Mar 2018 07:44:21: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 16 Mar 2018 07:44:21: start model_add_line... INFO @ Fri, 16 Mar 2018 07:44:21: start X-correlation... INFO @ Fri, 16 Mar 2018 07:44:21: end of X-cor INFO @ Fri, 16 Mar 2018 07:44:21: #2 finished! INFO @ Fri, 16 Mar 2018 07:44:21: #2 predicted fragment length is 141 bps INFO @ Fri, 16 Mar 2018 07:44:21: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 16 Mar 2018 07:44:21: #2.2 Generate R script for model : SRX3068962.20_model.r INFO @ Fri, 16 Mar 2018 07:44:21: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:38: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:42: #4 Write output xls file... SRX3068962.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:42: #4 Write peak in narrowPeak format file... SRX3068962.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:42: #4 Write summits bed file... SRX3068962.10_summits.bed INFO @ Fri, 16 Mar 2018 07:44:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2751 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:44:44: #4 Write output xls file... SRX3068962.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:44: #4 Write peak in narrowPeak format file... SRX3068962.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:44: #4 Write summits bed file... SRX3068962.05_summits.bed INFO @ Fri, 16 Mar 2018 07:44:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5424 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:44:47: #4 Write output xls file... SRX3068962.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:47: #4 Write peak in narrowPeak format file... SRX3068962.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:47: #4 Write summits bed file... SRX3068962.20_summits.bed INFO @ Fri, 16 Mar 2018 07:44:47: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1197 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。