Job ID = 10201971 sra ファイルのダウンロード中... Completed: 599408K bytes transferred in 18 seconds (264301K 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 17633815 spots for /home/okishinya/chipatlas/results/ce10/SRX2576640/SRR5272597.sra Written 17633815 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: 00:11:04 17633815 reads; of these: 17633815 (100.00%) were unpaired; of these: 2089770 (11.85%) aligned 0 times 12947088 (73.42%) aligned exactly 1 time 2596957 (14.73%) aligned >1 times 88.15% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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 8 files... [bam_rmdupse_core] 6951760 / 15544045 = 0.4472 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 13:26:28: # Command line: callpeak -t SRX2576640.bam -f BAM -g ce -n SRX2576640.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576640.10 # format = BAM # ChIP-seq file = ['SRX2576640.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 13:26:28: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:26:28: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:26:28: # Command line: callpeak -t SRX2576640.bam -f BAM -g ce -n SRX2576640.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576640.20 # format = BAM # ChIP-seq file = ['SRX2576640.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 13:26:28: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:26:28: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:26:28: # Command line: callpeak -t SRX2576640.bam -f BAM -g ce -n SRX2576640.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576640.05 # format = BAM # ChIP-seq file = ['SRX2576640.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 13:26:28: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:26:28: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:26:45: 1000000 INFO @ Mon, 13 Nov 2017 13:26:49: 1000000 INFO @ Mon, 13 Nov 2017 13:26:50: 1000000 INFO @ Mon, 13 Nov 2017 13:27:02: 2000000 INFO @ Mon, 13 Nov 2017 13:27:09: 2000000 INFO @ Mon, 13 Nov 2017 13:27:13: 2000000 INFO @ Mon, 13 Nov 2017 13:27:19: 3000000 INFO @ Mon, 13 Nov 2017 13:27:29: 3000000 INFO @ Mon, 13 Nov 2017 13:27:35: 3000000 INFO @ Mon, 13 Nov 2017 13:27:37: 4000000 INFO @ Mon, 13 Nov 2017 13:27:51: 4000000 INFO @ Mon, 13 Nov 2017 13:27:54: 5000000 INFO @ Mon, 13 Nov 2017 13:27:58: 4000000 INFO @ Mon, 13 Nov 2017 13:28:11: 6000000 INFO @ Mon, 13 Nov 2017 13:28:14: 5000000 INFO @ Mon, 13 Nov 2017 13:28:22: 5000000 INFO @ Mon, 13 Nov 2017 13:28:29: 7000000 INFO @ Mon, 13 Nov 2017 13:28:36: 6000000 INFO @ Mon, 13 Nov 2017 13:28:45: 6000000 INFO @ Mon, 13 Nov 2017 13:28:46: 8000000 INFO @ Mon, 13 Nov 2017 13:28:56: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:28:56: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:28:56: #1 total tags in treatment: 8592285 INFO @ Mon, 13 Nov 2017 13:28:56: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:28:56: #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 13:28:56: #1 tags after filtering in treatment: 8592285 INFO @ Mon, 13 Nov 2017 13:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:28:56: #1 finished! INFO @ Mon, 13 Nov 2017 13:28:56: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:28:57: #2 number of paired peaks: 1389 INFO @ Mon, 13 Nov 2017 13:28:57: start model_add_line... INFO @ Mon, 13 Nov 2017 13:28:57: start X-correlation... INFO @ Mon, 13 Nov 2017 13:28:57: end of X-cor INFO @ Mon, 13 Nov 2017 13:28:57: #2 finished! INFO @ Mon, 13 Nov 2017 13:28:57: #2 predicted fragment length is 173 bps INFO @ Mon, 13 Nov 2017 13:28:57: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 13 Nov 2017 13:28:57: #2.2 Generate R script for model : SRX2576640.10_model.r INFO @ Mon, 13 Nov 2017 13:28:57: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:28:58: 7000000 INFO @ Mon, 13 Nov 2017 13:29:08: 7000000 INFO @ Mon, 13 Nov 2017 13:29:19: 8000000 INFO @ Mon, 13 Nov 2017 13:29:28: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:29:32: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:32: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:32: #1 total tags in treatment: 8592285 INFO @ Mon, 13 Nov 2017 13:29:32: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:32: #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 13:29:32: 8000000 INFO @ Mon, 13 Nov 2017 13:29:32: #1 tags after filtering in treatment: 8592285 INFO @ Mon, 13 Nov 2017 13:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:32: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:32: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:33: #2 number of paired peaks: 1389 INFO @ Mon, 13 Nov 2017 13:29:33: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:34: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:34: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:34: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:34: #2 predicted fragment length is 173 bps INFO @ Mon, 13 Nov 2017 13:29:34: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 13 Nov 2017 13:29:34: #2.2 Generate R script for model : SRX2576640.05_model.r INFO @ Mon, 13 Nov 2017 13:29:34: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:43: #4 Write output xls file... SRX2576640.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:29:43: #4 Write peak in narrowPeak format file... SRX2576640.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:29:43: #4 Write summits bed file... SRX2576640.10_summits.bed INFO @ Mon, 13 Nov 2017 13:29:43: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (2637 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:29:45: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:45: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:45: #1 total tags in treatment: 8592285 INFO @ Mon, 13 Nov 2017 13:29:45: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:45: #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 13:29:46: #1 tags after filtering in treatment: 8592285 INFO @ Mon, 13 Nov 2017 13:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:46: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:46: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:47: #2 number of paired peaks: 1389 INFO @ Mon, 13 Nov 2017 13:29:47: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:47: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:47: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:47: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:47: #2 predicted fragment length is 173 bps INFO @ Mon, 13 Nov 2017 13:29:47: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 13 Nov 2017 13:29:47: #2.2 Generate R script for model : SRX2576640.20_model.r INFO @ Mon, 13 Nov 2017 13:29:47: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:30:04: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:18: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:19: #4 Write output xls file... SRX2576640.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:19: #4 Write peak in narrowPeak format file... SRX2576640.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:19: #4 Write summits bed file... SRX2576640.05_summits.bed INFO @ Mon, 13 Nov 2017 13:30:19: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3424 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:30:32: #4 Write output xls file... SRX2576640.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:32: #4 Write peak in narrowPeak format file... SRX2576640.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:32: #4 Write summits bed file... SRX2576640.20_summits.bed INFO @ Mon, 13 Nov 2017 13:30:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1816 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。