Job ID = 11240699 sra ファイルのダウンロード中... Completed: 85637K bytes transferred in 4 seconds (157025K 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... Read 4120114 spots for /home/okishinya/chipatlas/results/ce10/SRX4456922/SRR7591863.sra Written 4120114 spots for /home/okishinya/chipatlas/results/ce10/SRX4456922/SRR7591863.sra 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: 00:01:01 4120114 reads; of these: 4120114 (100.00%) were unpaired; of these: 295776 (7.18%) aligned 0 times 3335714 (80.96%) aligned exactly 1 time 488624 (11.86%) aligned >1 times 92.82% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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_rmdupse_core] 383994 / 3824338 = 0.1004 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 @ Sun, 07 Oct 2018 20:29:34: # Command line: callpeak -t SRX4456922.bam -f BAM -g ce -n SRX4456922.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4456922.05 # format = BAM # ChIP-seq file = ['SRX4456922.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 @ Sun, 07 Oct 2018 20:29:34: # Command line: callpeak -t SRX4456922.bam -f BAM -g ce -n SRX4456922.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4456922.20 # format = BAM # ChIP-seq file = ['SRX4456922.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 @ Sun, 07 Oct 2018 20:29:34: # Command line: callpeak -t SRX4456922.bam -f BAM -g ce -n SRX4456922.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4456922.10 # format = BAM # ChIP-seq file = ['SRX4456922.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 @ Sun, 07 Oct 2018 20:29:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:29:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:29:34: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:29:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:29:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:29:34: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:29:41: 1000000 INFO @ Sun, 07 Oct 2018 20:29:41: 1000000 INFO @ Sun, 07 Oct 2018 20:29:41: 1000000 INFO @ Sun, 07 Oct 2018 20:29:47: 2000000 INFO @ Sun, 07 Oct 2018 20:29:48: 2000000 INFO @ Sun, 07 Oct 2018 20:29:48: 2000000 INFO @ Sun, 07 Oct 2018 20:29:54: 3000000 INFO @ Sun, 07 Oct 2018 20:29:54: 3000000 INFO @ Sun, 07 Oct 2018 20:29:54: 3000000 INFO @ Sun, 07 Oct 2018 20:29:57: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:29:57: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:29:57: #1 total tags in treatment: 3440344 INFO @ Sun, 07 Oct 2018 20:29:57: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:29:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:29:57: #1 tags after filtering in treatment: 3440344 INFO @ Sun, 07 Oct 2018 20:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:29:57: #1 finished! INFO @ Sun, 07 Oct 2018 20:29:57: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:29:57: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:29:57: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:29:57: #1 total tags in treatment: 3440344 INFO @ Sun, 07 Oct 2018 20:29:57: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:29:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:29:57: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:29:57: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:29:57: #1 total tags in treatment: 3440344 INFO @ Sun, 07 Oct 2018 20:29:57: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:29:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:29:57: #1 tags after filtering in treatment: 3440344 INFO @ Sun, 07 Oct 2018 20:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:29:57: #1 finished! INFO @ Sun, 07 Oct 2018 20:29:57: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:29:57: #1 tags after filtering in treatment: 3440344 INFO @ Sun, 07 Oct 2018 20:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:29:57: #1 finished! INFO @ Sun, 07 Oct 2018 20:29:57: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:29:57: #2 number of paired peaks: 2610 INFO @ Sun, 07 Oct 2018 20:29:57: start model_add_line... INFO @ Sun, 07 Oct 2018 20:29:57: start X-correlation... INFO @ Sun, 07 Oct 2018 20:29:57: end of X-cor INFO @ Sun, 07 Oct 2018 20:29:57: #2 finished! INFO @ Sun, 07 Oct 2018 20:29:57: #2 predicted fragment length is 163 bps INFO @ Sun, 07 Oct 2018 20:29:57: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 07 Oct 2018 20:29:57: #2.2 Generate R script for model : SRX4456922.20_model.r INFO @ Sun, 07 Oct 2018 20:29:57: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:29:58: #2 number of paired peaks: 2610 INFO @ Sun, 07 Oct 2018 20:29:58: start model_add_line... INFO @ Sun, 07 Oct 2018 20:29:58: #2 number of paired peaks: 2610 INFO @ Sun, 07 Oct 2018 20:29:58: start model_add_line... INFO @ Sun, 07 Oct 2018 20:29:58: start X-correlation... INFO @ Sun, 07 Oct 2018 20:29:58: end of X-cor INFO @ Sun, 07 Oct 2018 20:29:58: #2 finished! INFO @ Sun, 07 Oct 2018 20:29:58: #2 predicted fragment length is 163 bps INFO @ Sun, 07 Oct 2018 20:29:58: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 07 Oct 2018 20:29:58: #2.2 Generate R script for model : SRX4456922.05_model.r INFO @ Sun, 07 Oct 2018 20:29:58: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:29:58: start X-correlation... INFO @ Sun, 07 Oct 2018 20:29:58: end of X-cor INFO @ Sun, 07 Oct 2018 20:29:58: #2 finished! INFO @ Sun, 07 Oct 2018 20:29:58: #2 predicted fragment length is 163 bps INFO @ Sun, 07 Oct 2018 20:29:58: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 07 Oct 2018 20:29:58: #2.2 Generate R script for model : SRX4456922.10_model.r INFO @ Sun, 07 Oct 2018 20:29:58: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:30:06: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:30:07: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:30:07: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:30:11: #4 Write output xls file... SRX4456922.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write peak in narrowPeak format file... SRX4456922.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write summits bed file... SRX4456922.05_summits.bed INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write output xls file... SRX4456922.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:30:12: Done! INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write peak in narrowPeak format file... SRX4456922.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write summits bed file... SRX4456922.20_summits.bed INFO @ Sun, 07 Oct 2018 20:30:12: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 3 millis pass2 - checking and writing primary data (2511 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write output xls file... SRX4456922.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write peak in narrowPeak format file... SRX4456922.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:30:12: #4 Write summits bed file... SRX4456922.10_summits.bed INFO @ Sun, 07 Oct 2018 20:30:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1124 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。