Job ID = 11240735 sra ファイルのダウンロード中... Completed: 377895K bytes transferred in 13 seconds (236169K 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 23209502 spots for /home/okishinya/chipatlas/results/dm3/SRX4669019/SRR7817544.sra Written 23209502 spots for /home/okishinya/chipatlas/results/dm3/SRX4669019/SRR7817544.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:55 23209502 reads; of these: 23209502 (100.00%) were unpaired; of these: 4589041 (19.77%) aligned 0 times 15196898 (65.48%) aligned exactly 1 time 3423563 (14.75%) aligned >1 times 80.23% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 11188927 / 18620461 = 0.6009 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 20:39:20: # Command line: callpeak -t SRX4669019.bam -f BAM -g dm -n SRX4669019.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669019.10 # format = BAM # ChIP-seq file = ['SRX4669019.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 @ Sun, 07 Oct 2018 20:39:20: # Command line: callpeak -t SRX4669019.bam -f BAM -g dm -n SRX4669019.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669019.05 # format = BAM # ChIP-seq file = ['SRX4669019.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 @ Sun, 07 Oct 2018 20:39:20: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:39:20: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:39:20: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:39:20: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:39:20: # Command line: callpeak -t SRX4669019.bam -f BAM -g dm -n SRX4669019.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669019.20 # format = BAM # ChIP-seq file = ['SRX4669019.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 @ Sun, 07 Oct 2018 20:39:20: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:39:20: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:39:26: 1000000 INFO @ Sun, 07 Oct 2018 20:39:26: 1000000 INFO @ Sun, 07 Oct 2018 20:39:26: 1000000 INFO @ Sun, 07 Oct 2018 20:39:32: 2000000 INFO @ Sun, 07 Oct 2018 20:39:32: 2000000 INFO @ Sun, 07 Oct 2018 20:39:33: 2000000 INFO @ Sun, 07 Oct 2018 20:39:38: 3000000 INFO @ Sun, 07 Oct 2018 20:39:38: 3000000 INFO @ Sun, 07 Oct 2018 20:39:39: 3000000 INFO @ Sun, 07 Oct 2018 20:39:44: 4000000 INFO @ Sun, 07 Oct 2018 20:39:44: 4000000 INFO @ Sun, 07 Oct 2018 20:39:45: 4000000 INFO @ Sun, 07 Oct 2018 20:39:50: 5000000 INFO @ Sun, 07 Oct 2018 20:39:50: 5000000 INFO @ Sun, 07 Oct 2018 20:39:51: 5000000 INFO @ Sun, 07 Oct 2018 20:39:56: 6000000 INFO @ Sun, 07 Oct 2018 20:39:56: 6000000 INFO @ Sun, 07 Oct 2018 20:39:57: 6000000 INFO @ Sun, 07 Oct 2018 20:40:02: 7000000 INFO @ Sun, 07 Oct 2018 20:40:03: 7000000 INFO @ Sun, 07 Oct 2018 20:40:03: 7000000 INFO @ Sun, 07 Oct 2018 20:40:05: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:40:05: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:40:05: #1 total tags in treatment: 7431534 INFO @ Sun, 07 Oct 2018 20:40:05: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:40:05: #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 20:40:05: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:40:05: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:40:05: #1 total tags in treatment: 7431534 INFO @ Sun, 07 Oct 2018 20:40:05: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:40:05: #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 20:40:05: #1 tags after filtering in treatment: 7431534 INFO @ Sun, 07 Oct 2018 20:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:40:05: #1 finished! INFO @ Sun, 07 Oct 2018 20:40:05: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:40:05: #1 tags after filtering in treatment: 7431534 INFO @ Sun, 07 Oct 2018 20:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:40:05: #1 finished! INFO @ Sun, 07 Oct 2018 20:40:05: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:40:05: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:40:05: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:40:05: #1 total tags in treatment: 7431534 INFO @ Sun, 07 Oct 2018 20:40:05: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:40:05: #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 20:40:06: #1 tags after filtering in treatment: 7431534 INFO @ Sun, 07 Oct 2018 20:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:40:06: #1 finished! INFO @ Sun, 07 Oct 2018 20:40:06: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:40:06: #2 number of paired peaks: 1472 INFO @ Sun, 07 Oct 2018 20:40:06: start model_add_line... INFO @ Sun, 07 Oct 2018 20:40:06: #2 number of paired peaks: 1472 INFO @ Sun, 07 Oct 2018 20:40:06: start model_add_line... INFO @ Sun, 07 Oct 2018 20:40:06: start X-correlation... INFO @ Sun, 07 Oct 2018 20:40:06: start X-correlation... INFO @ Sun, 07 Oct 2018 20:40:06: end of X-cor INFO @ Sun, 07 Oct 2018 20:40:06: end of X-cor INFO @ Sun, 07 Oct 2018 20:40:06: #2 finished! INFO @ Sun, 07 Oct 2018 20:40:06: #2 finished! INFO @ Sun, 07 Oct 2018 20:40:06: #2 predicted fragment length is 109 bps INFO @ Sun, 07 Oct 2018 20:40:06: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 07 Oct 2018 20:40:06: #2.2 Generate R script for model : SRX4669019.05_model.r INFO @ Sun, 07 Oct 2018 20:40:06: #2 predicted fragment length is 109 bps INFO @ Sun, 07 Oct 2018 20:40:06: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 07 Oct 2018 20:40:06: #2.2 Generate R script for model : SRX4669019.10_model.r INFO @ Sun, 07 Oct 2018 20:40:06: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:40:06: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:40:06: #2 number of paired peaks: 1472 INFO @ Sun, 07 Oct 2018 20:40:06: start model_add_line... INFO @ Sun, 07 Oct 2018 20:40:06: start X-correlation... INFO @ Sun, 07 Oct 2018 20:40:06: end of X-cor INFO @ Sun, 07 Oct 2018 20:40:06: #2 finished! INFO @ Sun, 07 Oct 2018 20:40:06: #2 predicted fragment length is 109 bps INFO @ Sun, 07 Oct 2018 20:40:06: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 07 Oct 2018 20:40:06: #2.2 Generate R script for model : SRX4669019.20_model.r INFO @ Sun, 07 Oct 2018 20:40:06: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:40:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:40:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:40:25: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write output xls file... SRX4669019.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write peak in narrowPeak format file... SRX4669019.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write summits bed file... SRX4669019.05_summits.bed INFO @ Sun, 07 Oct 2018 20:40:34: Done! INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write output xls file... SRX4669019.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write peak in narrowPeak format file... SRX4669019.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write summits bed file... SRX4669019.10_summits.bed INFO @ Sun, 07 Oct 2018 20:40:34: Done! INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write output xls file... SRX4669019.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write peak in narrowPeak format file... SRX4669019.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:40:34: #4 Write summits bed file... SRX4669019.20_summits.bed INFO @ Sun, 07 Oct 2018 20:40:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1957 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9213 records, 4 fields): 232 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5164 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。