Job ID = 11293694 sra ファイルのダウンロード中... Completed: 560560K bytes transferred in 28 seconds (162893K 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 16958488 spots for /home/okishinya/chipatlas/results/dm3/SRX4375855/SRR7506509.sra Written 16958488 spots for /home/okishinya/chipatlas/results/dm3/SRX4375855/SRR7506509.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: 00:04:46 16958488 reads; of these: 16958488 (100.00%) were unpaired; of these: 3458571 (20.39%) aligned 0 times 10889124 (64.21%) aligned exactly 1 time 2610793 (15.40%) aligned >1 times 79.61% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 4299217 / 13499917 = 0.3185 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, 04 Nov 2018 17:57:05: # Command line: callpeak -t SRX4375855.bam -f BAM -g dm -n SRX4375855.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375855.20 # format = BAM # ChIP-seq file = ['SRX4375855.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, 04 Nov 2018 17:57:05: # Command line: callpeak -t SRX4375855.bam -f BAM -g dm -n SRX4375855.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375855.10 # format = BAM # ChIP-seq file = ['SRX4375855.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, 04 Nov 2018 17:57:05: # Command line: callpeak -t SRX4375855.bam -f BAM -g dm -n SRX4375855.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375855.05 # format = BAM # ChIP-seq file = ['SRX4375855.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, 04 Nov 2018 17:57:05: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:05: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:05: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:05: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:05: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:05: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:11: 1000000 INFO @ Sun, 04 Nov 2018 17:57:11: 1000000 INFO @ Sun, 04 Nov 2018 17:57:11: 1000000 INFO @ Sun, 04 Nov 2018 17:57:17: 2000000 INFO @ Sun, 04 Nov 2018 17:57:17: 2000000 INFO @ Sun, 04 Nov 2018 17:57:17: 2000000 INFO @ Sun, 04 Nov 2018 17:57:23: 3000000 INFO @ Sun, 04 Nov 2018 17:57:23: 3000000 INFO @ Sun, 04 Nov 2018 17:57:24: 3000000 INFO @ Sun, 04 Nov 2018 17:57:28: 4000000 INFO @ Sun, 04 Nov 2018 17:57:30: 4000000 INFO @ Sun, 04 Nov 2018 17:57:30: 4000000 INFO @ Sun, 04 Nov 2018 17:57:34: 5000000 INFO @ Sun, 04 Nov 2018 17:57:36: 5000000 INFO @ Sun, 04 Nov 2018 17:57:36: 5000000 INFO @ Sun, 04 Nov 2018 17:57:40: 6000000 INFO @ Sun, 04 Nov 2018 17:57:42: 6000000 INFO @ Sun, 04 Nov 2018 17:57:42: 6000000 INFO @ Sun, 04 Nov 2018 17:57:46: 7000000 INFO @ Sun, 04 Nov 2018 17:57:48: 7000000 INFO @ Sun, 04 Nov 2018 17:57:49: 7000000 INFO @ Sun, 04 Nov 2018 17:57:52: 8000000 INFO @ Sun, 04 Nov 2018 17:57:55: 8000000 INFO @ Sun, 04 Nov 2018 17:57:55: 8000000 INFO @ Sun, 04 Nov 2018 17:57:58: 9000000 INFO @ Sun, 04 Nov 2018 17:57:59: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:57:59: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:57:59: #1 total tags in treatment: 9200700 INFO @ Sun, 04 Nov 2018 17:57:59: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:57:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:57:59: #1 tags after filtering in treatment: 9200700 INFO @ Sun, 04 Nov 2018 17:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:57:59: #1 finished! INFO @ Sun, 04 Nov 2018 17:57:59: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:01: #2 number of paired peaks: 8640 INFO @ Sun, 04 Nov 2018 17:58:01: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:01: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:01: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:01: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:01: #2 predicted fragment length is 222 bps INFO @ Sun, 04 Nov 2018 17:58:01: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 04 Nov 2018 17:58:01: #2.2 Generate R script for model : SRX4375855.10_model.r INFO @ Sun, 04 Nov 2018 17:58:01: 9000000 INFO @ Sun, 04 Nov 2018 17:58:01: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:02: 9000000 INFO @ Sun, 04 Nov 2018 17:58:03: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:03: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:03: #1 total tags in treatment: 9200700 INFO @ Sun, 04 Nov 2018 17:58:03: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:03: #1 tags after filtering in treatment: 9200700 INFO @ Sun, 04 Nov 2018 17:58:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:03: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:03: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:03: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:03: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:03: #1 total tags in treatment: 9200700 INFO @ Sun, 04 Nov 2018 17:58:03: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:03: #1 tags after filtering in treatment: 9200700 INFO @ Sun, 04 Nov 2018 17:58:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:03: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:03: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:04: #2 number of paired peaks: 8640 INFO @ Sun, 04 Nov 2018 17:58:04: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:04: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:04: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:04: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:04: #2 predicted fragment length is 222 bps INFO @ Sun, 04 Nov 2018 17:58:04: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 04 Nov 2018 17:58:04: #2.2 Generate R script for model : SRX4375855.05_model.r INFO @ Sun, 04 Nov 2018 17:58:04: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:05: #2 number of paired peaks: 8640 INFO @ Sun, 04 Nov 2018 17:58:05: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:05: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:05: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:05: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:05: #2 predicted fragment length is 222 bps INFO @ Sun, 04 Nov 2018 17:58:05: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 04 Nov 2018 17:58:05: #2.2 Generate R script for model : SRX4375855.20_model.r INFO @ Sun, 04 Nov 2018 17:58:05: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:42: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:43: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:53: #4 Write output xls file... SRX4375855.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:58:53: #4 Write peak in narrowPeak format file... SRX4375855.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:58:53: #4 Write summits bed file... SRX4375855.10_summits.bed INFO @ Sun, 04 Nov 2018 17:58:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8062 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:58:55: #4 Write output xls file... SRX4375855.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:58:56: #4 Write peak in narrowPeak format file... SRX4375855.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:58:56: #4 Write output xls file... SRX4375855.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:58:56: #4 Write summits bed file... SRX4375855.05_summits.bed INFO @ Sun, 04 Nov 2018 17:58:56: Done! INFO @ Sun, 04 Nov 2018 17:58:56: #4 Write peak in narrowPeak format file... SRX4375855.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:58:56: #4 Write summits bed file... SRX4375855.20_summits.bed INFO @ Sun, 04 Nov 2018 17:58:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9598 records, 4 fields): 16 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6251 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。