Job ID = 10043486 sra ファイルのダウンロード中... Completed: 1258141K bytes transferred in 26 seconds (382897K bits/sec), in 2 files, 3 directories. 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 15068330 spots for /home/okishinya/chipatlas/results/dm3/SRX2165270/SRR4244769.sra Written 15068330 spots total Written 15221560 spots for /home/okishinya/chipatlas/results/dm3/SRX2165270/SRR4244770.sra Written 15221560 spots total 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: 00:13:41 30289890 reads; of these: 30289890 (100.00%) were unpaired; of these: 5756144 (19.00%) aligned 0 times 16651864 (54.97%) aligned exactly 1 time 7881882 (26.02%) aligned >1 times 81.00% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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 12 files... [bam_rmdupse_core] 17236382 / 24533746 = 0.7026 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, 02 Oct 2017 03:48:09: # Command line: callpeak -t SRX2165270.bam -f BAM -g dm -n SRX2165270.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165270.05 # format = BAM # ChIP-seq file = ['SRX2165270.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 @ Mon, 02 Oct 2017 03:48:09: # Command line: callpeak -t SRX2165270.bam -f BAM -g dm -n SRX2165270.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165270.20 # format = BAM # ChIP-seq file = ['SRX2165270.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 @ Mon, 02 Oct 2017 03:48:09: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:48:09: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:48:09: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:48:09: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:48:09: # Command line: callpeak -t SRX2165270.bam -f BAM -g dm -n SRX2165270.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165270.10 # format = BAM # ChIP-seq file = ['SRX2165270.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 @ Mon, 02 Oct 2017 03:48:09: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:48:09: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:48:16: 1000000 INFO @ Mon, 02 Oct 2017 03:48:16: 1000000 INFO @ Mon, 02 Oct 2017 03:48:16: 1000000 INFO @ Mon, 02 Oct 2017 03:48:23: 2000000 INFO @ Mon, 02 Oct 2017 03:48:24: 2000000 INFO @ Mon, 02 Oct 2017 03:48:24: 2000000 INFO @ Mon, 02 Oct 2017 03:48:30: 3000000 INFO @ Mon, 02 Oct 2017 03:48:32: 3000000 INFO @ Mon, 02 Oct 2017 03:48:32: 3000000 INFO @ Mon, 02 Oct 2017 03:48:37: 4000000 INFO @ Mon, 02 Oct 2017 03:48:39: 4000000 INFO @ Mon, 02 Oct 2017 03:48:39: 4000000 INFO @ Mon, 02 Oct 2017 03:48:44: 5000000 INFO @ Mon, 02 Oct 2017 03:48:47: 5000000 INFO @ Mon, 02 Oct 2017 03:48:47: 5000000 INFO @ Mon, 02 Oct 2017 03:48:51: 6000000 INFO @ Mon, 02 Oct 2017 03:48:55: 6000000 INFO @ Mon, 02 Oct 2017 03:48:55: 6000000 INFO @ Mon, 02 Oct 2017 03:48:58: 7000000 INFO @ Mon, 02 Oct 2017 03:49:00: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:49:00: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:49:00: #1 total tags in treatment: 7297364 INFO @ Mon, 02 Oct 2017 03:49:00: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:49:00: #1 tags after filtering in treatment: 7297364 INFO @ Mon, 02 Oct 2017 03:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:49:00: #1 finished! INFO @ Mon, 02 Oct 2017 03:49:00: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:49:01: #2 number of paired peaks: 1012 INFO @ Mon, 02 Oct 2017 03:49:01: start model_add_line... INFO @ Mon, 02 Oct 2017 03:49:01: start X-correlation... INFO @ Mon, 02 Oct 2017 03:49:01: end of X-cor INFO @ Mon, 02 Oct 2017 03:49:01: #2 finished! INFO @ Mon, 02 Oct 2017 03:49:01: #2 predicted fragment length is 65 bps INFO @ Mon, 02 Oct 2017 03:49:01: #2 alternative fragment length(s) may be 65 bps INFO @ Mon, 02 Oct 2017 03:49:01: #2.2 Generate R script for model : SRX2165270.05_model.r WARNING @ Mon, 02 Oct 2017 03:49:01: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:49:01: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Mon, 02 Oct 2017 03:49:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:49:01: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:49:02: 7000000 INFO @ Mon, 02 Oct 2017 03:49:02: 7000000 INFO @ Mon, 02 Oct 2017 03:49:05: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:49:05: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:49:05: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:49:05: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:49:05: #1 total tags in treatment: 7297364 INFO @ Mon, 02 Oct 2017 03:49:05: #1 total tags in treatment: 7297364 INFO @ Mon, 02 Oct 2017 03:49:05: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:49:05: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:49:05: #1 tags after filtering in treatment: 7297364 INFO @ Mon, 02 Oct 2017 03:49:05: #1 tags after filtering in treatment: 7297364 INFO @ Mon, 02 Oct 2017 03:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:49:05: #1 finished! INFO @ Mon, 02 Oct 2017 03:49:05: #1 finished! INFO @ Mon, 02 Oct 2017 03:49:05: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:49:05: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:49:06: #2 number of paired peaks: 1012 INFO @ Mon, 02 Oct 2017 03:49:06: start model_add_line... INFO @ Mon, 02 Oct 2017 03:49:06: #2 number of paired peaks: 1012 INFO @ Mon, 02 Oct 2017 03:49:06: start model_add_line... INFO @ Mon, 02 Oct 2017 03:49:06: start X-correlation... INFO @ Mon, 02 Oct 2017 03:49:06: start X-correlation... INFO @ Mon, 02 Oct 2017 03:49:06: end of X-cor INFO @ Mon, 02 Oct 2017 03:49:06: end of X-cor INFO @ Mon, 02 Oct 2017 03:49:06: #2 finished! INFO @ Mon, 02 Oct 2017 03:49:06: #2 finished! INFO @ Mon, 02 Oct 2017 03:49:06: #2 predicted fragment length is 65 bps INFO @ Mon, 02 Oct 2017 03:49:06: #2 predicted fragment length is 65 bps INFO @ Mon, 02 Oct 2017 03:49:06: #2 alternative fragment length(s) may be 65 bps INFO @ Mon, 02 Oct 2017 03:49:06: #2 alternative fragment length(s) may be 65 bps INFO @ Mon, 02 Oct 2017 03:49:06: #2.2 Generate R script for model : SRX2165270.20_model.r INFO @ Mon, 02 Oct 2017 03:49:06: #2.2 Generate R script for model : SRX2165270.10_model.r WARNING @ Mon, 02 Oct 2017 03:49:06: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:49:06: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Mon, 02 Oct 2017 03:49:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:49:06: #3 Call peaks... WARNING @ Mon, 02 Oct 2017 03:49:06: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Mon, 02 Oct 2017 03:49:06: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 02 Oct 2017 03:49:06: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Mon, 02 Oct 2017 03:49:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:49:06: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:49:19: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:49:23: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:49:23: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:49:29: #4 Write output xls file... SRX2165270.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:49:29: #4 Write peak in narrowPeak format file... SRX2165270.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:49:29: #4 Write summits bed file... SRX2165270.05_summits.bed INFO @ Mon, 02 Oct 2017 03:49:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3072 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:49:32: #4 Write output xls file... SRX2165270.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:49:32: #4 Write peak in narrowPeak format file... SRX2165270.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:49:32: #4 Write summits bed file... SRX2165270.10_summits.bed INFO @ Mon, 02 Oct 2017 03:49:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1674 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:49:34: #4 Write output xls file... SRX2165270.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:49:34: #4 Write peak in narrowPeak format file... SRX2165270.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:49:34: #4 Write summits bed file... SRX2165270.20_summits.bed INFO @ Mon, 02 Oct 2017 03:49:34: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (1103 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。