Job ID = 10043505 sra ファイルのダウンロード中... Completed: 1938249K bytes transferred in 40 seconds (391908K 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 26248602 spots for /home/okishinya/chipatlas/results/dm3/SRX2165287/SRR4244803.sra Written 26248602 spots total Written 25235086 spots for /home/okishinya/chipatlas/results/dm3/SRX2165287/SRR4244804.sra Written 25235086 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: 00:23:29 51483688 reads; of these: 51483688 (100.00%) were unpaired; of these: 5778217 (11.22%) aligned 0 times 31439231 (61.07%) aligned exactly 1 time 14266240 (27.71%) aligned >1 times 88.78% overall alignment rate Time searching: 00:23:29 Overall time: 00:23:29 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 20 files... [bam_rmdupse_core] 37535236 / 45705471 = 0.8212 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 04:03:40: # Command line: callpeak -t SRX2165287.bam -f BAM -g dm -n SRX2165287.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165287.10 # format = BAM # ChIP-seq file = ['SRX2165287.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 04:03:40: # Command line: callpeak -t SRX2165287.bam -f BAM -g dm -n SRX2165287.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165287.20 # format = BAM # ChIP-seq file = ['SRX2165287.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 04:03:40: # Command line: callpeak -t SRX2165287.bam -f BAM -g dm -n SRX2165287.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165287.05 # format = BAM # ChIP-seq file = ['SRX2165287.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 04:03:40: #1 read tag files... INFO @ Mon, 02 Oct 2017 04:03:40: #1 read tag files... INFO @ Mon, 02 Oct 2017 04:03:40: #1 read tag files... INFO @ Mon, 02 Oct 2017 04:03:40: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 04:03:40: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 04:03:40: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 04:03:46: 1000000 INFO @ Mon, 02 Oct 2017 04:03:47: 1000000 INFO @ Mon, 02 Oct 2017 04:03:47: 1000000 INFO @ Mon, 02 Oct 2017 04:03:53: 2000000 INFO @ Mon, 02 Oct 2017 04:03:53: 2000000 INFO @ Mon, 02 Oct 2017 04:03:53: 2000000 INFO @ Mon, 02 Oct 2017 04:04:00: 3000000 INFO @ Mon, 02 Oct 2017 04:04:00: 3000000 INFO @ Mon, 02 Oct 2017 04:04:00: 3000000 INFO @ Mon, 02 Oct 2017 04:04:07: 4000000 INFO @ Mon, 02 Oct 2017 04:04:07: 4000000 INFO @ Mon, 02 Oct 2017 04:04:07: 4000000 INFO @ Mon, 02 Oct 2017 04:04:14: 5000000 INFO @ Mon, 02 Oct 2017 04:04:14: 5000000 INFO @ Mon, 02 Oct 2017 04:04:14: 5000000 INFO @ Mon, 02 Oct 2017 04:04:21: 6000000 INFO @ Mon, 02 Oct 2017 04:04:21: 6000000 INFO @ Mon, 02 Oct 2017 04:04:21: 6000000 INFO @ Mon, 02 Oct 2017 04:04:28: 7000000 INFO @ Mon, 02 Oct 2017 04:04:28: 7000000 INFO @ Mon, 02 Oct 2017 04:04:28: 7000000 INFO @ Mon, 02 Oct 2017 04:04:35: 8000000 INFO @ Mon, 02 Oct 2017 04:04:35: 8000000 INFO @ Mon, 02 Oct 2017 04:04:35: 8000000 INFO @ Mon, 02 Oct 2017 04:04:36: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 04:04:36: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 04:04:36: #1 total tags in treatment: 8170235 INFO @ Mon, 02 Oct 2017 04:04:36: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 04:04:36: #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 04:04:36: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 04:04:36: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 04:04:36: #1 total tags in treatment: 8170235 INFO @ Mon, 02 Oct 2017 04:04:36: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 04:04:36: #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 04:04:36: #1 tags after filtering in treatment: 8170235 INFO @ Mon, 02 Oct 2017 04:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 04:04:36: #1 finished! INFO @ Mon, 02 Oct 2017 04:04:36: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 04:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 04:04:36: #1 tags after filtering in treatment: 8170235 INFO @ Mon, 02 Oct 2017 04:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 04:04:36: #1 finished! INFO @ Mon, 02 Oct 2017 04:04:36: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 04:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 04:04:36: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 04:04:36: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 04:04:36: #1 total tags in treatment: 8170235 INFO @ Mon, 02 Oct 2017 04:04:36: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 04:04:36: #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 04:04:37: #1 tags after filtering in treatment: 8170235 INFO @ Mon, 02 Oct 2017 04:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 04:04:37: #1 finished! INFO @ Mon, 02 Oct 2017 04:04:37: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 04:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 04:04:37: #2 number of paired peaks: 1951 INFO @ Mon, 02 Oct 2017 04:04:37: start model_add_line... INFO @ Mon, 02 Oct 2017 04:04:37: #2 number of paired peaks: 1951 INFO @ Mon, 02 Oct 2017 04:04:37: start model_add_line... INFO @ Mon, 02 Oct 2017 04:04:37: start X-correlation... INFO @ Mon, 02 Oct 2017 04:04:37: start X-correlation... INFO @ Mon, 02 Oct 2017 04:04:38: #2 number of paired peaks: 1951 INFO @ Mon, 02 Oct 2017 04:04:38: start model_add_line... INFO @ Mon, 02 Oct 2017 04:04:38: end of X-cor INFO @ Mon, 02 Oct 2017 04:04:38: end of X-cor INFO @ Mon, 02 Oct 2017 04:04:38: #2 finished! INFO @ Mon, 02 Oct 2017 04:04:38: #2 finished! INFO @ Mon, 02 Oct 2017 04:04:38: #2 predicted fragment length is 87 bps INFO @ Mon, 02 Oct 2017 04:04:38: #2 predicted fragment length is 87 bps INFO @ Mon, 02 Oct 2017 04:04:38: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 02 Oct 2017 04:04:38: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 02 Oct 2017 04:04:38: #2.2 Generate R script for model : SRX2165287.20_model.r INFO @ Mon, 02 Oct 2017 04:04:38: #2.2 Generate R script for model : SRX2165287.10_model.r WARNING @ Mon, 02 Oct 2017 04:04:38: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 04:04:38: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Mon, 02 Oct 2017 04:04:38: #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 04:04:38: #3 Call peaks... WARNING @ Mon, 02 Oct 2017 04:04:38: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 04:04:38: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Mon, 02 Oct 2017 04:04:38: #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 04:04:38: #3 Call peaks... INFO @ Mon, 02 Oct 2017 04:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:04:38: start X-correlation... INFO @ Mon, 02 Oct 2017 04:04:38: end of X-cor INFO @ Mon, 02 Oct 2017 04:04:38: #2 finished! INFO @ Mon, 02 Oct 2017 04:04:38: #2 predicted fragment length is 87 bps INFO @ Mon, 02 Oct 2017 04:04:38: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 02 Oct 2017 04:04:38: #2.2 Generate R script for model : SRX2165287.05_model.r WARNING @ Mon, 02 Oct 2017 04:04:38: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 04:04:38: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Mon, 02 Oct 2017 04:04:38: #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 04:04:38: #3 Call peaks... INFO @ Mon, 02 Oct 2017 04:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:04:58: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:04:59: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:05:00: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:05:09: #4 Write output xls file... SRX2165287.20_peaks.xls INFO @ Mon, 02 Oct 2017 04:05:10: #4 Write peak in narrowPeak format file... SRX2165287.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:05:10: #4 Write summits bed file... SRX2165287.20_summits.bed INFO @ Mon, 02 Oct 2017 04:05:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1922 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 04:05:12: #4 Write output xls file... SRX2165287.10_peaks.xls INFO @ Mon, 02 Oct 2017 04:05:12: #4 Write output xls file... SRX2165287.05_peaks.xls INFO @ Mon, 02 Oct 2017 04:05:12: #4 Write peak in narrowPeak format file... SRX2165287.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:05:12: #4 Write summits bed file... SRX2165287.10_summits.bed INFO @ Mon, 02 Oct 2017 04:05:12: Done! INFO @ Mon, 02 Oct 2017 04:05:12: #4 Write peak in narrowPeak format file... SRX2165287.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:05:12: #4 Write summits bed file... SRX2165287.05_summits.bed pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3966 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 04:05:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9468 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。