Job ID = 9371427 sra ファイルのダウンロード中... Completed: 1037079K bytes transferred in 15 seconds (553703K 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: PAIRED fastq に変換中... Written 3404325 spots for /home/okishinya/chipatlas/results/dm3/SRX1958586/SRR4011804.sra Written 3404325 spots total Written 5310636 spots for /home/okishinya/chipatlas/results/dm3/SRX1958586/SRR3928900.sra Written 5310636 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: 01:21:41 8714961 reads; of these: 8714961 (100.00%) were paired; of these: 1572003 (18.04%) aligned concordantly 0 times 4820811 (55.32%) aligned concordantly exactly 1 time 2322147 (26.65%) aligned concordantly >1 times ---- 1572003 pairs aligned concordantly 0 times; of these: 452144 (28.76%) aligned discordantly 1 time ---- 1119859 pairs aligned 0 times concordantly or discordantly; of these: 2239718 mates make up the pairs; of these: 1716074 (76.62%) aligned 0 times 121134 (5.41%) aligned exactly 1 time 402510 (17.97%) aligned >1 times 90.15% overall alignment rate Time searching: 01:21:41 Overall time: 01:21:41 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 473133 / 7539796 = 0.0628 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 @ Fri, 04 Aug 2017 15:28:45: # Command line: callpeak -t SRX1958586.bam -f BAM -g dm -n SRX1958586.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1958586.10 # format = BAM # ChIP-seq file = ['SRX1958586.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 @ Fri, 04 Aug 2017 15:28:45: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:28:45: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:28:45: # Command line: callpeak -t SRX1958586.bam -f BAM -g dm -n SRX1958586.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1958586.05 # format = BAM # ChIP-seq file = ['SRX1958586.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 @ Fri, 04 Aug 2017 15:28:45: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:28:45: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:28:45: # Command line: callpeak -t SRX1958586.bam -f BAM -g dm -n SRX1958586.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1958586.20 # format = BAM # ChIP-seq file = ['SRX1958586.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 @ Fri, 04 Aug 2017 15:28:45: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:28:45: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:28:57: 1000000 INFO @ Fri, 04 Aug 2017 15:28:58: 1000000 INFO @ Fri, 04 Aug 2017 15:29:00: 1000000 INFO @ Fri, 04 Aug 2017 15:29:11: 2000000 INFO @ Fri, 04 Aug 2017 15:29:11: 2000000 INFO @ Fri, 04 Aug 2017 15:29:22: 2000000 INFO @ Fri, 04 Aug 2017 15:29:23: 3000000 INFO @ Fri, 04 Aug 2017 15:29:32: 3000000 INFO @ Fri, 04 Aug 2017 15:29:44: 3000000 INFO @ Fri, 04 Aug 2017 15:29:44: 4000000 INFO @ Fri, 04 Aug 2017 15:29:56: 4000000 INFO @ Fri, 04 Aug 2017 15:30:03: 5000000 INFO @ Fri, 04 Aug 2017 15:30:06: 4000000 INFO @ Fri, 04 Aug 2017 15:30:13: 5000000 INFO @ Fri, 04 Aug 2017 15:30:20: 5000000 INFO @ Fri, 04 Aug 2017 15:30:23: 6000000 INFO @ Fri, 04 Aug 2017 15:30:31: 6000000 INFO @ Fri, 04 Aug 2017 15:30:31: 6000000 INFO @ Fri, 04 Aug 2017 15:30:42: 7000000 INFO @ Fri, 04 Aug 2017 15:30:46: 7000000 INFO @ Fri, 04 Aug 2017 15:30:48: 7000000 INFO @ Fri, 04 Aug 2017 15:31:00: 8000000 INFO @ Fri, 04 Aug 2017 15:31:02: 8000000 INFO @ Fri, 04 Aug 2017 15:31:05: 8000000 INFO @ Fri, 04 Aug 2017 15:31:16: 9000000 INFO @ Fri, 04 Aug 2017 15:31:18: 9000000 INFO @ Fri, 04 Aug 2017 15:31:25: 9000000 INFO @ Fri, 04 Aug 2017 15:31:32: 10000000 INFO @ Fri, 04 Aug 2017 15:31:33: 10000000 INFO @ Fri, 04 Aug 2017 15:31:44: 11000000 INFO @ Fri, 04 Aug 2017 15:31:46: 10000000 INFO @ Fri, 04 Aug 2017 15:31:52: 11000000 INFO @ Fri, 04 Aug 2017 15:31:58: 12000000 INFO @ Fri, 04 Aug 2017 15:32:07: 11000000 INFO @ Fri, 04 Aug 2017 15:32:10: 12000000 INFO @ Fri, 04 Aug 2017 15:32:11: 13000000 INFO @ Fri, 04 Aug 2017 15:32:24: 13000000 INFO @ Fri, 04 Aug 2017 15:32:25: 14000000 INFO @ Fri, 04 Aug 2017 15:32:26: 12000000 INFO @ Fri, 04 Aug 2017 15:32:37: #1 tag size is determined as 113 bps INFO @ Fri, 04 Aug 2017 15:32:37: #1 tag size = 113 INFO @ Fri, 04 Aug 2017 15:32:37: #1 total tags in treatment: 6684079 INFO @ Fri, 04 Aug 2017 15:32:37: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:32:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:32:37: #1 tags after filtering in treatment: 6215205 INFO @ Fri, 04 Aug 2017 15:32:37: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 Aug 2017 15:32:37: #1 finished! INFO @ Fri, 04 Aug 2017 15:32:37: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:32:38: #2 number of paired peaks: 1374 INFO @ Fri, 04 Aug 2017 15:32:38: start model_add_line... INFO @ Fri, 04 Aug 2017 15:32:38: start X-correlation... INFO @ Fri, 04 Aug 2017 15:32:38: end of X-cor INFO @ Fri, 04 Aug 2017 15:32:38: #2 finished! INFO @ Fri, 04 Aug 2017 15:32:38: #2 predicted fragment length is 164 bps INFO @ Fri, 04 Aug 2017 15:32:38: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 04 Aug 2017 15:32:38: #2.2 Generate R script for model : SRX1958586.20_model.r WARNING @ Fri, 04 Aug 2017 15:32:38: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:32:38: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 04 Aug 2017 15:32:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:32:38: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:32:40: 14000000 INFO @ Fri, 04 Aug 2017 15:32:47: 13000000 INFO @ Fri, 04 Aug 2017 15:32:51: #1 tag size is determined as 113 bps INFO @ Fri, 04 Aug 2017 15:32:51: #1 tag size = 113 INFO @ Fri, 04 Aug 2017 15:32:51: #1 total tags in treatment: 6684079 INFO @ Fri, 04 Aug 2017 15:32:51: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:32:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:32:51: #1 tags after filtering in treatment: 6215205 INFO @ Fri, 04 Aug 2017 15:32:51: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 Aug 2017 15:32:51: #1 finished! INFO @ Fri, 04 Aug 2017 15:32:51: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:32:52: #2 number of paired peaks: 1374 INFO @ Fri, 04 Aug 2017 15:32:52: start model_add_line... INFO @ Fri, 04 Aug 2017 15:32:52: start X-correlation... INFO @ Fri, 04 Aug 2017 15:32:52: end of X-cor INFO @ Fri, 04 Aug 2017 15:32:52: #2 finished! INFO @ Fri, 04 Aug 2017 15:32:52: #2 predicted fragment length is 164 bps INFO @ Fri, 04 Aug 2017 15:32:52: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 04 Aug 2017 15:32:52: #2.2 Generate R script for model : SRX1958586.10_model.r WARNING @ Fri, 04 Aug 2017 15:32:52: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:32:52: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 04 Aug 2017 15:32:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:32:52: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:33:00: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:33:06: 14000000 INFO @ Fri, 04 Aug 2017 15:33:12: #4 Write output xls file... SRX1958586.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:33:12: #4 Write peak in narrowPeak format file... SRX1958586.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:33:12: #4 Write summits bed file... SRX1958586.20_summits.bed INFO @ Fri, 04 Aug 2017 15:33:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (961 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:33:13: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:33:23: #1 tag size is determined as 113 bps INFO @ Fri, 04 Aug 2017 15:33:23: #1 tag size = 113 INFO @ Fri, 04 Aug 2017 15:33:23: #1 total tags in treatment: 6684079 INFO @ Fri, 04 Aug 2017 15:33:23: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:33:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:33:23: #1 tags after filtering in treatment: 6215205 INFO @ Fri, 04 Aug 2017 15:33:23: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 Aug 2017 15:33:23: #1 finished! INFO @ Fri, 04 Aug 2017 15:33:23: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:33:24: #2 number of paired peaks: 1374 INFO @ Fri, 04 Aug 2017 15:33:24: start model_add_line... INFO @ Fri, 04 Aug 2017 15:33:24: start X-correlation... INFO @ Fri, 04 Aug 2017 15:33:24: end of X-cor INFO @ Fri, 04 Aug 2017 15:33:24: #2 finished! INFO @ Fri, 04 Aug 2017 15:33:24: #2 predicted fragment length is 164 bps INFO @ Fri, 04 Aug 2017 15:33:24: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 04 Aug 2017 15:33:24: #2.2 Generate R script for model : SRX1958586.05_model.r WARNING @ Fri, 04 Aug 2017 15:33:24: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:33:24: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 04 Aug 2017 15:33:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:33:24: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:33:24: #4 Write output xls file... SRX1958586.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:33:24: #4 Write peak in narrowPeak format file... SRX1958586.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:33:24: #4 Write summits bed file... SRX1958586.10_summits.bed INFO @ Fri, 04 Aug 2017 15:33:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1651 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:33:45: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:33:57: #4 Write output xls file... SRX1958586.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:33:57: #4 Write peak in narrowPeak format file... SRX1958586.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:33:57: #4 Write summits bed file... SRX1958586.05_summits.bed INFO @ Fri, 04 Aug 2017 15:33:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2813 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。