Job ID = 10202004 sra ファイルのダウンロード中... Completed: 886880K bytes transferred in 79 seconds (91534K 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: PAIRED fastq に変換中... Written 10247819 spots for /home/okishinya/chipatlas/results/dm3/SRX2965248/SRR5765706.sra Written 10247819 spots total 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: 00:36:31 10247819 reads; of these: 10247819 (100.00%) were paired; of these: 3063668 (29.90%) aligned concordantly 0 times 5270362 (51.43%) aligned concordantly exactly 1 time 1913789 (18.68%) aligned concordantly >1 times ---- 3063668 pairs aligned concordantly 0 times; of these: 928989 (30.32%) aligned discordantly 1 time ---- 2134679 pairs aligned 0 times concordantly or discordantly; of these: 4269358 mates make up the pairs; of these: 3504487 (82.08%) aligned 0 times 163575 (3.83%) aligned exactly 1 time 601296 (14.08%) aligned >1 times 82.90% overall alignment rate Time searching: 00:36:32 Overall time: 00:36:32 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] 566795 / 8036152 = 0.0705 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, 13 Nov 2017 13:54:52: # Command line: callpeak -t SRX2965248.bam -f BAM -g dm -n SRX2965248.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965248.05 # format = BAM # ChIP-seq file = ['SRX2965248.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, 13 Nov 2017 13:54:52: # Command line: callpeak -t SRX2965248.bam -f BAM -g dm -n SRX2965248.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965248.10 # format = BAM # ChIP-seq file = ['SRX2965248.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, 13 Nov 2017 13:54:52: # Command line: callpeak -t SRX2965248.bam -f BAM -g dm -n SRX2965248.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965248.20 # format = BAM # ChIP-seq file = ['SRX2965248.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, 13 Nov 2017 13:54:52: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:54:52: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:54:52: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:54:52: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:54:52: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:54:52: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:55:01: 1000000 INFO @ Mon, 13 Nov 2017 13:55:01: 1000000 INFO @ Mon, 13 Nov 2017 13:55:01: 1000000 INFO @ Mon, 13 Nov 2017 13:55:09: 2000000 INFO @ Mon, 13 Nov 2017 13:55:10: 2000000 INFO @ Mon, 13 Nov 2017 13:55:10: 2000000 INFO @ Mon, 13 Nov 2017 13:55:18: 3000000 INFO @ Mon, 13 Nov 2017 13:55:19: 3000000 INFO @ Mon, 13 Nov 2017 13:55:19: 3000000 INFO @ Mon, 13 Nov 2017 13:55:26: 4000000 INFO @ Mon, 13 Nov 2017 13:55:27: 4000000 INFO @ Mon, 13 Nov 2017 13:55:27: 4000000 INFO @ Mon, 13 Nov 2017 13:55:34: 5000000 INFO @ Mon, 13 Nov 2017 13:55:36: 5000000 INFO @ Mon, 13 Nov 2017 13:55:36: 5000000 INFO @ Mon, 13 Nov 2017 13:55:43: 6000000 INFO @ Mon, 13 Nov 2017 13:55:44: 6000000 INFO @ Mon, 13 Nov 2017 13:55:44: 6000000 INFO @ Mon, 13 Nov 2017 13:55:51: 7000000 INFO @ Mon, 13 Nov 2017 13:55:53: 7000000 INFO @ Mon, 13 Nov 2017 13:55:53: 7000000 INFO @ Mon, 13 Nov 2017 13:55:59: 8000000 INFO @ Mon, 13 Nov 2017 13:56:02: 8000000 INFO @ Mon, 13 Nov 2017 13:56:02: 8000000 INFO @ Mon, 13 Nov 2017 13:56:07: 9000000 INFO @ Mon, 13 Nov 2017 13:56:10: 9000000 INFO @ Mon, 13 Nov 2017 13:56:10: 9000000 INFO @ Mon, 13 Nov 2017 13:56:15: 10000000 INFO @ Mon, 13 Nov 2017 13:56:19: 10000000 INFO @ Mon, 13 Nov 2017 13:56:19: 10000000 INFO @ Mon, 13 Nov 2017 13:56:24: 11000000 INFO @ Mon, 13 Nov 2017 13:56:28: 11000000 INFO @ Mon, 13 Nov 2017 13:56:28: 11000000 INFO @ Mon, 13 Nov 2017 13:56:32: 12000000 INFO @ Mon, 13 Nov 2017 13:56:36: 12000000 INFO @ Mon, 13 Nov 2017 13:56:36: 12000000 INFO @ Mon, 13 Nov 2017 13:56:40: 13000000 INFO @ Mon, 13 Nov 2017 13:56:45: 13000000 INFO @ Mon, 13 Nov 2017 13:56:45: 13000000 INFO @ Mon, 13 Nov 2017 13:56:48: 14000000 INFO @ Mon, 13 Nov 2017 13:56:54: 14000000 INFO @ Mon, 13 Nov 2017 13:56:54: 14000000 INFO @ Mon, 13 Nov 2017 13:56:56: 15000000 INFO @ Mon, 13 Nov 2017 13:57:02: 15000000 INFO @ Mon, 13 Nov 2017 13:57:02: 15000000 INFO @ Mon, 13 Nov 2017 13:57:03: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 13:57:03: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 13:57:03: #1 total tags in treatment: 6644029 INFO @ Mon, 13 Nov 2017 13:57:03: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:57:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:57:04: #1 tags after filtering in treatment: 6406941 INFO @ Mon, 13 Nov 2017 13:57:04: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 13 Nov 2017 13:57:04: #1 finished! INFO @ Mon, 13 Nov 2017 13:57:04: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:57:04: #2 number of paired peaks: 1104 INFO @ Mon, 13 Nov 2017 13:57:04: start model_add_line... INFO @ Mon, 13 Nov 2017 13:57:04: start X-correlation... INFO @ Mon, 13 Nov 2017 13:57:05: end of X-cor INFO @ Mon, 13 Nov 2017 13:57:05: #2 finished! INFO @ Mon, 13 Nov 2017 13:57:05: #2 predicted fragment length is 181 bps INFO @ Mon, 13 Nov 2017 13:57:05: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 13 Nov 2017 13:57:05: #2.2 Generate R script for model : SRX2965248.10_model.r WARNING @ Mon, 13 Nov 2017 13:57:05: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:57:05: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Mon, 13 Nov 2017 13:57:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:57:05: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:57:10: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 13:57:10: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 13:57:10: #1 total tags in treatment: 6644029 INFO @ Mon, 13 Nov 2017 13:57:10: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:57:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:57:10: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 13:57:10: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 13:57:10: #1 total tags in treatment: 6644029 INFO @ Mon, 13 Nov 2017 13:57:10: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:57:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:57:10: #1 tags after filtering in treatment: 6406941 INFO @ Mon, 13 Nov 2017 13:57:10: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 13 Nov 2017 13:57:10: #1 finished! INFO @ Mon, 13 Nov 2017 13:57:10: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:57:10: #1 tags after filtering in treatment: 6406941 INFO @ Mon, 13 Nov 2017 13:57:10: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 13 Nov 2017 13:57:10: #1 finished! INFO @ Mon, 13 Nov 2017 13:57:10: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:57:10: #2 number of paired peaks: 1104 INFO @ Mon, 13 Nov 2017 13:57:10: start model_add_line... INFO @ Mon, 13 Nov 2017 13:57:10: #2 number of paired peaks: 1104 INFO @ Mon, 13 Nov 2017 13:57:10: start model_add_line... INFO @ Mon, 13 Nov 2017 13:57:10: start X-correlation... INFO @ Mon, 13 Nov 2017 13:57:10: end of X-cor INFO @ Mon, 13 Nov 2017 13:57:10: #2 finished! INFO @ Mon, 13 Nov 2017 13:57:10: #2 predicted fragment length is 181 bps INFO @ Mon, 13 Nov 2017 13:57:10: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 13 Nov 2017 13:57:10: #2.2 Generate R script for model : SRX2965248.05_model.r WARNING @ Mon, 13 Nov 2017 13:57:10: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:57:10: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Mon, 13 Nov 2017 13:57:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:57:10: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:57:10: start X-correlation... INFO @ Mon, 13 Nov 2017 13:57:10: end of X-cor INFO @ Mon, 13 Nov 2017 13:57:10: #2 finished! INFO @ Mon, 13 Nov 2017 13:57:10: #2 predicted fragment length is 181 bps INFO @ Mon, 13 Nov 2017 13:57:10: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 13 Nov 2017 13:57:10: #2.2 Generate R script for model : SRX2965248.20_model.r WARNING @ Mon, 13 Nov 2017 13:57:10: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:57:10: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Mon, 13 Nov 2017 13:57:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:57:10: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:57:21: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:57:26: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:57:27: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:57:30: #4 Write output xls file... SRX2965248.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:57:30: #4 Write peak in narrowPeak format file... SRX2965248.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:57:30: #4 Write summits bed file... SRX2965248.10_summits.bed INFO @ Mon, 13 Nov 2017 13:57:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1068 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:57:34: #4 Write output xls file... SRX2965248.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:57:34: #4 Write peak in narrowPeak format file... SRX2965248.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:57:34: #4 Write summits bed file... SRX2965248.05_summits.bed INFO @ Mon, 13 Nov 2017 13:57:34: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1717 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:57:34: #4 Write output xls file... SRX2965248.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:57:34: #4 Write peak in narrowPeak format file... SRX2965248.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:57:34: #4 Write summits bed file... SRX2965248.20_summits.bed INFO @ Mon, 13 Nov 2017 13:57:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (570 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。