Job ID = 10202002 sra ファイルのダウンロード中... Completed: 993400K bytes transferred in 73 seconds (110291K 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 11653167 spots for /home/okishinya/chipatlas/results/dm3/SRX2965246/SRR5765704.sra Written 11653167 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: 00:46:34 11653167 reads; of these: 11653167 (100.00%) were paired; of these: 3240621 (27.81%) aligned concordantly 0 times 5858086 (50.27%) aligned concordantly exactly 1 time 2554460 (21.92%) aligned concordantly >1 times ---- 3240621 pairs aligned concordantly 0 times; of these: 1126894 (34.77%) aligned discordantly 1 time ---- 2113727 pairs aligned 0 times concordantly or discordantly; of these: 4227454 mates make up the pairs; of these: 3322984 (78.60%) aligned 0 times 180271 (4.26%) aligned exactly 1 time 724199 (17.13%) aligned >1 times 85.74% overall alignment rate Time searching: 00:46:34 Overall time: 00:46:35 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 16 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] 648776 / 9428354 = 0.0688 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 14:05:39: # Command line: callpeak -t SRX2965246.bam -f BAM -g dm -n SRX2965246.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965246.05 # format = BAM # ChIP-seq file = ['SRX2965246.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 14:05:39: # Command line: callpeak -t SRX2965246.bam -f BAM -g dm -n SRX2965246.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965246.20 # format = BAM # ChIP-seq file = ['SRX2965246.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 14:05:39: # Command line: callpeak -t SRX2965246.bam -f BAM -g dm -n SRX2965246.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965246.10 # format = BAM # ChIP-seq file = ['SRX2965246.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 14:05:39: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:05:39: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:05:39: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:05:39: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:05:39: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:05:39: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:05:50: 1000000 INFO @ Mon, 13 Nov 2017 14:05:50: 1000000 INFO @ Mon, 13 Nov 2017 14:05:50: 1000000 INFO @ Mon, 13 Nov 2017 14:06:01: 2000000 INFO @ Mon, 13 Nov 2017 14:06:01: 2000000 INFO @ Mon, 13 Nov 2017 14:06:01: 2000000 INFO @ Mon, 13 Nov 2017 14:06:11: 3000000 INFO @ Mon, 13 Nov 2017 14:06:11: 3000000 INFO @ Mon, 13 Nov 2017 14:06:11: 3000000 INFO @ Mon, 13 Nov 2017 14:06:20: 4000000 INFO @ Mon, 13 Nov 2017 14:06:21: 4000000 INFO @ Mon, 13 Nov 2017 14:06:21: 4000000 INFO @ Mon, 13 Nov 2017 14:06:29: 5000000 INFO @ Mon, 13 Nov 2017 14:06:30: 5000000 INFO @ Mon, 13 Nov 2017 14:06:30: 5000000 INFO @ Mon, 13 Nov 2017 14:06:37: 6000000 INFO @ Mon, 13 Nov 2017 14:06:39: 6000000 INFO @ Mon, 13 Nov 2017 14:06:39: 6000000 INFO @ Mon, 13 Nov 2017 14:06:46: 7000000 INFO @ Mon, 13 Nov 2017 14:06:49: 7000000 INFO @ Mon, 13 Nov 2017 14:06:49: 7000000 INFO @ Mon, 13 Nov 2017 14:06:55: 8000000 INFO @ Mon, 13 Nov 2017 14:06:58: 8000000 INFO @ Mon, 13 Nov 2017 14:06:58: 8000000 INFO @ Mon, 13 Nov 2017 14:07:04: 9000000 INFO @ Mon, 13 Nov 2017 14:07:08: 9000000 INFO @ Mon, 13 Nov 2017 14:07:08: 9000000 INFO @ Mon, 13 Nov 2017 14:07:13: 10000000 INFO @ Mon, 13 Nov 2017 14:07:17: 10000000 INFO @ Mon, 13 Nov 2017 14:07:17: 10000000 INFO @ Mon, 13 Nov 2017 14:07:22: 11000000 INFO @ Mon, 13 Nov 2017 14:07:26: 11000000 INFO @ Mon, 13 Nov 2017 14:07:26: 11000000 INFO @ Mon, 13 Nov 2017 14:07:31: 12000000 INFO @ Mon, 13 Nov 2017 14:07:35: 12000000 INFO @ Mon, 13 Nov 2017 14:07:35: 12000000 INFO @ Mon, 13 Nov 2017 14:07:40: 13000000 INFO @ Mon, 13 Nov 2017 14:07:44: 13000000 INFO @ Mon, 13 Nov 2017 14:07:44: 13000000 INFO @ Mon, 13 Nov 2017 14:07:49: 14000000 INFO @ Mon, 13 Nov 2017 14:07:53: 14000000 INFO @ Mon, 13 Nov 2017 14:07:53: 14000000 INFO @ Mon, 13 Nov 2017 14:07:58: 15000000 INFO @ Mon, 13 Nov 2017 14:08:03: 15000000 INFO @ Mon, 13 Nov 2017 14:08:03: 15000000 INFO @ Mon, 13 Nov 2017 14:08:07: 16000000 INFO @ Mon, 13 Nov 2017 14:08:12: 16000000 INFO @ Mon, 13 Nov 2017 14:08:12: 16000000 INFO @ Mon, 13 Nov 2017 14:08:16: 17000000 INFO @ Mon, 13 Nov 2017 14:08:21: 17000000 INFO @ Mon, 13 Nov 2017 14:08:21: 17000000 INFO @ Mon, 13 Nov 2017 14:08:25: 18000000 INFO @ Mon, 13 Nov 2017 14:08:30: 18000000 INFO @ Mon, 13 Nov 2017 14:08:30: 18000000 INFO @ Mon, 13 Nov 2017 14:08:31: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:08:31: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:08:31: #1 total tags in treatment: 7791782 INFO @ Mon, 13 Nov 2017 14:08:31: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:08:31: #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 14:08:31: #1 tags after filtering in treatment: 7447842 INFO @ Mon, 13 Nov 2017 14:08:31: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 13 Nov 2017 14:08:31: #1 finished! INFO @ Mon, 13 Nov 2017 14:08:31: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:08:32: #2 number of paired peaks: 1164 INFO @ Mon, 13 Nov 2017 14:08:32: start model_add_line... INFO @ Mon, 13 Nov 2017 14:08:32: start X-correlation... INFO @ Mon, 13 Nov 2017 14:08:32: end of X-cor INFO @ Mon, 13 Nov 2017 14:08:32: #2 finished! INFO @ Mon, 13 Nov 2017 14:08:32: #2 predicted fragment length is 171 bps INFO @ Mon, 13 Nov 2017 14:08:32: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 13 Nov 2017 14:08:32: #2.2 Generate R script for model : SRX2965246.20_model.r WARNING @ Mon, 13 Nov 2017 14:08:32: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:08:32: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Mon, 13 Nov 2017 14:08:32: #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 14:08:32: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:08:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:08:36: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:08:36: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:08:36: #1 total tags in treatment: 7791782 INFO @ Mon, 13 Nov 2017 14:08:36: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:08:36: #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 14:08:36: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:08:36: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:08:36: #1 total tags in treatment: 7791782 INFO @ Mon, 13 Nov 2017 14:08:36: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:08:36: #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 14:08:36: #1 tags after filtering in treatment: 7447842 INFO @ Mon, 13 Nov 2017 14:08:36: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 13 Nov 2017 14:08:36: #1 finished! INFO @ Mon, 13 Nov 2017 14:08:36: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:08:36: #1 tags after filtering in treatment: 7447842 INFO @ Mon, 13 Nov 2017 14:08:36: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 13 Nov 2017 14:08:36: #1 finished! INFO @ Mon, 13 Nov 2017 14:08:36: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:08:37: #2 number of paired peaks: 1164 INFO @ Mon, 13 Nov 2017 14:08:37: start model_add_line... INFO @ Mon, 13 Nov 2017 14:08:37: #2 number of paired peaks: 1164 INFO @ Mon, 13 Nov 2017 14:08:37: start model_add_line... INFO @ Mon, 13 Nov 2017 14:08:37: start X-correlation... INFO @ Mon, 13 Nov 2017 14:08:37: end of X-cor INFO @ Mon, 13 Nov 2017 14:08:37: #2 finished! INFO @ Mon, 13 Nov 2017 14:08:37: #2 predicted fragment length is 171 bps INFO @ Mon, 13 Nov 2017 14:08:37: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 13 Nov 2017 14:08:37: #2.2 Generate R script for model : SRX2965246.05_model.r WARNING @ Mon, 13 Nov 2017 14:08:37: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:08:37: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Mon, 13 Nov 2017 14:08:37: #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 14:08:37: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:08:37: start X-correlation... INFO @ Mon, 13 Nov 2017 14:08:37: end of X-cor INFO @ Mon, 13 Nov 2017 14:08:37: #2 finished! INFO @ Mon, 13 Nov 2017 14:08:37: #2 predicted fragment length is 171 bps INFO @ Mon, 13 Nov 2017 14:08:37: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 13 Nov 2017 14:08:37: #2.2 Generate R script for model : SRX2965246.10_model.r WARNING @ Mon, 13 Nov 2017 14:08:37: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:08:37: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Mon, 13 Nov 2017 14:08:37: #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 14:08:37: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:08:55: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:08:57: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:09:01: #4 Write output xls file... SRX2965246.20_peaks.xls INFO @ Mon, 13 Nov 2017 14:09:01: #4 Write peak in narrowPeak format file... SRX2965246.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:09:01: #4 Write summits bed file... SRX2965246.20_summits.bed INFO @ Mon, 13 Nov 2017 14:09:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 14:09:05: #4 Write output xls file... SRX2965246.05_peaks.xls INFO @ Mon, 13 Nov 2017 14:09:05: #4 Write peak in narrowPeak format file... SRX2965246.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:09:05: #4 Write summits bed file... SRX2965246.05_summits.bed INFO @ Mon, 13 Nov 2017 14:09:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2166 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 14:09:07: #4 Write output xls file... SRX2965246.10_peaks.xls INFO @ Mon, 13 Nov 2017 14:09:07: #4 Write peak in narrowPeak format file... SRX2965246.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:09:07: #4 Write summits bed file... SRX2965246.10_summits.bed INFO @ Mon, 13 Nov 2017 14:09:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1376 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。