Job ID = 9370043 sra ファイルのダウンロード中... Completed: 977240K bytes transferred in 18 seconds (436717K bits/sec), in 1 file, 2 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 7568721 spots for /home/okishinya/chipatlas/results/ce10/SRX2035135/SRR4044259.sra Written 7568721 spots total 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: 00:00:01 Multiseed full-index search: 00:22:34 7568721 reads; of these: 7568721 (100.00%) were paired; of these: 674814 (8.92%) aligned concordantly 0 times 5877865 (77.66%) aligned concordantly exactly 1 time 1016042 (13.42%) aligned concordantly >1 times ---- 674814 pairs aligned concordantly 0 times; of these: 422415 (62.60%) aligned discordantly 1 time ---- 252399 pairs aligned 0 times concordantly or discordantly; of these: 504798 mates make up the pairs; of these: 332263 (65.82%) aligned 0 times 70984 (14.06%) aligned exactly 1 time 101551 (20.12%) aligned >1 times 97.81% overall alignment rate Time searching: 00:22:35 Overall time: 00:22:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 35225 / 7263929 = 0.0048 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 12:25:45: # Command line: callpeak -t SRX2035135.bam -f BAM -g ce -n SRX2035135.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2035135.10 # format = BAM # ChIP-seq file = ['SRX2035135.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:25:45: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:25:45: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:25:45: # Command line: callpeak -t SRX2035135.bam -f BAM -g ce -n SRX2035135.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2035135.20 # format = BAM # ChIP-seq file = ['SRX2035135.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:25:45: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:25:45: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:25:45: # Command line: callpeak -t SRX2035135.bam -f BAM -g ce -n SRX2035135.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2035135.05 # format = BAM # ChIP-seq file = ['SRX2035135.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:25:45: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:25:45: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:26:02: 1000000 INFO @ Fri, 04 Aug 2017 12:26:03: 1000000 INFO @ Fri, 04 Aug 2017 12:26:04: 1000000 INFO @ Fri, 04 Aug 2017 12:26:20: 2000000 INFO @ Fri, 04 Aug 2017 12:26:24: 2000000 INFO @ Fri, 04 Aug 2017 12:26:25: 2000000 INFO @ Fri, 04 Aug 2017 12:26:38: 3000000 INFO @ Fri, 04 Aug 2017 12:26:46: 3000000 INFO @ Fri, 04 Aug 2017 12:26:46: 3000000 INFO @ Fri, 04 Aug 2017 12:26:56: 4000000 INFO @ Fri, 04 Aug 2017 12:27:07: 4000000 INFO @ Fri, 04 Aug 2017 12:27:08: 4000000 INFO @ Fri, 04 Aug 2017 12:27:14: 5000000 INFO @ Fri, 04 Aug 2017 12:27:29: 5000000 INFO @ Fri, 04 Aug 2017 12:27:30: 5000000 INFO @ Fri, 04 Aug 2017 12:27:32: 6000000 INFO @ Fri, 04 Aug 2017 12:27:50: 7000000 INFO @ Fri, 04 Aug 2017 12:27:51: 6000000 INFO @ Fri, 04 Aug 2017 12:27:51: 6000000 INFO @ Fri, 04 Aug 2017 12:28:08: 8000000 INFO @ Fri, 04 Aug 2017 12:28:12: 7000000 INFO @ Fri, 04 Aug 2017 12:28:13: 7000000 INFO @ Fri, 04 Aug 2017 12:28:25: 9000000 INFO @ Fri, 04 Aug 2017 12:28:33: 8000000 INFO @ Fri, 04 Aug 2017 12:28:33: 8000000 INFO @ Fri, 04 Aug 2017 12:28:43: 10000000 INFO @ Fri, 04 Aug 2017 12:28:54: 9000000 INFO @ Fri, 04 Aug 2017 12:28:55: 9000000 INFO @ Fri, 04 Aug 2017 12:29:01: 11000000 INFO @ Fri, 04 Aug 2017 12:29:16: 10000000 INFO @ Fri, 04 Aug 2017 12:29:17: 10000000 INFO @ Fri, 04 Aug 2017 12:29:18: 12000000 INFO @ Fri, 04 Aug 2017 12:29:35: 13000000 INFO @ Fri, 04 Aug 2017 12:29:37: 11000000 INFO @ Fri, 04 Aug 2017 12:29:38: 11000000 INFO @ Fri, 04 Aug 2017 12:29:53: 14000000 INFO @ Fri, 04 Aug 2017 12:29:58: 12000000 INFO @ Fri, 04 Aug 2017 12:29:59: 12000000 INFO @ Fri, 04 Aug 2017 12:30:05: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:30:05: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:30:05: #1 total tags in treatment: 6859438 INFO @ Fri, 04 Aug 2017 12:30:05: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:30:05: #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 12:30:05: #1 tags after filtering in treatment: 6342552 INFO @ Fri, 04 Aug 2017 12:30:05: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 12:30:05: #1 finished! INFO @ Fri, 04 Aug 2017 12:30:05: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:30:06: #2 number of paired peaks: 394 WARNING @ Fri, 04 Aug 2017 12:30:06: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 04 Aug 2017 12:30:06: start model_add_line... INFO @ Fri, 04 Aug 2017 12:30:06: start X-correlation... INFO @ Fri, 04 Aug 2017 12:30:06: end of X-cor INFO @ Fri, 04 Aug 2017 12:30:06: #2 finished! INFO @ Fri, 04 Aug 2017 12:30:06: #2 predicted fragment length is 179 bps INFO @ Fri, 04 Aug 2017 12:30:06: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 04 Aug 2017 12:30:06: #2.2 Generate R script for model : SRX2035135.05_model.r WARNING @ Fri, 04 Aug 2017 12:30:06: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:30:06: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 04 Aug 2017 12:30:06: #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 12:30:06: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:30:19: 13000000 INFO @ Fri, 04 Aug 2017 12:30:20: 13000000 INFO @ Fri, 04 Aug 2017 12:30:30: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:30:41: 14000000 INFO @ Fri, 04 Aug 2017 12:30:42: 14000000 INFO @ Fri, 04 Aug 2017 12:30:44: #4 Write output xls file... SRX2035135.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:30:44: #4 Write peak in narrowPeak format file... SRX2035135.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:30:44: #4 Write summits bed file... SRX2035135.05_summits.bed INFO @ Fri, 04 Aug 2017 12:30:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (665 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:30:57: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:30:57: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:30:57: #1 total tags in treatment: 6859438 INFO @ Fri, 04 Aug 2017 12:30:57: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:30:57: #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 12:30:57: #1 tags after filtering in treatment: 6342552 INFO @ Fri, 04 Aug 2017 12:30:57: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 12:30:57: #1 finished! INFO @ Fri, 04 Aug 2017 12:30:57: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:30:58: #2 number of paired peaks: 394 WARNING @ Fri, 04 Aug 2017 12:30:58: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 04 Aug 2017 12:30:58: start model_add_line... INFO @ Fri, 04 Aug 2017 12:30:58: start X-correlation... INFO @ Fri, 04 Aug 2017 12:30:58: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:30:58: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:30:58: #1 total tags in treatment: 6859438 INFO @ Fri, 04 Aug 2017 12:30:58: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:30:58: #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 12:30:58: end of X-cor INFO @ Fri, 04 Aug 2017 12:30:58: #2 finished! INFO @ Fri, 04 Aug 2017 12:30:58: #2 predicted fragment length is 179 bps INFO @ Fri, 04 Aug 2017 12:30:58: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 04 Aug 2017 12:30:58: #2.2 Generate R script for model : SRX2035135.10_model.r WARNING @ Fri, 04 Aug 2017 12:30:58: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:30:58: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 04 Aug 2017 12:30:58: #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 12:30:58: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:30:58: #1 tags after filtering in treatment: 6342552 INFO @ Fri, 04 Aug 2017 12:30:58: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 12:30:58: #1 finished! INFO @ Fri, 04 Aug 2017 12:30:58: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:30:59: #2 number of paired peaks: 394 WARNING @ Fri, 04 Aug 2017 12:30:59: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 04 Aug 2017 12:30:59: start model_add_line... INFO @ Fri, 04 Aug 2017 12:30:59: start X-correlation... INFO @ Fri, 04 Aug 2017 12:30:59: end of X-cor INFO @ Fri, 04 Aug 2017 12:30:59: #2 finished! INFO @ Fri, 04 Aug 2017 12:30:59: #2 predicted fragment length is 179 bps INFO @ Fri, 04 Aug 2017 12:30:59: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 04 Aug 2017 12:30:59: #2.2 Generate R script for model : SRX2035135.20_model.r WARNING @ Fri, 04 Aug 2017 12:30:59: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:30:59: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 04 Aug 2017 12:30:59: #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 12:30:59: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:31:19: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:31:20: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:31:30: #4 Write output xls file... SRX2035135.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:31:30: #4 Write peak in narrowPeak format file... SRX2035135.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:31:30: #4 Write summits bed file... SRX2035135.20_summits.bed INFO @ Fri, 04 Aug 2017 12:31:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:31:31: #4 Write output xls file... SRX2035135.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:31:31: #4 Write peak in narrowPeak format file... SRX2035135.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:31:31: #4 Write summits bed file... SRX2035135.10_summits.bed INFO @ Fri, 04 Aug 2017 12:31:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (281 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。