Job ID = 9370016 sra ファイルのダウンロード中... Completed: 1024815K bytes transferred in 18 seconds (465731K 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 7936022 spots for /home/okishinya/chipatlas/results/ce10/SRX2035138/SRR4044262.sra Written 7936022 spots total rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:21:23 7936022 reads; of these: 7936022 (100.00%) were paired; of these: 655085 (8.25%) aligned concordantly 0 times 6288190 (79.24%) aligned concordantly exactly 1 time 992747 (12.51%) aligned concordantly >1 times ---- 655085 pairs aligned concordantly 0 times; of these: 409846 (62.56%) aligned discordantly 1 time ---- 245239 pairs aligned 0 times concordantly or discordantly; of these: 490478 mates make up the pairs; of these: 311816 (63.57%) aligned 0 times 78081 (15.92%) aligned exactly 1 time 100581 (20.51%) aligned >1 times 98.04% overall alignment rate Time searching: 00:21:23 Overall time: 00:21:23 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] 72137 / 7624623 = 0.0095 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 12:20:47: # Command line: callpeak -t SRX2035138.bam -f BAM -g ce -n SRX2035138.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2035138.10 # format = BAM # ChIP-seq file = ['SRX2035138.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 12:20:47: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:20:47: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:20:47: # Command line: callpeak -t SRX2035138.bam -f BAM -g ce -n SRX2035138.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2035138.20 # format = BAM # ChIP-seq file = ['SRX2035138.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 12:20:48: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:20:48: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:20:48: # Command line: callpeak -t SRX2035138.bam -f BAM -g ce -n SRX2035138.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2035138.05 # format = BAM # ChIP-seq file = ['SRX2035138.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 12:20:48: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:20:48: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:20:57: 1000000 INFO @ Fri, 04 Aug 2017 12:20:59: 1000000 INFO @ Fri, 04 Aug 2017 12:20:59: 1000000 INFO @ Fri, 04 Aug 2017 12:21:07: 2000000 INFO @ Fri, 04 Aug 2017 12:21:09: 2000000 INFO @ Fri, 04 Aug 2017 12:21:09: 2000000 INFO @ Fri, 04 Aug 2017 12:21:18: 3000000 INFO @ Fri, 04 Aug 2017 12:21:21: 3000000 INFO @ Fri, 04 Aug 2017 12:21:21: 3000000 INFO @ Fri, 04 Aug 2017 12:21:29: 4000000 INFO @ Fri, 04 Aug 2017 12:21:32: 4000000 INFO @ Fri, 04 Aug 2017 12:21:33: 4000000 INFO @ Fri, 04 Aug 2017 12:21:41: 5000000 INFO @ Fri, 04 Aug 2017 12:21:44: 5000000 INFO @ Fri, 04 Aug 2017 12:21:44: 5000000 INFO @ Fri, 04 Aug 2017 12:21:54: 6000000 INFO @ Fri, 04 Aug 2017 12:21:54: 6000000 INFO @ Fri, 04 Aug 2017 12:21:57: 6000000 INFO @ Fri, 04 Aug 2017 12:22:05: 7000000 INFO @ Fri, 04 Aug 2017 12:22:05: 7000000 INFO @ Fri, 04 Aug 2017 12:22:07: 7000000 INFO @ Fri, 04 Aug 2017 12:22:15: 8000000 INFO @ Fri, 04 Aug 2017 12:22:15: 8000000 INFO @ Fri, 04 Aug 2017 12:22:17: 8000000 INFO @ Fri, 04 Aug 2017 12:22:24: 9000000 INFO @ Fri, 04 Aug 2017 12:22:25: 9000000 INFO @ Fri, 04 Aug 2017 12:22:26: 9000000 INFO @ Fri, 04 Aug 2017 12:22:34: 10000000 INFO @ Fri, 04 Aug 2017 12:22:35: 10000000 INFO @ Fri, 04 Aug 2017 12:22:36: 10000000 INFO @ Fri, 04 Aug 2017 12:22:44: 11000000 INFO @ Fri, 04 Aug 2017 12:22:45: 11000000 INFO @ Fri, 04 Aug 2017 12:22:46: 11000000 INFO @ Fri, 04 Aug 2017 12:22:56: 12000000 INFO @ Fri, 04 Aug 2017 12:22:56: 12000000 INFO @ Fri, 04 Aug 2017 12:22:57: 12000000 INFO @ Fri, 04 Aug 2017 12:23:07: 13000000 INFO @ Fri, 04 Aug 2017 12:23:08: 13000000 INFO @ Fri, 04 Aug 2017 12:23:10: 13000000 INFO @ Fri, 04 Aug 2017 12:23:16: 14000000 INFO @ Fri, 04 Aug 2017 12:23:20: 14000000 INFO @ Fri, 04 Aug 2017 12:23:21: 14000000 INFO @ Fri, 04 Aug 2017 12:23:25: 15000000 INFO @ Fri, 04 Aug 2017 12:23:29: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:23:29: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:23:29: #1 total tags in treatment: 7212243 INFO @ Fri, 04 Aug 2017 12:23:29: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:23:29: #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 12:23:29: #1 tags after filtering in treatment: 6591333 INFO @ Fri, 04 Aug 2017 12:23:29: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 04 Aug 2017 12:23:29: #1 finished! INFO @ Fri, 04 Aug 2017 12:23:29: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:23:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:23:30: #2 number of paired peaks: 329 WARNING @ Fri, 04 Aug 2017 12:23:30: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Fri, 04 Aug 2017 12:23:30: start model_add_line... INFO @ Fri, 04 Aug 2017 12:23:30: start X-correlation... INFO @ Fri, 04 Aug 2017 12:23:30: end of X-cor INFO @ Fri, 04 Aug 2017 12:23:30: #2 finished! INFO @ Fri, 04 Aug 2017 12:23:30: #2 predicted fragment length is 172 bps INFO @ Fri, 04 Aug 2017 12:23:30: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 04 Aug 2017 12:23:30: #2.2 Generate R script for model : SRX2035138.20_model.r WARNING @ Fri, 04 Aug 2017 12:23:30: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:23:30: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 04 Aug 2017 12:23:30: #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 12:23:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:23:31: 15000000 INFO @ Fri, 04 Aug 2017 12:23:32: 15000000 INFO @ Fri, 04 Aug 2017 12:23:35: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:23:35: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:23:35: #1 total tags in treatment: 7212243 INFO @ Fri, 04 Aug 2017 12:23:35: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:23:35: #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 12:23:35: #1 tags after filtering in treatment: 6591333 INFO @ Fri, 04 Aug 2017 12:23:35: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 04 Aug 2017 12:23:35: #1 finished! INFO @ Fri, 04 Aug 2017 12:23:35: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:23:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:23:36: #2 number of paired peaks: 329 WARNING @ Fri, 04 Aug 2017 12:23:36: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Fri, 04 Aug 2017 12:23:36: start model_add_line... INFO @ Fri, 04 Aug 2017 12:23:36: start X-correlation... INFO @ Fri, 04 Aug 2017 12:23:36: end of X-cor INFO @ Fri, 04 Aug 2017 12:23:36: #2 finished! INFO @ Fri, 04 Aug 2017 12:23:36: #2 predicted fragment length is 172 bps INFO @ Fri, 04 Aug 2017 12:23:36: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 04 Aug 2017 12:23:36: #2.2 Generate R script for model : SRX2035138.05_model.r WARNING @ Fri, 04 Aug 2017 12:23:36: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:23:36: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 04 Aug 2017 12:23:36: #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 12:23:36: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:23:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:23:36: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:23:36: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:23:36: #1 total tags in treatment: 7212243 INFO @ Fri, 04 Aug 2017 12:23:36: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:23:36: #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 12:23:37: #1 tags after filtering in treatment: 6591333 INFO @ Fri, 04 Aug 2017 12:23:37: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 04 Aug 2017 12:23:37: #1 finished! INFO @ Fri, 04 Aug 2017 12:23:37: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:23:37: #2 number of paired peaks: 329 WARNING @ Fri, 04 Aug 2017 12:23:37: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Fri, 04 Aug 2017 12:23:37: start model_add_line... INFO @ Fri, 04 Aug 2017 12:23:37: start X-correlation... INFO @ Fri, 04 Aug 2017 12:23:37: end of X-cor INFO @ Fri, 04 Aug 2017 12:23:37: #2 finished! INFO @ Fri, 04 Aug 2017 12:23:37: #2 predicted fragment length is 172 bps INFO @ Fri, 04 Aug 2017 12:23:37: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 04 Aug 2017 12:23:37: #2.2 Generate R script for model : SRX2035138.10_model.r WARNING @ Fri, 04 Aug 2017 12:23:37: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:23:37: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 04 Aug 2017 12:23:37: #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 12:23:37: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:23:48: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:23:54: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:23:55: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:23:58: #4 Write output xls file... SRX2035138.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:23:58: #4 Write peak in narrowPeak format file... SRX2035138.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:23:58: #4 Write summits bed file... SRX2035138.20_summits.bed INFO @ Fri, 04 Aug 2017 12:23:58: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (143 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:24:04: #4 Write output xls file... SRX2035138.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:24:04: #4 Write peak in narrowPeak format file... SRX2035138.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:24:04: #4 Write summits bed file... SRX2035138.05_summits.bed INFO @ Fri, 04 Aug 2017 12:24:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (376 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:24:05: #4 Write output xls file... SRX2035138.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:24:05: #4 Write peak in narrowPeak format file... SRX2035138.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:24:05: #4 Write summits bed file... SRX2035138.10_summits.bed INFO @ Fri, 04 Aug 2017 12:24:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (238 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。