Job ID = 9157273 sra ファイルのダウンロード中... Completed: 621453K bytes transferred in 7 seconds (726049K 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: SINGLE fastq に変換中... Written 13747279 spots for /home/okishinya/chipatlas/results/ce10/SRX2350749/SRR5024058.sra Written 13747279 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: 00:00:00 Multiseed full-index search: 00:03:44 13747279 reads; of these: 13747279 (100.00%) were unpaired; of these: 265416 (1.93%) aligned 0 times 11833085 (86.08%) aligned exactly 1 time 1648778 (11.99%) aligned >1 times 98.07% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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_rmdupse_core] 1940897 / 13481863 = 0.1440 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 @ Tue, 27 Jun 2017 11:23:26: # Command line: callpeak -t SRX2350749.bam -f BAM -g ce -n SRX2350749.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350749.10 # format = BAM # ChIP-seq file = ['SRX2350749.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 @ Tue, 27 Jun 2017 11:23:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:26: # Command line: callpeak -t SRX2350749.bam -f BAM -g ce -n SRX2350749.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350749.05 # format = BAM # ChIP-seq file = ['SRX2350749.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 @ Tue, 27 Jun 2017 11:23:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:26: # Command line: callpeak -t SRX2350749.bam -f BAM -g ce -n SRX2350749.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350749.20 # format = BAM # ChIP-seq file = ['SRX2350749.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 @ Tue, 27 Jun 2017 11:23:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:33: 1000000 INFO @ Tue, 27 Jun 2017 11:23:33: 1000000 INFO @ Tue, 27 Jun 2017 11:23:33: 1000000 INFO @ Tue, 27 Jun 2017 11:23:41: 2000000 INFO @ Tue, 27 Jun 2017 11:23:41: 2000000 INFO @ Tue, 27 Jun 2017 11:23:41: 2000000 INFO @ Tue, 27 Jun 2017 11:23:50: 3000000 INFO @ Tue, 27 Jun 2017 11:23:50: 3000000 INFO @ Tue, 27 Jun 2017 11:23:50: 3000000 INFO @ Tue, 27 Jun 2017 11:23:58: 4000000 INFO @ Tue, 27 Jun 2017 11:23:58: 4000000 INFO @ Tue, 27 Jun 2017 11:23:58: 4000000 INFO @ Tue, 27 Jun 2017 11:24:06: 5000000 INFO @ Tue, 27 Jun 2017 11:24:06: 5000000 INFO @ Tue, 27 Jun 2017 11:24:07: 5000000 INFO @ Tue, 27 Jun 2017 11:24:14: 6000000 INFO @ Tue, 27 Jun 2017 11:24:15: 6000000 INFO @ Tue, 27 Jun 2017 11:24:15: 6000000 INFO @ Tue, 27 Jun 2017 11:24:23: 7000000 INFO @ Tue, 27 Jun 2017 11:24:23: 7000000 INFO @ Tue, 27 Jun 2017 11:24:23: 7000000 INFO @ Tue, 27 Jun 2017 11:24:31: 8000000 INFO @ Tue, 27 Jun 2017 11:24:31: 8000000 INFO @ Tue, 27 Jun 2017 11:24:31: 8000000 INFO @ Tue, 27 Jun 2017 11:24:38: 9000000 INFO @ Tue, 27 Jun 2017 11:24:39: 9000000 INFO @ Tue, 27 Jun 2017 11:24:39: 9000000 INFO @ Tue, 27 Jun 2017 11:24:46: 10000000 INFO @ Tue, 27 Jun 2017 11:24:46: 10000000 INFO @ Tue, 27 Jun 2017 11:24:46: 10000000 INFO @ Tue, 27 Jun 2017 11:24:53: 11000000 INFO @ Tue, 27 Jun 2017 11:24:53: 11000000 INFO @ Tue, 27 Jun 2017 11:24:54: 11000000 INFO @ Tue, 27 Jun 2017 11:24:57: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:57: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:57: #1 total tags in treatment: 11540966 INFO @ Tue, 27 Jun 2017 11:24:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:24:57: #1 tags after filtering in treatment: 11540966 INFO @ Tue, 27 Jun 2017 11:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:57: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:57: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:57: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:57: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:57: #1 total tags in treatment: 11540966 INFO @ Tue, 27 Jun 2017 11:24:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:24:58: #1 tags after filtering in treatment: 11540966 INFO @ Tue, 27 Jun 2017 11:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:58: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:58: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:58: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:58: #1 total tags in treatment: 11540966 INFO @ Tue, 27 Jun 2017 11:24:58: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:24:58: #2 number of paired peaks: 152 WARNING @ Tue, 27 Jun 2017 11:24:58: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:58: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:58: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:58: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:58: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:58: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:24:58: #2 alternative fragment length(s) may be 2,51,211,490,518,578 bps INFO @ Tue, 27 Jun 2017 11:24:58: #2.2 Generate R script for model : SRX2350749.10_model.r WARNING @ Tue, 27 Jun 2017 11:24:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:58: #2 You may need to consider one of the other alternative d(s): 2,51,211,490,518,578 WARNING @ Tue, 27 Jun 2017 11:24:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:24:58: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:58: #1 tags after filtering in treatment: 11540966 INFO @ Tue, 27 Jun 2017 11:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:58: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:58: #2 number of paired peaks: 152 WARNING @ Tue, 27 Jun 2017 11:24:58: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:58: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:59: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:59: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:59: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:59: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:24:59: #2 alternative fragment length(s) may be 2,51,211,490,518,578 bps INFO @ Tue, 27 Jun 2017 11:24:59: #2.2 Generate R script for model : SRX2350749.20_model.r WARNING @ Tue, 27 Jun 2017 11:24:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:59: #2 You may need to consider one of the other alternative d(s): 2,51,211,490,518,578 WARNING @ Tue, 27 Jun 2017 11:24:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:24:59: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:59: #2 number of paired peaks: 152 WARNING @ Tue, 27 Jun 2017 11:24:59: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:59: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:59: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:59: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:59: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:59: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:24:59: #2 alternative fragment length(s) may be 2,51,211,490,518,578 bps INFO @ Tue, 27 Jun 2017 11:24:59: #2.2 Generate R script for model : SRX2350749.05_model.r WARNING @ Tue, 27 Jun 2017 11:24:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:59: #2 You may need to consider one of the other alternative d(s): 2,51,211,490,518,578 WARNING @ Tue, 27 Jun 2017 11:24:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:24:59: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:37: #4 Write output xls file... SRX2350749.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:37: #4 Write peak in narrowPeak format file... SRX2350749.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:37: #4 Write summits bed file... SRX2350749.20_summits.bed INFO @ Tue, 27 Jun 2017 11:25:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (90 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:25:37: #4 Write output xls file... SRX2350749.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:37: #4 Write peak in narrowPeak format file... SRX2350749.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:37: #4 Write summits bed file... SRX2350749.05_summits.bed INFO @ Tue, 27 Jun 2017 11:25:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (746 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:25:38: #4 Write output xls file... SRX2350749.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:38: #4 Write peak in narrowPeak format file... SRX2350749.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:38: #4 Write summits bed file... SRX2350749.10_summits.bed INFO @ Tue, 27 Jun 2017 11:25:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。