Job ID = 9370838 sra ファイルのダウンロード中... Completed: 1156367K bytes transferred in 16 seconds (564730K 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 6653455 spots for /home/okishinya/chipatlas/results/dm3/SRX1958588/SRR3928902.sra Written 6653455 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:44:04 6653455 reads; of these: 6653455 (100.00%) were paired; of these: 437730 (6.58%) aligned concordantly 0 times 4811208 (72.31%) aligned concordantly exactly 1 time 1404517 (21.11%) aligned concordantly >1 times ---- 437730 pairs aligned concordantly 0 times; of these: 26034 (5.95%) aligned discordantly 1 time ---- 411696 pairs aligned 0 times concordantly or discordantly; of these: 823392 mates make up the pairs; of these: 594335 (72.18%) aligned 0 times 148848 (18.08%) aligned exactly 1 time 80209 (9.74%) aligned >1 times 95.53% overall alignment rate Time searching: 00:44:05 Overall time: 00:44:05 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] 199577 / 5419426 = 0.0368 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 14:30:49: # Command line: callpeak -t SRX1958588.bam -f BAM -g dm -n SRX1958588.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1958588.10 # format = BAM # ChIP-seq file = ['SRX1958588.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 @ Fri, 04 Aug 2017 14:30:49: # Command line: callpeak -t SRX1958588.bam -f BAM -g dm -n SRX1958588.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1958588.20 # format = BAM # ChIP-seq file = ['SRX1958588.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 @ Fri, 04 Aug 2017 14:30:49: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:30:49: # Command line: callpeak -t SRX1958588.bam -f BAM -g dm -n SRX1958588.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1958588.05 # format = BAM # ChIP-seq file = ['SRX1958588.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 @ Fri, 04 Aug 2017 14:30:49: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:30:49: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:30:49: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:30:49: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:30:49: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:31:01: 1000000 INFO @ Fri, 04 Aug 2017 14:31:01: 1000000 INFO @ Fri, 04 Aug 2017 14:31:01: 1000000 INFO @ Fri, 04 Aug 2017 14:31:12: 2000000 INFO @ Fri, 04 Aug 2017 14:31:13: 2000000 INFO @ Fri, 04 Aug 2017 14:31:13: 2000000 INFO @ Fri, 04 Aug 2017 14:31:22: 3000000 INFO @ Fri, 04 Aug 2017 14:31:24: 3000000 INFO @ Fri, 04 Aug 2017 14:31:24: 3000000 INFO @ Fri, 04 Aug 2017 14:31:34: 4000000 INFO @ Fri, 04 Aug 2017 14:31:35: 4000000 INFO @ Fri, 04 Aug 2017 14:31:36: 4000000 INFO @ Fri, 04 Aug 2017 14:31:45: 5000000 INFO @ Fri, 04 Aug 2017 14:31:46: 5000000 INFO @ Fri, 04 Aug 2017 14:31:47: 5000000 INFO @ Fri, 04 Aug 2017 14:31:56: 6000000 INFO @ Fri, 04 Aug 2017 14:31:58: 6000000 INFO @ Fri, 04 Aug 2017 14:31:58: 6000000 INFO @ Fri, 04 Aug 2017 14:32:07: 7000000 INFO @ Fri, 04 Aug 2017 14:32:09: 7000000 INFO @ Fri, 04 Aug 2017 14:32:10: 7000000 INFO @ Fri, 04 Aug 2017 14:32:19: 8000000 INFO @ Fri, 04 Aug 2017 14:32:20: 8000000 INFO @ Fri, 04 Aug 2017 14:32:21: 8000000 INFO @ Fri, 04 Aug 2017 14:32:30: 9000000 INFO @ Fri, 04 Aug 2017 14:32:32: 9000000 INFO @ Fri, 04 Aug 2017 14:32:32: 9000000 INFO @ Fri, 04 Aug 2017 14:32:41: 10000000 INFO @ Fri, 04 Aug 2017 14:32:43: 10000000 INFO @ Fri, 04 Aug 2017 14:32:44: 10000000 INFO @ Fri, 04 Aug 2017 14:32:52: 11000000 INFO @ Fri, 04 Aug 2017 14:32:54: 11000000 INFO @ Fri, 04 Aug 2017 14:32:55: 11000000 INFO @ Fri, 04 Aug 2017 14:33:04: 12000000 INFO @ Fri, 04 Aug 2017 14:33:05: 12000000 INFO @ Fri, 04 Aug 2017 14:33:06: 12000000 INFO @ Fri, 04 Aug 2017 14:33:07: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:33:07: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:33:07: #1 total tags in treatment: 6016263 INFO @ Fri, 04 Aug 2017 14:33:07: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:33:07: #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 14:33:08: #1 tags after filtering in treatment: 5564131 INFO @ Fri, 04 Aug 2017 14:33:08: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 14:33:08: #1 finished! INFO @ Fri, 04 Aug 2017 14:33:08: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:33:08: #2 number of paired peaks: 919 WARNING @ Fri, 04 Aug 2017 14:33:08: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Fri, 04 Aug 2017 14:33:08: start model_add_line... INFO @ Fri, 04 Aug 2017 14:33:08: start X-correlation... INFO @ Fri, 04 Aug 2017 14:33:08: end of X-cor INFO @ Fri, 04 Aug 2017 14:33:08: #2 finished! INFO @ Fri, 04 Aug 2017 14:33:08: #2 predicted fragment length is 178 bps INFO @ Fri, 04 Aug 2017 14:33:08: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 04 Aug 2017 14:33:08: #2.2 Generate R script for model : SRX1958588.10_model.r WARNING @ Fri, 04 Aug 2017 14:33:08: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:33:08: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Fri, 04 Aug 2017 14:33:08: #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 14:33:08: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:33:09: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:33:09: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:33:09: #1 total tags in treatment: 6016263 INFO @ Fri, 04 Aug 2017 14:33:09: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:33:09: #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 14:33:09: #1 tags after filtering in treatment: 5564131 INFO @ Fri, 04 Aug 2017 14:33:09: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 14:33:09: #1 finished! INFO @ Fri, 04 Aug 2017 14:33:09: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:33:10: #2 number of paired peaks: 919 WARNING @ Fri, 04 Aug 2017 14:33:10: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Fri, 04 Aug 2017 14:33:10: start model_add_line... INFO @ Fri, 04 Aug 2017 14:33:10: start X-correlation... INFO @ Fri, 04 Aug 2017 14:33:10: end of X-cor INFO @ Fri, 04 Aug 2017 14:33:10: #2 finished! INFO @ Fri, 04 Aug 2017 14:33:10: #2 predicted fragment length is 178 bps INFO @ Fri, 04 Aug 2017 14:33:10: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 04 Aug 2017 14:33:10: #2.2 Generate R script for model : SRX1958588.20_model.r WARNING @ Fri, 04 Aug 2017 14:33:10: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:33:10: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Fri, 04 Aug 2017 14:33:10: #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 14:33:10: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:33:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:33:10: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:33:10: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:33:10: #1 total tags in treatment: 6016263 INFO @ Fri, 04 Aug 2017 14:33:10: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:33:10: #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 14:33:10: #1 tags after filtering in treatment: 5564131 INFO @ Fri, 04 Aug 2017 14:33:10: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 14:33:10: #1 finished! INFO @ Fri, 04 Aug 2017 14:33:10: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:33:11: #2 number of paired peaks: 919 WARNING @ Fri, 04 Aug 2017 14:33:11: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Fri, 04 Aug 2017 14:33:11: start model_add_line... INFO @ Fri, 04 Aug 2017 14:33:11: start X-correlation... INFO @ Fri, 04 Aug 2017 14:33:11: end of X-cor INFO @ Fri, 04 Aug 2017 14:33:11: #2 finished! INFO @ Fri, 04 Aug 2017 14:33:11: #2 predicted fragment length is 178 bps INFO @ Fri, 04 Aug 2017 14:33:11: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 04 Aug 2017 14:33:11: #2.2 Generate R script for model : SRX1958588.05_model.r WARNING @ Fri, 04 Aug 2017 14:33:11: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:33:11: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Fri, 04 Aug 2017 14:33:11: #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 14:33:11: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:33:24: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:33:26: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:33:26: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:33:33: #4 Write output xls file... SRX1958588.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:33:33: #4 Write peak in narrowPeak format file... SRX1958588.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:33:33: #4 Write summits bed file... SRX1958588.10_summits.bed INFO @ Fri, 04 Aug 2017 14:33:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1385 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:33:35: #4 Write output xls file... SRX1958588.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:33:35: #4 Write peak in narrowPeak format file... SRX1958588.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:33:35: #4 Write summits bed file... SRX1958588.20_summits.bed INFO @ Fri, 04 Aug 2017 14:33:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (770 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:33:35: #4 Write output xls file... SRX1958588.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:33:36: #4 Write peak in narrowPeak format file... SRX1958588.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:33:36: #4 Write summits bed file... SRX1958588.05_summits.bed INFO @ Fri, 04 Aug 2017 14:33:36: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (3535 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。