Job ID = 9371925 sra ファイルのダウンロード中... Completed: 1287212K bytes transferred in 38 seconds (271540K 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 14900035 spots for /home/okishinya/chipatlas/results/dm3/SRX2548346/SRR5241490.sra Written 14900035 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:46:42 14900035 reads; of these: 14900035 (100.00%) were paired; of these: 5017567 (33.67%) aligned concordantly 0 times 7355400 (49.36%) aligned concordantly exactly 1 time 2527068 (16.96%) aligned concordantly >1 times ---- 5017567 pairs aligned concordantly 0 times; of these: 1449939 (28.90%) aligned discordantly 1 time ---- 3567628 pairs aligned 0 times concordantly or discordantly; of these: 7135256 mates make up the pairs; of these: 5871697 (82.29%) aligned 0 times 498688 (6.99%) aligned exactly 1 time 764871 (10.72%) aligned >1 times 80.30% overall alignment rate Time searching: 01:46:43 Overall time: 01:46:43 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] 258010 / 11184173 = 0.0231 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 17:00:11: # Command line: callpeak -t SRX2548346.bam -f BAM -g dm -n SRX2548346.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548346.05 # format = BAM # ChIP-seq file = ['SRX2548346.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 17:00:11: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:00:11: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:00:11: # Command line: callpeak -t SRX2548346.bam -f BAM -g dm -n SRX2548346.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548346.10 # format = BAM # ChIP-seq file = ['SRX2548346.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 17:00:11: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:00:11: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:00:11: # Command line: callpeak -t SRX2548346.bam -f BAM -g dm -n SRX2548346.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548346.20 # format = BAM # ChIP-seq file = ['SRX2548346.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 17:00:11: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:00:11: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:00:43: 1000000 INFO @ Fri, 04 Aug 2017 17:00:43: 1000000 INFO @ Fri, 04 Aug 2017 17:00:45: 1000000 INFO @ Fri, 04 Aug 2017 17:01:10: 2000000 INFO @ Fri, 04 Aug 2017 17:01:12: 2000000 INFO @ Fri, 04 Aug 2017 17:01:18: 2000000 INFO @ Fri, 04 Aug 2017 17:01:39: 3000000 INFO @ Fri, 04 Aug 2017 17:01:44: 3000000 INFO @ Fri, 04 Aug 2017 17:01:51: 3000000 INFO @ Fri, 04 Aug 2017 17:02:14: 4000000 INFO @ Fri, 04 Aug 2017 17:02:16: 4000000 INFO @ Fri, 04 Aug 2017 17:02:22: 4000000 INFO @ Fri, 04 Aug 2017 17:02:43: 5000000 INFO @ Fri, 04 Aug 2017 17:02:50: 5000000 INFO @ Fri, 04 Aug 2017 17:02:55: 5000000 INFO @ Fri, 04 Aug 2017 17:03:16: 6000000 INFO @ Fri, 04 Aug 2017 17:03:25: 6000000 INFO @ Fri, 04 Aug 2017 17:03:26: 6000000 INFO @ Fri, 04 Aug 2017 17:03:52: 7000000 INFO @ Fri, 04 Aug 2017 17:03:56: 7000000 INFO @ Fri, 04 Aug 2017 17:03:57: 7000000 INFO @ Fri, 04 Aug 2017 17:04:22: 8000000 INFO @ Fri, 04 Aug 2017 17:04:26: 8000000 INFO @ Fri, 04 Aug 2017 17:04:27: 8000000 INFO @ Fri, 04 Aug 2017 17:04:53: 9000000 INFO @ Fri, 04 Aug 2017 17:04:58: 9000000 INFO @ Fri, 04 Aug 2017 17:05:00: 9000000 INFO @ Fri, 04 Aug 2017 17:05:15: 10000000 INFO @ Fri, 04 Aug 2017 17:05:28: 10000000 INFO @ Fri, 04 Aug 2017 17:05:32: 10000000 INFO @ Fri, 04 Aug 2017 17:05:44: 11000000 INFO @ Fri, 04 Aug 2017 17:05:49: 11000000 INFO @ Fri, 04 Aug 2017 17:06:06: 11000000 INFO @ Fri, 04 Aug 2017 17:06:15: 12000000 INFO @ Fri, 04 Aug 2017 17:06:16: 12000000 INFO @ Fri, 04 Aug 2017 17:06:37: 12000000 INFO @ Fri, 04 Aug 2017 17:06:44: 13000000 INFO @ Fri, 04 Aug 2017 17:06:48: 13000000 INFO @ Fri, 04 Aug 2017 17:07:07: 13000000 INFO @ Fri, 04 Aug 2017 17:07:11: 14000000 INFO @ Fri, 04 Aug 2017 17:07:20: 14000000 INFO @ Fri, 04 Aug 2017 17:07:41: 14000000 INFO @ Fri, 04 Aug 2017 17:07:41: 15000000 INFO @ Fri, 04 Aug 2017 17:07:51: 15000000 INFO @ Fri, 04 Aug 2017 17:07:59: 16000000 INFO @ Fri, 04 Aug 2017 17:08:15: 16000000 INFO @ Fri, 04 Aug 2017 17:08:16: 15000000 INFO @ Fri, 04 Aug 2017 17:08:17: 17000000 INFO @ Fri, 04 Aug 2017 17:08:37: 18000000 INFO @ Fri, 04 Aug 2017 17:08:44: 17000000 INFO @ Fri, 04 Aug 2017 17:08:45: 16000000 INFO @ Fri, 04 Aug 2017 17:09:05: 19000000 INFO @ Fri, 04 Aug 2017 17:09:17: 17000000 INFO @ Fri, 04 Aug 2017 17:09:21: 18000000 INFO @ Fri, 04 Aug 2017 17:09:31: 20000000 INFO @ Fri, 04 Aug 2017 17:09:50: 18000000 INFO @ Fri, 04 Aug 2017 17:09:51: 19000000 INFO @ Fri, 04 Aug 2017 17:10:01: 21000000 INFO @ Fri, 04 Aug 2017 17:10:20: 20000000 INFO @ Fri, 04 Aug 2017 17:10:22: 19000000 INFO @ Fri, 04 Aug 2017 17:10:38: 22000000 INFO @ Fri, 04 Aug 2017 17:10:53: 20000000 INFO @ Fri, 04 Aug 2017 17:10:53: 21000000 INFO @ Fri, 04 Aug 2017 17:11:15: 23000000 INFO @ Fri, 04 Aug 2017 17:11:26: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:11:26: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:11:26: #1 total tags in treatment: 9630366 INFO @ Fri, 04 Aug 2017 17:11:26: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:11:26: #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 17:11:26: #1 tags after filtering in treatment: 9194974 INFO @ Fri, 04 Aug 2017 17:11:26: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 04 Aug 2017 17:11:26: #1 finished! INFO @ Fri, 04 Aug 2017 17:11:26: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:11:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:11:27: #2 number of paired peaks: 314 WARNING @ Fri, 04 Aug 2017 17:11:27: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 04 Aug 2017 17:11:27: start model_add_line... INFO @ Fri, 04 Aug 2017 17:11:28: start X-correlation... INFO @ Fri, 04 Aug 2017 17:11:28: end of X-cor INFO @ Fri, 04 Aug 2017 17:11:28: #2 finished! INFO @ Fri, 04 Aug 2017 17:11:28: #2 predicted fragment length is 170 bps INFO @ Fri, 04 Aug 2017 17:11:28: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 04 Aug 2017 17:11:28: #2.2 Generate R script for model : SRX2548346.10_model.r WARNING @ Fri, 04 Aug 2017 17:11:28: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 17:11:28: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Fri, 04 Aug 2017 17:11:28: #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 17:11:28: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:11:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:11:29: 22000000 INFO @ Fri, 04 Aug 2017 17:11:30: 21000000 INFO @ Fri, 04 Aug 2017 17:11:57: 23000000 INFO @ Fri, 04 Aug 2017 17:12:00: 22000000 INFO @ Fri, 04 Aug 2017 17:12:00: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:12:11: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:12:11: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:12:11: #1 total tags in treatment: 9630366 INFO @ Fri, 04 Aug 2017 17:12:11: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:12:11: #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 17:12:11: #1 tags after filtering in treatment: 9194974 INFO @ Fri, 04 Aug 2017 17:12:11: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 04 Aug 2017 17:12:11: #1 finished! INFO @ Fri, 04 Aug 2017 17:12:11: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:12:12: #2 number of paired peaks: 314 WARNING @ Fri, 04 Aug 2017 17:12:12: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 04 Aug 2017 17:12:12: start model_add_line... INFO @ Fri, 04 Aug 2017 17:12:12: start X-correlation... INFO @ Fri, 04 Aug 2017 17:12:12: end of X-cor INFO @ Fri, 04 Aug 2017 17:12:12: #2 finished! INFO @ Fri, 04 Aug 2017 17:12:12: #2 predicted fragment length is 170 bps INFO @ Fri, 04 Aug 2017 17:12:12: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 04 Aug 2017 17:12:12: #2.2 Generate R script for model : SRX2548346.05_model.r WARNING @ Fri, 04 Aug 2017 17:12:12: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 17:12:12: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Fri, 04 Aug 2017 17:12:12: #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 17:12:12: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:12:19: #4 Write output xls file... SRX2548346.10_peaks.xls INFO @ Fri, 04 Aug 2017 17:12:19: #4 Write peak in narrowPeak format file... SRX2548346.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:12:19: #4 Write summits bed file... SRX2548346.10_summits.bed INFO @ Fri, 04 Aug 2017 17:12:19: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1205 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 17:12:33: 23000000 INFO @ Fri, 04 Aug 2017 17:12:43: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:12:47: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:12:47: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:12:47: #1 total tags in treatment: 9630366 INFO @ Fri, 04 Aug 2017 17:12:47: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:12:47: #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 17:12:47: #1 tags after filtering in treatment: 9194974 INFO @ Fri, 04 Aug 2017 17:12:47: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 04 Aug 2017 17:12:47: #1 finished! INFO @ Fri, 04 Aug 2017 17:12:47: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:12:48: #2 number of paired peaks: 314 WARNING @ Fri, 04 Aug 2017 17:12:48: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 04 Aug 2017 17:12:48: start model_add_line... INFO @ Fri, 04 Aug 2017 17:12:49: start X-correlation... INFO @ Fri, 04 Aug 2017 17:12:49: end of X-cor INFO @ Fri, 04 Aug 2017 17:12:49: #2 finished! INFO @ Fri, 04 Aug 2017 17:12:49: #2 predicted fragment length is 170 bps INFO @ Fri, 04 Aug 2017 17:12:49: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 04 Aug 2017 17:12:49: #2.2 Generate R script for model : SRX2548346.20_model.r WARNING @ Fri, 04 Aug 2017 17:12:49: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 17:12:49: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Fri, 04 Aug 2017 17:12:49: #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 17:12:49: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:13:01: #4 Write output xls file... SRX2548346.05_peaks.xls INFO @ Fri, 04 Aug 2017 17:13:01: #4 Write peak in narrowPeak format file... SRX2548346.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:13:01: #4 Write summits bed file... SRX2548346.05_summits.bed INFO @ Fri, 04 Aug 2017 17:13:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1889 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 17:13:18: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:13:37: #4 Write output xls file... SRX2548346.20_peaks.xls INFO @ Fri, 04 Aug 2017 17:13:37: #4 Write peak in narrowPeak format file... SRX2548346.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:13:37: #4 Write summits bed file... SRX2548346.20_summits.bed INFO @ Fri, 04 Aug 2017 17:13:37: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (713 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。