Job ID = 11171260 sra ファイルのダウンロード中... Completed: 1943992K bytes transferred in 73 seconds (217256K bits/sec), in 1 file. 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... Read 29656878 spots for /home/okishinya/chipatlas/results/dm3/SRX2982447/SRR5803098.sra Written 29656878 spots for /home/okishinya/chipatlas/results/dm3/SRX2982447/SRR5803098.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 01:10:44 29656878 reads; of these: 29656878 (100.00%) were paired; of these: 2863218 (9.65%) aligned concordantly 0 times 21295946 (71.81%) aligned concordantly exactly 1 time 5497714 (18.54%) aligned concordantly >1 times ---- 2863218 pairs aligned concordantly 0 times; of these: 31876 (1.11%) aligned discordantly 1 time ---- 2831342 pairs aligned 0 times concordantly or discordantly; of these: 5662684 mates make up the pairs; of these: 4377525 (77.30%) aligned 0 times 850756 (15.02%) aligned exactly 1 time 434403 (7.67%) aligned >1 times 92.62% overall alignment rate Time searching: 01:10:44 Overall time: 01:10:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 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] 8388009 / 26792928 = 0.3131 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 @ Sat, 08 Sep 2018 14:52:02: # Command line: callpeak -t SRX2982447.bam -f BAM -g dm -n SRX2982447.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2982447.10 # format = BAM # ChIP-seq file = ['SRX2982447.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 @ Sat, 08 Sep 2018 14:52:02: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:52:02: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:52:02: # Command line: callpeak -t SRX2982447.bam -f BAM -g dm -n SRX2982447.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2982447.20 # format = BAM # ChIP-seq file = ['SRX2982447.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 @ Sat, 08 Sep 2018 14:52:02: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:52:02: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:52:02: # Command line: callpeak -t SRX2982447.bam -f BAM -g dm -n SRX2982447.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2982447.05 # format = BAM # ChIP-seq file = ['SRX2982447.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 @ Sat, 08 Sep 2018 14:52:02: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:52:02: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:52:09: 1000000 INFO @ Sat, 08 Sep 2018 14:52:09: 1000000 INFO @ Sat, 08 Sep 2018 14:52:09: 1000000 INFO @ Sat, 08 Sep 2018 14:52:16: 2000000 INFO @ Sat, 08 Sep 2018 14:52:16: 2000000 INFO @ Sat, 08 Sep 2018 14:52:16: 2000000 INFO @ Sat, 08 Sep 2018 14:52:22: 3000000 INFO @ Sat, 08 Sep 2018 14:52:22: 3000000 INFO @ Sat, 08 Sep 2018 14:52:23: 3000000 INFO @ Sat, 08 Sep 2018 14:52:29: 4000000 INFO @ Sat, 08 Sep 2018 14:52:29: 4000000 INFO @ Sat, 08 Sep 2018 14:52:29: 4000000 INFO @ Sat, 08 Sep 2018 14:52:36: 5000000 INFO @ Sat, 08 Sep 2018 14:52:36: 5000000 INFO @ Sat, 08 Sep 2018 14:52:36: 5000000 INFO @ Sat, 08 Sep 2018 14:52:43: 6000000 INFO @ Sat, 08 Sep 2018 14:52:43: 6000000 INFO @ Sat, 08 Sep 2018 14:52:43: 6000000 INFO @ Sat, 08 Sep 2018 14:52:50: 7000000 INFO @ Sat, 08 Sep 2018 14:52:50: 7000000 INFO @ Sat, 08 Sep 2018 14:52:50: 7000000 INFO @ Sat, 08 Sep 2018 14:52:56: 8000000 INFO @ Sat, 08 Sep 2018 14:52:57: 8000000 INFO @ Sat, 08 Sep 2018 14:52:57: 8000000 INFO @ Sat, 08 Sep 2018 14:53:03: 9000000 INFO @ Sat, 08 Sep 2018 14:53:04: 9000000 INFO @ Sat, 08 Sep 2018 14:53:04: 9000000 INFO @ Sat, 08 Sep 2018 14:53:10: 10000000 INFO @ Sat, 08 Sep 2018 14:53:11: 10000000 INFO @ Sat, 08 Sep 2018 14:53:11: 10000000 INFO @ Sat, 08 Sep 2018 14:53:17: 11000000 INFO @ Sat, 08 Sep 2018 14:53:17: 11000000 INFO @ Sat, 08 Sep 2018 14:53:18: 11000000 INFO @ Sat, 08 Sep 2018 14:53:24: 12000000 INFO @ Sat, 08 Sep 2018 14:53:24: 12000000 INFO @ Sat, 08 Sep 2018 14:53:24: 12000000 INFO @ Sat, 08 Sep 2018 14:53:31: 13000000 INFO @ Sat, 08 Sep 2018 14:53:31: 13000000 INFO @ Sat, 08 Sep 2018 14:53:31: 13000000 INFO @ Sat, 08 Sep 2018 14:53:37: 14000000 INFO @ Sat, 08 Sep 2018 14:53:38: 14000000 INFO @ Sat, 08 Sep 2018 14:53:38: 14000000 INFO @ Sat, 08 Sep 2018 14:53:44: 15000000 INFO @ Sat, 08 Sep 2018 14:53:45: 15000000 INFO @ Sat, 08 Sep 2018 14:53:45: 15000000 INFO @ Sat, 08 Sep 2018 14:53:51: 16000000 INFO @ Sat, 08 Sep 2018 14:53:52: 16000000 INFO @ Sat, 08 Sep 2018 14:53:52: 16000000 INFO @ Sat, 08 Sep 2018 14:53:58: 17000000 INFO @ Sat, 08 Sep 2018 14:53:58: 17000000 INFO @ Sat, 08 Sep 2018 14:53:59: 17000000 INFO @ Sat, 08 Sep 2018 14:54:05: 18000000 INFO @ Sat, 08 Sep 2018 14:54:05: 18000000 INFO @ Sat, 08 Sep 2018 14:54:05: 18000000 INFO @ Sat, 08 Sep 2018 14:54:11: 19000000 INFO @ Sat, 08 Sep 2018 14:54:12: 19000000 INFO @ Sat, 08 Sep 2018 14:54:12: 19000000 INFO @ Sat, 08 Sep 2018 14:54:18: 20000000 INFO @ Sat, 08 Sep 2018 14:54:19: 20000000 INFO @ Sat, 08 Sep 2018 14:54:19: 20000000 INFO @ Sat, 08 Sep 2018 14:54:25: 21000000 INFO @ Sat, 08 Sep 2018 14:54:26: 21000000 INFO @ Sat, 08 Sep 2018 14:54:26: 21000000 INFO @ Sat, 08 Sep 2018 14:54:32: 22000000 INFO @ Sat, 08 Sep 2018 14:54:33: 22000000 INFO @ Sat, 08 Sep 2018 14:54:33: 22000000 INFO @ Sat, 08 Sep 2018 14:54:39: 23000000 INFO @ Sat, 08 Sep 2018 14:54:39: 23000000 INFO @ Sat, 08 Sep 2018 14:54:40: 23000000 INFO @ Sat, 08 Sep 2018 14:54:45: 24000000 INFO @ Sat, 08 Sep 2018 14:54:46: 24000000 INFO @ Sat, 08 Sep 2018 14:54:46: 24000000 INFO @ Sat, 08 Sep 2018 14:54:52: 25000000 INFO @ Sat, 08 Sep 2018 14:54:53: 25000000 INFO @ Sat, 08 Sep 2018 14:54:53: 25000000 INFO @ Sat, 08 Sep 2018 14:54:59: 26000000 INFO @ Sat, 08 Sep 2018 14:55:00: 26000000 INFO @ Sat, 08 Sep 2018 14:55:00: 26000000 INFO @ Sat, 08 Sep 2018 14:55:05: 27000000 INFO @ Sat, 08 Sep 2018 14:55:07: 27000000 INFO @ Sat, 08 Sep 2018 14:55:07: 27000000 INFO @ Sat, 08 Sep 2018 14:55:12: 28000000 INFO @ Sat, 08 Sep 2018 14:55:14: 28000000 INFO @ Sat, 08 Sep 2018 14:55:14: 28000000 INFO @ Sat, 08 Sep 2018 14:55:18: 29000000 INFO @ Sat, 08 Sep 2018 14:55:21: 29000000 INFO @ Sat, 08 Sep 2018 14:55:21: 29000000 INFO @ Sat, 08 Sep 2018 14:55:25: 30000000 INFO @ Sat, 08 Sep 2018 14:55:28: 30000000 INFO @ Sat, 08 Sep 2018 14:55:28: 30000000 INFO @ Sat, 08 Sep 2018 14:55:32: 31000000 INFO @ Sat, 08 Sep 2018 14:55:35: 31000000 INFO @ Sat, 08 Sep 2018 14:55:35: 31000000 INFO @ Sat, 08 Sep 2018 14:55:38: 32000000 INFO @ Sat, 08 Sep 2018 14:55:42: 32000000 INFO @ Sat, 08 Sep 2018 14:55:42: 32000000 INFO @ Sat, 08 Sep 2018 14:55:45: 33000000 INFO @ Sat, 08 Sep 2018 14:55:49: 33000000 INFO @ Sat, 08 Sep 2018 14:55:49: 33000000 INFO @ Sat, 08 Sep 2018 14:55:52: 34000000 INFO @ Sat, 08 Sep 2018 14:55:56: 34000000 INFO @ Sat, 08 Sep 2018 14:55:56: 34000000 INFO @ Sat, 08 Sep 2018 14:55:58: 35000000 INFO @ Sat, 08 Sep 2018 14:56:03: 35000000 INFO @ Sat, 08 Sep 2018 14:56:04: 35000000 INFO @ Sat, 08 Sep 2018 14:56:05: 36000000 INFO @ Sat, 08 Sep 2018 14:56:10: 36000000 INFO @ Sat, 08 Sep 2018 14:56:11: 36000000 INFO @ Sat, 08 Sep 2018 14:56:12: 37000000 INFO @ Sat, 08 Sep 2018 14:56:18: 37000000 INFO @ Sat, 08 Sep 2018 14:56:18: 37000000 INFO @ Sat, 08 Sep 2018 14:56:18: 38000000 INFO @ Sat, 08 Sep 2018 14:56:20: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:56:20: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:56:20: #1 total tags in treatment: 18411560 INFO @ Sat, 08 Sep 2018 14:56:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:56:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:56:20: #1 tags after filtering in treatment: 16765425 INFO @ Sat, 08 Sep 2018 14:56:20: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Sep 2018 14:56:20: #1 finished! INFO @ Sat, 08 Sep 2018 14:56:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:56:21: #2 number of paired peaks: 169 WARNING @ Sat, 08 Sep 2018 14:56:21: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 08 Sep 2018 14:56:21: start model_add_line... INFO @ Sat, 08 Sep 2018 14:56:21: start X-correlation... INFO @ Sat, 08 Sep 2018 14:56:21: end of X-cor INFO @ Sat, 08 Sep 2018 14:56:21: #2 finished! INFO @ Sat, 08 Sep 2018 14:56:21: #2 predicted fragment length is 145 bps INFO @ Sat, 08 Sep 2018 14:56:21: #2 alternative fragment length(s) may be 1,122,128,145,181,206,233,432,525,545 bps INFO @ Sat, 08 Sep 2018 14:56:21: #2.2 Generate R script for model : SRX2982447.20_model.r WARNING @ Sat, 08 Sep 2018 14:56:21: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:56:21: #2 You may need to consider one of the other alternative d(s): 1,122,128,145,181,206,233,432,525,545 WARNING @ Sat, 08 Sep 2018 14:56:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:56:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:56:25: 38000000 INFO @ Sat, 08 Sep 2018 14:56:25: 38000000 INFO @ Sat, 08 Sep 2018 14:56:26: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:56:26: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:56:26: #1 total tags in treatment: 18411560 INFO @ Sat, 08 Sep 2018 14:56:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:56:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:56:26: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:56:26: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:56:26: #1 total tags in treatment: 18411560 INFO @ Sat, 08 Sep 2018 14:56:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:56:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:56:26: #1 tags after filtering in treatment: 16765425 INFO @ Sat, 08 Sep 2018 14:56:26: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Sep 2018 14:56:26: #1 finished! INFO @ Sat, 08 Sep 2018 14:56:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:56:26: #1 tags after filtering in treatment: 16765425 INFO @ Sat, 08 Sep 2018 14:56:26: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Sep 2018 14:56:26: #1 finished! INFO @ Sat, 08 Sep 2018 14:56:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:56:27: #2 number of paired peaks: 169 WARNING @ Sat, 08 Sep 2018 14:56:27: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 08 Sep 2018 14:56:27: start model_add_line... INFO @ Sat, 08 Sep 2018 14:56:27: start X-correlation... INFO @ Sat, 08 Sep 2018 14:56:27: end of X-cor INFO @ Sat, 08 Sep 2018 14:56:27: #2 finished! INFO @ Sat, 08 Sep 2018 14:56:27: #2 predicted fragment length is 145 bps INFO @ Sat, 08 Sep 2018 14:56:27: #2 alternative fragment length(s) may be 1,122,128,145,181,206,233,432,525,545 bps INFO @ Sat, 08 Sep 2018 14:56:27: #2.2 Generate R script for model : SRX2982447.10_model.r WARNING @ Sat, 08 Sep 2018 14:56:27: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:56:27: #2 You may need to consider one of the other alternative d(s): 1,122,128,145,181,206,233,432,525,545 WARNING @ Sat, 08 Sep 2018 14:56:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:56:27: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:56:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:56:28: #2 number of paired peaks: 169 WARNING @ Sat, 08 Sep 2018 14:56:28: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 08 Sep 2018 14:56:28: start model_add_line... INFO @ Sat, 08 Sep 2018 14:56:28: start X-correlation... INFO @ Sat, 08 Sep 2018 14:56:28: end of X-cor INFO @ Sat, 08 Sep 2018 14:56:28: #2 finished! INFO @ Sat, 08 Sep 2018 14:56:28: #2 predicted fragment length is 145 bps INFO @ Sat, 08 Sep 2018 14:56:28: #2 alternative fragment length(s) may be 1,122,128,145,181,206,233,432,525,545 bps INFO @ Sat, 08 Sep 2018 14:56:28: #2.2 Generate R script for model : SRX2982447.05_model.r WARNING @ Sat, 08 Sep 2018 14:56:28: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:56:28: #2 You may need to consider one of the other alternative d(s): 1,122,128,145,181,206,233,432,525,545 WARNING @ Sat, 08 Sep 2018 14:56:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:56:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:56:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:57:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:57:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:57:16: #4 Write output xls file... SRX2982447.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:57:17: #4 Write peak in narrowPeak format file... SRX2982447.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:57:17: #4 Write summits bed file... SRX2982447.20_summits.bed INFO @ Sat, 08 Sep 2018 14:57:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:57:21: #4 Write output xls file... SRX2982447.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:57:21: #4 Write peak in narrowPeak format file... SRX2982447.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:57:21: #4 Write summits bed file... SRX2982447.05_summits.bed INFO @ Sat, 08 Sep 2018 14:57:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1006 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:57:22: #4 Write output xls file... SRX2982447.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:57:22: #4 Write peak in narrowPeak format file... SRX2982447.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:57:22: #4 Write summits bed file... SRX2982447.10_summits.bed INFO @ Sat, 08 Sep 2018 14:57:22: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (383 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。