Job ID = 10202001 sra ファイルのダウンロード中... Completed: 1691742K bytes transferred in 132 seconds (104294K 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... Written 19647582 spots for /home/okishinya/chipatlas/results/dm3/SRX2965245/SRR5765703.sra Written 19647582 spots total 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: 01:14:23 19647582 reads; of these: 19647582 (100.00%) were paired; of these: 5267515 (26.81%) aligned concordantly 0 times 10638747 (54.15%) aligned concordantly exactly 1 time 3741320 (19.04%) aligned concordantly >1 times ---- 5267515 pairs aligned concordantly 0 times; of these: 2277795 (43.24%) aligned discordantly 1 time ---- 2989720 pairs aligned 0 times concordantly or discordantly; of these: 5979440 mates make up the pairs; of these: 4263835 (71.31%) aligned 0 times 359431 (6.01%) aligned exactly 1 time 1356174 (22.68%) aligned >1 times 89.15% overall alignment rate Time searching: 01:14:23 Overall time: 01:14:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 576695 / 16478946 = 0.0350 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 @ Mon, 13 Nov 2017 14:42:09: # Command line: callpeak -t SRX2965245.bam -f BAM -g dm -n SRX2965245.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965245.05 # format = BAM # ChIP-seq file = ['SRX2965245.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 @ Mon, 13 Nov 2017 14:42:09: # Command line: callpeak -t SRX2965245.bam -f BAM -g dm -n SRX2965245.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965245.10 # format = BAM # ChIP-seq file = ['SRX2965245.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 @ Mon, 13 Nov 2017 14:42:09: # Command line: callpeak -t SRX2965245.bam -f BAM -g dm -n SRX2965245.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965245.20 # format = BAM # ChIP-seq file = ['SRX2965245.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 @ Mon, 13 Nov 2017 14:42:09: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:42:09: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:42:09: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:42:09: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:42:09: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:42:09: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:42:18: 1000000 INFO @ Mon, 13 Nov 2017 14:42:18: 1000000 INFO @ Mon, 13 Nov 2017 14:42:19: 1000000 INFO @ Mon, 13 Nov 2017 14:42:27: 2000000 INFO @ Mon, 13 Nov 2017 14:42:27: 2000000 INFO @ Mon, 13 Nov 2017 14:42:29: 2000000 INFO @ Mon, 13 Nov 2017 14:42:36: 3000000 INFO @ Mon, 13 Nov 2017 14:42:36: 3000000 INFO @ Mon, 13 Nov 2017 14:42:39: 3000000 INFO @ Mon, 13 Nov 2017 14:42:45: 4000000 INFO @ Mon, 13 Nov 2017 14:42:46: 4000000 INFO @ Mon, 13 Nov 2017 14:42:49: 4000000 INFO @ Mon, 13 Nov 2017 14:42:53: 5000000 INFO @ Mon, 13 Nov 2017 14:42:55: 5000000 INFO @ Mon, 13 Nov 2017 14:42:59: 5000000 INFO @ Mon, 13 Nov 2017 14:43:02: 6000000 INFO @ Mon, 13 Nov 2017 14:43:04: 6000000 INFO @ Mon, 13 Nov 2017 14:43:09: 6000000 INFO @ Mon, 13 Nov 2017 14:43:11: 7000000 INFO @ Mon, 13 Nov 2017 14:43:13: 7000000 INFO @ Mon, 13 Nov 2017 14:43:19: 7000000 INFO @ Mon, 13 Nov 2017 14:43:20: 8000000 INFO @ Mon, 13 Nov 2017 14:43:22: 8000000 INFO @ Mon, 13 Nov 2017 14:43:29: 9000000 INFO @ Mon, 13 Nov 2017 14:43:29: 8000000 INFO @ Mon, 13 Nov 2017 14:43:31: 9000000 INFO @ Mon, 13 Nov 2017 14:43:38: 10000000 INFO @ Mon, 13 Nov 2017 14:43:39: 9000000 INFO @ Mon, 13 Nov 2017 14:43:41: 10000000 INFO @ Mon, 13 Nov 2017 14:43:46: 11000000 INFO @ Mon, 13 Nov 2017 14:43:49: 10000000 INFO @ Mon, 13 Nov 2017 14:43:50: 11000000 INFO @ Mon, 13 Nov 2017 14:43:55: 12000000 INFO @ Mon, 13 Nov 2017 14:43:59: 12000000 INFO @ Mon, 13 Nov 2017 14:43:59: 11000000 INFO @ Mon, 13 Nov 2017 14:44:04: 13000000 INFO @ Mon, 13 Nov 2017 14:44:08: 13000000 INFO @ Mon, 13 Nov 2017 14:44:09: 12000000 INFO @ Mon, 13 Nov 2017 14:44:13: 14000000 INFO @ Mon, 13 Nov 2017 14:44:18: 14000000 INFO @ Mon, 13 Nov 2017 14:44:19: 13000000 INFO @ Mon, 13 Nov 2017 14:44:21: 15000000 INFO @ Mon, 13 Nov 2017 14:44:27: 15000000 INFO @ Mon, 13 Nov 2017 14:44:29: 14000000 INFO @ Mon, 13 Nov 2017 14:44:30: 16000000 INFO @ Mon, 13 Nov 2017 14:44:37: 16000000 INFO @ Mon, 13 Nov 2017 14:44:39: 17000000 INFO @ Mon, 13 Nov 2017 14:44:40: 15000000 INFO @ Mon, 13 Nov 2017 14:44:47: 17000000 INFO @ Mon, 13 Nov 2017 14:44:47: 18000000 INFO @ Mon, 13 Nov 2017 14:44:50: 16000000 INFO @ Mon, 13 Nov 2017 14:44:56: 19000000 INFO @ Mon, 13 Nov 2017 14:44:57: 18000000 INFO @ Mon, 13 Nov 2017 14:45:01: 17000000 INFO @ Mon, 13 Nov 2017 14:45:04: 20000000 INFO @ Mon, 13 Nov 2017 14:45:07: 19000000 INFO @ Mon, 13 Nov 2017 14:45:11: 18000000 INFO @ Mon, 13 Nov 2017 14:45:13: 21000000 INFO @ Mon, 13 Nov 2017 14:45:16: 20000000 INFO @ Mon, 13 Nov 2017 14:45:22: 22000000 INFO @ Mon, 13 Nov 2017 14:45:22: 19000000 INFO @ Mon, 13 Nov 2017 14:45:26: 21000000 INFO @ Mon, 13 Nov 2017 14:45:30: 23000000 INFO @ Mon, 13 Nov 2017 14:45:32: 20000000 INFO @ Mon, 13 Nov 2017 14:45:35: 22000000 INFO @ Mon, 13 Nov 2017 14:45:39: 24000000 INFO @ Mon, 13 Nov 2017 14:45:42: 21000000 INFO @ Mon, 13 Nov 2017 14:45:45: 23000000 INFO @ Mon, 13 Nov 2017 14:45:47: 25000000 INFO @ Mon, 13 Nov 2017 14:45:53: 22000000 INFO @ Mon, 13 Nov 2017 14:45:55: 24000000 INFO @ Mon, 13 Nov 2017 14:45:56: 26000000 INFO @ Mon, 13 Nov 2017 14:46:03: 23000000 INFO @ Mon, 13 Nov 2017 14:46:04: 27000000 INFO @ Mon, 13 Nov 2017 14:46:05: 25000000 INFO @ Mon, 13 Nov 2017 14:46:13: 28000000 INFO @ Mon, 13 Nov 2017 14:46:13: 24000000 INFO @ Mon, 13 Nov 2017 14:46:14: 26000000 INFO @ Mon, 13 Nov 2017 14:46:21: 29000000 INFO @ Mon, 13 Nov 2017 14:46:24: 27000000 INFO @ Mon, 13 Nov 2017 14:46:24: 25000000 INFO @ Mon, 13 Nov 2017 14:46:30: 30000000 INFO @ Mon, 13 Nov 2017 14:46:34: 28000000 INFO @ Mon, 13 Nov 2017 14:46:34: 26000000 INFO @ Mon, 13 Nov 2017 14:46:39: 31000000 INFO @ Mon, 13 Nov 2017 14:46:43: 29000000 INFO @ Mon, 13 Nov 2017 14:46:45: 27000000 INFO @ Mon, 13 Nov 2017 14:46:47: 32000000 INFO @ Mon, 13 Nov 2017 14:46:53: 30000000 INFO @ Mon, 13 Nov 2017 14:46:55: 28000000 INFO @ Mon, 13 Nov 2017 14:46:56: 33000000 INFO @ Mon, 13 Nov 2017 14:47:03: 31000000 INFO @ Mon, 13 Nov 2017 14:47:04: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:47:04: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:47:04: #1 total tags in treatment: 13824111 INFO @ Mon, 13 Nov 2017 14:47:04: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:47:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 14:47:04: #1 tags after filtering in treatment: 12911258 INFO @ Mon, 13 Nov 2017 14:47:04: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 13 Nov 2017 14:47:04: #1 finished! INFO @ Mon, 13 Nov 2017 14:47:04: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:47:05: #2 number of paired peaks: 848 WARNING @ Mon, 13 Nov 2017 14:47:05: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Mon, 13 Nov 2017 14:47:05: start model_add_line... INFO @ Mon, 13 Nov 2017 14:47:05: start X-correlation... INFO @ Mon, 13 Nov 2017 14:47:05: end of X-cor INFO @ Mon, 13 Nov 2017 14:47:05: #2 finished! INFO @ Mon, 13 Nov 2017 14:47:05: #2 predicted fragment length is 169 bps INFO @ Mon, 13 Nov 2017 14:47:05: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 13 Nov 2017 14:47:05: #2.2 Generate R script for model : SRX2965245.10_model.r WARNING @ Mon, 13 Nov 2017 14:47:05: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:47:05: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Mon, 13 Nov 2017 14:47:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 14:47:05: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:47:05: 29000000 INFO @ Mon, 13 Nov 2017 14:47:13: 32000000 INFO @ Mon, 13 Nov 2017 14:47:16: 30000000 INFO @ Mon, 13 Nov 2017 14:47:22: 33000000 INFO @ Mon, 13 Nov 2017 14:47:26: 31000000 INFO @ Mon, 13 Nov 2017 14:47:31: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:47:31: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:47:31: #1 total tags in treatment: 13824111 INFO @ Mon, 13 Nov 2017 14:47:31: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:47:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 14:47:31: #1 tags after filtering in treatment: 12911258 INFO @ Mon, 13 Nov 2017 14:47:31: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 13 Nov 2017 14:47:31: #1 finished! INFO @ Mon, 13 Nov 2017 14:47:31: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:47:32: #2 number of paired peaks: 848 WARNING @ Mon, 13 Nov 2017 14:47:32: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Mon, 13 Nov 2017 14:47:32: start model_add_line... INFO @ Mon, 13 Nov 2017 14:47:32: start X-correlation... INFO @ Mon, 13 Nov 2017 14:47:32: end of X-cor INFO @ Mon, 13 Nov 2017 14:47:32: #2 finished! INFO @ Mon, 13 Nov 2017 14:47:32: #2 predicted fragment length is 169 bps INFO @ Mon, 13 Nov 2017 14:47:32: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 13 Nov 2017 14:47:32: #2.2 Generate R script for model : SRX2965245.05_model.r WARNING @ Mon, 13 Nov 2017 14:47:32: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:47:32: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Mon, 13 Nov 2017 14:47:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 14:47:32: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:47:36: 32000000 INFO @ Mon, 13 Nov 2017 14:47:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:47:44: 33000000 INFO @ Mon, 13 Nov 2017 14:47:51: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:47:51: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:47:51: #1 total tags in treatment: 13824111 INFO @ Mon, 13 Nov 2017 14:47:51: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:47:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 14:47:51: #1 tags after filtering in treatment: 12911258 INFO @ Mon, 13 Nov 2017 14:47:51: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 13 Nov 2017 14:47:51: #1 finished! INFO @ Mon, 13 Nov 2017 14:47:51: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:47:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:47:52: #2 number of paired peaks: 848 WARNING @ Mon, 13 Nov 2017 14:47:52: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Mon, 13 Nov 2017 14:47:52: start model_add_line... INFO @ Mon, 13 Nov 2017 14:47:52: start X-correlation... INFO @ Mon, 13 Nov 2017 14:47:52: end of X-cor INFO @ Mon, 13 Nov 2017 14:47:52: #2 finished! INFO @ Mon, 13 Nov 2017 14:47:52: #2 predicted fragment length is 169 bps INFO @ Mon, 13 Nov 2017 14:47:52: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 13 Nov 2017 14:47:52: #2.2 Generate R script for model : SRX2965245.20_model.r WARNING @ Mon, 13 Nov 2017 14:47:52: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:47:52: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Mon, 13 Nov 2017 14:47:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 14:47:52: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:47:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:47:54: #4 Write output xls file... SRX2965245.10_peaks.xls INFO @ Mon, 13 Nov 2017 14:47:54: #4 Write peak in narrowPeak format file... SRX2965245.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:47:54: #4 Write summits bed file... SRX2965245.10_summits.bed INFO @ Mon, 13 Nov 2017 14:47:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 14:48:04: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:48:22: #4 Write output xls file... SRX2965245.05_peaks.xls INFO @ Mon, 13 Nov 2017 14:48:22: #4 Write peak in narrowPeak format file... SRX2965245.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:48:22: #4 Write summits bed file... SRX2965245.05_summits.bed INFO @ Mon, 13 Nov 2017 14:48:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2323 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 14:48:24: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:48:40: #4 Write output xls file... SRX2965245.20_peaks.xls INFO @ Mon, 13 Nov 2017 14:48:40: #4 Write peak in narrowPeak format file... SRX2965245.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:48:40: #4 Write summits bed file... SRX2965245.20_summits.bed INFO @ Mon, 13 Nov 2017 14:48:40: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (936 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。