Job ID = 11597668 sra ファイルのダウンロード中... Completed: 4091516K bytes transferred in 75 seconds (444935K 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 30362235 spots for /home/okishinya/chipatlas/results/ce10/ERX1485062/ERR1414279.sra Written 30362235 spots for /home/okishinya/chipatlas/results/ce10/ERX1485062/ERR1414279.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: 00:52:17 30362235 reads; of these: 30362235 (100.00%) were paired; of these: 386088 (1.27%) aligned concordantly 0 times 26442126 (87.09%) aligned concordantly exactly 1 time 3534021 (11.64%) aligned concordantly >1 times ---- 386088 pairs aligned concordantly 0 times; of these: 15684 (4.06%) aligned discordantly 1 time ---- 370404 pairs aligned 0 times concordantly or discordantly; of these: 740808 mates make up the pairs; of these: 436964 (58.98%) aligned 0 times 231600 (31.26%) aligned exactly 1 time 72244 (9.75%) aligned >1 times 99.28% overall alignment rate Time searching: 00:52:17 Overall time: 00:52:17 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 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 13397531 / 29981417 = 0.4469 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 @ Wed, 30 Jan 2019 15:35:28: # Command line: callpeak -t ERX1485062.bam -f BAM -g ce -n ERX1485062.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1485062.20 # format = BAM # ChIP-seq file = ['ERX1485062.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 @ Wed, 30 Jan 2019 15:35:28: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:35:28: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:35:28: # Command line: callpeak -t ERX1485062.bam -f BAM -g ce -n ERX1485062.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1485062.10 # format = BAM # ChIP-seq file = ['ERX1485062.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 @ Wed, 30 Jan 2019 15:35:28: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:35:28: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:35:28: # Command line: callpeak -t ERX1485062.bam -f BAM -g ce -n ERX1485062.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1485062.05 # format = BAM # ChIP-seq file = ['ERX1485062.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 @ Wed, 30 Jan 2019 15:35:28: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:35:28: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:35:36: 1000000 INFO @ Wed, 30 Jan 2019 15:35:36: 1000000 INFO @ Wed, 30 Jan 2019 15:35:36: 1000000 INFO @ Wed, 30 Jan 2019 15:35:44: 2000000 INFO @ Wed, 30 Jan 2019 15:35:44: 2000000 INFO @ Wed, 30 Jan 2019 15:35:44: 2000000 INFO @ Wed, 30 Jan 2019 15:35:52: 3000000 INFO @ Wed, 30 Jan 2019 15:35:52: 3000000 INFO @ Wed, 30 Jan 2019 15:35:52: 3000000 INFO @ Wed, 30 Jan 2019 15:35:59: 4000000 INFO @ Wed, 30 Jan 2019 15:35:59: 4000000 INFO @ Wed, 30 Jan 2019 15:35:59: 4000000 INFO @ Wed, 30 Jan 2019 15:36:07: 5000000 INFO @ Wed, 30 Jan 2019 15:36:07: 5000000 INFO @ Wed, 30 Jan 2019 15:36:07: 5000000 INFO @ Wed, 30 Jan 2019 15:36:15: 6000000 INFO @ Wed, 30 Jan 2019 15:36:15: 6000000 INFO @ Wed, 30 Jan 2019 15:36:15: 6000000 INFO @ Wed, 30 Jan 2019 15:36:22: 7000000 INFO @ Wed, 30 Jan 2019 15:36:22: 7000000 INFO @ Wed, 30 Jan 2019 15:36:22: 7000000 INFO @ Wed, 30 Jan 2019 15:36:30: 8000000 INFO @ Wed, 30 Jan 2019 15:36:30: 8000000 INFO @ Wed, 30 Jan 2019 15:36:31: 8000000 INFO @ Wed, 30 Jan 2019 15:36:37: 9000000 INFO @ Wed, 30 Jan 2019 15:36:37: 9000000 INFO @ Wed, 30 Jan 2019 15:36:39: 9000000 INFO @ Wed, 30 Jan 2019 15:36:45: 10000000 INFO @ Wed, 30 Jan 2019 15:36:45: 10000000 INFO @ Wed, 30 Jan 2019 15:36:47: 10000000 INFO @ Wed, 30 Jan 2019 15:36:53: 11000000 INFO @ Wed, 30 Jan 2019 15:36:53: 11000000 INFO @ Wed, 30 Jan 2019 15:36:55: 11000000 INFO @ Wed, 30 Jan 2019 15:37:00: 12000000 INFO @ Wed, 30 Jan 2019 15:37:00: 12000000 INFO @ Wed, 30 Jan 2019 15:37:03: 12000000 INFO @ Wed, 30 Jan 2019 15:37:08: 13000000 INFO @ Wed, 30 Jan 2019 15:37:08: 13000000 INFO @ Wed, 30 Jan 2019 15:37:10: 13000000 INFO @ Wed, 30 Jan 2019 15:37:16: 14000000 INFO @ Wed, 30 Jan 2019 15:37:16: 14000000 INFO @ Wed, 30 Jan 2019 15:37:18: 14000000 INFO @ Wed, 30 Jan 2019 15:37:23: 15000000 INFO @ Wed, 30 Jan 2019 15:37:23: 15000000 INFO @ Wed, 30 Jan 2019 15:37:25: 15000000 INFO @ Wed, 30 Jan 2019 15:37:31: 16000000 INFO @ Wed, 30 Jan 2019 15:37:31: 16000000 INFO @ Wed, 30 Jan 2019 15:37:33: 16000000 INFO @ Wed, 30 Jan 2019 15:37:38: 17000000 INFO @ Wed, 30 Jan 2019 15:37:38: 17000000 INFO @ Wed, 30 Jan 2019 15:37:41: 17000000 INFO @ Wed, 30 Jan 2019 15:37:46: 18000000 INFO @ Wed, 30 Jan 2019 15:37:46: 18000000 INFO @ Wed, 30 Jan 2019 15:37:48: 18000000 INFO @ Wed, 30 Jan 2019 15:37:54: 19000000 INFO @ Wed, 30 Jan 2019 15:37:54: 19000000 INFO @ Wed, 30 Jan 2019 15:37:56: 19000000 INFO @ Wed, 30 Jan 2019 15:38:01: 20000000 INFO @ Wed, 30 Jan 2019 15:38:01: 20000000 INFO @ Wed, 30 Jan 2019 15:38:04: 20000000 INFO @ Wed, 30 Jan 2019 15:38:08: 21000000 INFO @ Wed, 30 Jan 2019 15:38:09: 21000000 INFO @ Wed, 30 Jan 2019 15:38:12: 21000000 INFO @ Wed, 30 Jan 2019 15:38:16: 22000000 INFO @ Wed, 30 Jan 2019 15:38:17: 22000000 INFO @ Wed, 30 Jan 2019 15:38:20: 22000000 INFO @ Wed, 30 Jan 2019 15:38:24: 23000000 INFO @ Wed, 30 Jan 2019 15:38:25: 23000000 INFO @ Wed, 30 Jan 2019 15:38:27: 23000000 INFO @ Wed, 30 Jan 2019 15:38:32: 24000000 INFO @ Wed, 30 Jan 2019 15:38:33: 24000000 INFO @ Wed, 30 Jan 2019 15:38:36: 24000000 INFO @ Wed, 30 Jan 2019 15:38:40: 25000000 INFO @ Wed, 30 Jan 2019 15:38:41: 25000000 INFO @ Wed, 30 Jan 2019 15:38:44: 25000000 INFO @ Wed, 30 Jan 2019 15:38:48: 26000000 INFO @ Wed, 30 Jan 2019 15:38:49: 26000000 INFO @ Wed, 30 Jan 2019 15:38:51: 26000000 INFO @ Wed, 30 Jan 2019 15:38:55: 27000000 INFO @ Wed, 30 Jan 2019 15:38:57: 27000000 INFO @ Wed, 30 Jan 2019 15:38:59: 27000000 INFO @ Wed, 30 Jan 2019 15:39:03: 28000000 INFO @ Wed, 30 Jan 2019 15:39:05: 28000000 INFO @ Wed, 30 Jan 2019 15:39:07: 28000000 INFO @ Wed, 30 Jan 2019 15:39:12: 29000000 INFO @ Wed, 30 Jan 2019 15:39:14: 29000000 INFO @ Wed, 30 Jan 2019 15:39:16: 29000000 INFO @ Wed, 30 Jan 2019 15:39:22: 30000000 INFO @ Wed, 30 Jan 2019 15:39:24: 30000000 INFO @ Wed, 30 Jan 2019 15:39:25: 30000000 INFO @ Wed, 30 Jan 2019 15:39:31: 31000000 INFO @ Wed, 30 Jan 2019 15:39:33: 31000000 INFO @ Wed, 30 Jan 2019 15:39:34: 31000000 INFO @ Wed, 30 Jan 2019 15:39:41: 32000000 INFO @ Wed, 30 Jan 2019 15:39:42: 32000000 INFO @ Wed, 30 Jan 2019 15:39:42: 32000000 INFO @ Wed, 30 Jan 2019 15:39:49: 33000000 INFO @ Wed, 30 Jan 2019 15:39:50: 33000000 INFO @ Wed, 30 Jan 2019 15:39:51: 33000000 INFO @ Wed, 30 Jan 2019 15:39:53: #1 tag size is determined as 101 bps INFO @ Wed, 30 Jan 2019 15:39:53: #1 tag size = 101 INFO @ Wed, 30 Jan 2019 15:39:53: #1 total tags in treatment: 16582743 INFO @ Wed, 30 Jan 2019 15:39:53: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:39:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:39:53: #1 tag size is determined as 101 bps INFO @ Wed, 30 Jan 2019 15:39:53: #1 tag size = 101 INFO @ Wed, 30 Jan 2019 15:39:53: #1 total tags in treatment: 16582743 INFO @ Wed, 30 Jan 2019 15:39:53: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:39:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:39:54: #1 tags after filtering in treatment: 14856622 INFO @ Wed, 30 Jan 2019 15:39:54: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 30 Jan 2019 15:39:54: #1 finished! INFO @ Wed, 30 Jan 2019 15:39:54: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:39:54: #1 tags after filtering in treatment: 14856622 INFO @ Wed, 30 Jan 2019 15:39:54: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 30 Jan 2019 15:39:54: #1 finished! INFO @ Wed, 30 Jan 2019 15:39:54: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:39:55: #1 tag size is determined as 101 bps INFO @ Wed, 30 Jan 2019 15:39:55: #1 tag size = 101 INFO @ Wed, 30 Jan 2019 15:39:55: #1 total tags in treatment: 16582743 INFO @ Wed, 30 Jan 2019 15:39:55: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:39:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:39:55: #2 number of paired peaks: 267 WARNING @ Wed, 30 Jan 2019 15:39:55: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Wed, 30 Jan 2019 15:39:55: start model_add_line... INFO @ Wed, 30 Jan 2019 15:39:55: #2 number of paired peaks: 267 WARNING @ Wed, 30 Jan 2019 15:39:55: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Wed, 30 Jan 2019 15:39:55: start model_add_line... INFO @ Wed, 30 Jan 2019 15:39:55: start X-correlation... INFO @ Wed, 30 Jan 2019 15:39:55: end of X-cor INFO @ Wed, 30 Jan 2019 15:39:55: #2 finished! INFO @ Wed, 30 Jan 2019 15:39:55: #2 predicted fragment length is 169 bps INFO @ Wed, 30 Jan 2019 15:39:55: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 30 Jan 2019 15:39:55: #2.2 Generate R script for model : ERX1485062.05_model.r WARNING @ Wed, 30 Jan 2019 15:39:55: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:39:55: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Wed, 30 Jan 2019 15:39:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:39:55: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:39:55: #1 tags after filtering in treatment: 14856622 INFO @ Wed, 30 Jan 2019 15:39:55: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 30 Jan 2019 15:39:55: #1 finished! INFO @ Wed, 30 Jan 2019 15:39:55: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:39:55: start X-correlation... INFO @ Wed, 30 Jan 2019 15:39:55: end of X-cor INFO @ Wed, 30 Jan 2019 15:39:55: #2 finished! INFO @ Wed, 30 Jan 2019 15:39:55: #2 predicted fragment length is 169 bps INFO @ Wed, 30 Jan 2019 15:39:55: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 30 Jan 2019 15:39:55: #2.2 Generate R script for model : ERX1485062.20_model.r WARNING @ Wed, 30 Jan 2019 15:39:55: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:39:55: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Wed, 30 Jan 2019 15:39:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:39:55: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:39:56: #2 number of paired peaks: 267 WARNING @ Wed, 30 Jan 2019 15:39:56: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Wed, 30 Jan 2019 15:39:56: start model_add_line... INFO @ Wed, 30 Jan 2019 15:39:56: start X-correlation... INFO @ Wed, 30 Jan 2019 15:39:56: end of X-cor INFO @ Wed, 30 Jan 2019 15:39:56: #2 finished! INFO @ Wed, 30 Jan 2019 15:39:56: #2 predicted fragment length is 169 bps INFO @ Wed, 30 Jan 2019 15:39:56: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 30 Jan 2019 15:39:56: #2.2 Generate R script for model : ERX1485062.10_model.r WARNING @ Wed, 30 Jan 2019 15:39:56: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:39:56: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Wed, 30 Jan 2019 15:39:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:39:56: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:39:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:40:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:40:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:40:30: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:40:46: #4 Write output xls file... ERX1485062.10_peaks.xls INFO @ Wed, 30 Jan 2019 15:40:46: #4 Write peak in narrowPeak format file... ERX1485062.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:40:46: #4 Write summits bed file... ERX1485062.10_summits.bed INFO @ Wed, 30 Jan 2019 15:40:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3512 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 15:40:47: #4 Write output xls file... ERX1485062.05_peaks.xls INFO @ Wed, 30 Jan 2019 15:40:47: #4 Write peak in narrowPeak format file... ERX1485062.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:40:47: #4 Write summits bed file... ERX1485062.05_summits.bed INFO @ Wed, 30 Jan 2019 15:40:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5940 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 15:40:48: #4 Write output xls file... ERX1485062.20_peaks.xls INFO @ Wed, 30 Jan 2019 15:40:48: #4 Write peak in narrowPeak format file... ERX1485062.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:40:48: #4 Write summits bed file... ERX1485062.20_summits.bed INFO @ Wed, 30 Jan 2019 15:40:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1657 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。