Job ID = 11170830 sra ファイルのダウンロード中... Completed: 3206495K bytes transferred in 172 seconds (152371K 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 26026647 spots for /home/okishinya/chipatlas/results/ce10/SRX3058057/SRR5892348.sra Written 26026647 spots for /home/okishinya/chipatlas/results/ce10/SRX3058057/SRR5892348.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: 00:00:01 Multiseed full-index search: 01:05:12 26026647 reads; of these: 26026647 (100.00%) were paired; of these: 3131619 (12.03%) aligned concordantly 0 times 19787623 (76.03%) aligned concordantly exactly 1 time 3107405 (11.94%) aligned concordantly >1 times ---- 3131619 pairs aligned concordantly 0 times; of these: 557728 (17.81%) aligned discordantly 1 time ---- 2573891 pairs aligned 0 times concordantly or discordantly; of these: 5147782 mates make up the pairs; of these: 4563195 (88.64%) aligned 0 times 380717 (7.40%) aligned exactly 1 time 203870 (3.96%) aligned >1 times 91.23% overall alignment rate Time searching: 01:05:13 Overall time: 01:05:13 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 36 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] 8784075 / 23365402 = 0.3759 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 12:55:36: # Command line: callpeak -t SRX3058057.bam -f BAM -g ce -n SRX3058057.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3058057.10 # format = BAM # ChIP-seq file = ['SRX3058057.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 @ Sat, 08 Sep 2018 12:55:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:55:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:55:36: # Command line: callpeak -t SRX3058057.bam -f BAM -g ce -n SRX3058057.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3058057.20 # format = BAM # ChIP-seq file = ['SRX3058057.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 @ Sat, 08 Sep 2018 12:55:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:55:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:55:36: # Command line: callpeak -t SRX3058057.bam -f BAM -g ce -n SRX3058057.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3058057.05 # format = BAM # ChIP-seq file = ['SRX3058057.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 @ Sat, 08 Sep 2018 12:55:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:55:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:55:45: 1000000 INFO @ Sat, 08 Sep 2018 12:55:45: 1000000 INFO @ Sat, 08 Sep 2018 12:55:45: 1000000 INFO @ Sat, 08 Sep 2018 12:55:53: 2000000 INFO @ Sat, 08 Sep 2018 12:55:54: 2000000 INFO @ Sat, 08 Sep 2018 12:55:54: 2000000 INFO @ Sat, 08 Sep 2018 12:56:02: 3000000 INFO @ Sat, 08 Sep 2018 12:56:02: 3000000 INFO @ Sat, 08 Sep 2018 12:56:02: 3000000 INFO @ Sat, 08 Sep 2018 12:56:11: 4000000 INFO @ Sat, 08 Sep 2018 12:56:11: 4000000 INFO @ Sat, 08 Sep 2018 12:56:11: 4000000 INFO @ Sat, 08 Sep 2018 12:56:19: 5000000 INFO @ Sat, 08 Sep 2018 12:56:20: 5000000 INFO @ Sat, 08 Sep 2018 12:56:20: 5000000 INFO @ Sat, 08 Sep 2018 12:56:28: 6000000 INFO @ Sat, 08 Sep 2018 12:56:29: 6000000 INFO @ Sat, 08 Sep 2018 12:56:29: 6000000 INFO @ Sat, 08 Sep 2018 12:56:37: 7000000 INFO @ Sat, 08 Sep 2018 12:56:38: 7000000 INFO @ Sat, 08 Sep 2018 12:56:38: 7000000 INFO @ Sat, 08 Sep 2018 12:56:45: 8000000 INFO @ Sat, 08 Sep 2018 12:56:47: 8000000 INFO @ Sat, 08 Sep 2018 12:56:47: 8000000 INFO @ Sat, 08 Sep 2018 12:56:54: 9000000 INFO @ Sat, 08 Sep 2018 12:56:56: 9000000 INFO @ Sat, 08 Sep 2018 12:56:56: 9000000 INFO @ Sat, 08 Sep 2018 12:57:03: 10000000 INFO @ Sat, 08 Sep 2018 12:57:04: 10000000 INFO @ Sat, 08 Sep 2018 12:57:04: 10000000 INFO @ Sat, 08 Sep 2018 12:57:12: 11000000 INFO @ Sat, 08 Sep 2018 12:57:13: 11000000 INFO @ Sat, 08 Sep 2018 12:57:13: 11000000 INFO @ Sat, 08 Sep 2018 12:57:20: 12000000 INFO @ Sat, 08 Sep 2018 12:57:22: 12000000 INFO @ Sat, 08 Sep 2018 12:57:22: 12000000 INFO @ Sat, 08 Sep 2018 12:57:29: 13000000 INFO @ Sat, 08 Sep 2018 12:57:31: 13000000 INFO @ Sat, 08 Sep 2018 12:57:31: 13000000 INFO @ Sat, 08 Sep 2018 12:57:38: 14000000 INFO @ Sat, 08 Sep 2018 12:57:40: 14000000 INFO @ Sat, 08 Sep 2018 12:57:40: 14000000 INFO @ Sat, 08 Sep 2018 12:57:47: 15000000 INFO @ Sat, 08 Sep 2018 12:57:49: 15000000 INFO @ Sat, 08 Sep 2018 12:57:49: 15000000 INFO @ Sat, 08 Sep 2018 12:57:55: 16000000 INFO @ Sat, 08 Sep 2018 12:57:58: 16000000 INFO @ Sat, 08 Sep 2018 12:57:58: 16000000 INFO @ Sat, 08 Sep 2018 12:58:04: 17000000 INFO @ Sat, 08 Sep 2018 12:58:06: 17000000 INFO @ Sat, 08 Sep 2018 12:58:06: 17000000 INFO @ Sat, 08 Sep 2018 12:58:13: 18000000 INFO @ Sat, 08 Sep 2018 12:58:15: 18000000 INFO @ Sat, 08 Sep 2018 12:58:15: 18000000 INFO @ Sat, 08 Sep 2018 12:58:21: 19000000 INFO @ Sat, 08 Sep 2018 12:58:24: 19000000 INFO @ Sat, 08 Sep 2018 12:58:24: 19000000 INFO @ Sat, 08 Sep 2018 12:58:30: 20000000 INFO @ Sat, 08 Sep 2018 12:58:33: 20000000 INFO @ Sat, 08 Sep 2018 12:58:33: 20000000 INFO @ Sat, 08 Sep 2018 12:58:38: 21000000 INFO @ Sat, 08 Sep 2018 12:58:41: 21000000 INFO @ Sat, 08 Sep 2018 12:58:41: 21000000 INFO @ Sat, 08 Sep 2018 12:58:47: 22000000 INFO @ Sat, 08 Sep 2018 12:58:50: 22000000 INFO @ Sat, 08 Sep 2018 12:58:50: 22000000 INFO @ Sat, 08 Sep 2018 12:58:55: 23000000 INFO @ Sat, 08 Sep 2018 12:58:59: 23000000 INFO @ Sat, 08 Sep 2018 12:58:59: 23000000 INFO @ Sat, 08 Sep 2018 12:59:04: 24000000 INFO @ Sat, 08 Sep 2018 12:59:08: 24000000 INFO @ Sat, 08 Sep 2018 12:59:08: 24000000 INFO @ Sat, 08 Sep 2018 12:59:12: 25000000 INFO @ Sat, 08 Sep 2018 12:59:16: 25000000 INFO @ Sat, 08 Sep 2018 12:59:16: 25000000 INFO @ Sat, 08 Sep 2018 12:59:21: 26000000 INFO @ Sat, 08 Sep 2018 12:59:25: 26000000 INFO @ Sat, 08 Sep 2018 12:59:25: 26000000 INFO @ Sat, 08 Sep 2018 12:59:29: 27000000 INFO @ Sat, 08 Sep 2018 12:59:34: 27000000 INFO @ Sat, 08 Sep 2018 12:59:34: 27000000 INFO @ Sat, 08 Sep 2018 12:59:38: 28000000 INFO @ Sat, 08 Sep 2018 12:59:43: 28000000 INFO @ Sat, 08 Sep 2018 12:59:43: 28000000 INFO @ Sat, 08 Sep 2018 12:59:46: 29000000 INFO @ Sat, 08 Sep 2018 12:59:53: 29000000 INFO @ Sat, 08 Sep 2018 12:59:53: 29000000 INFO @ Sat, 08 Sep 2018 12:59:54: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:59:54: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:59:54: #1 total tags in treatment: 14254573 INFO @ Sat, 08 Sep 2018 12:59:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:59:54: #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 12:59:54: #1 tags after filtering in treatment: 12680273 INFO @ Sat, 08 Sep 2018 12:59:54: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Sep 2018 12:59:54: #1 finished! INFO @ Sat, 08 Sep 2018 12:59:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:59:55: #2 number of paired peaks: 522 WARNING @ Sat, 08 Sep 2018 12:59:55: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 08 Sep 2018 12:59:55: start model_add_line... INFO @ Sat, 08 Sep 2018 12:59:56: start X-correlation... INFO @ Sat, 08 Sep 2018 12:59:56: end of X-cor INFO @ Sat, 08 Sep 2018 12:59:56: #2 finished! INFO @ Sat, 08 Sep 2018 12:59:56: #2 predicted fragment length is 217 bps INFO @ Sat, 08 Sep 2018 12:59:56: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 08 Sep 2018 12:59:56: #2.2 Generate R script for model : SRX3058057.20_model.r WARNING @ Sat, 08 Sep 2018 12:59:56: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:59:56: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 08 Sep 2018 12:59:56: #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 12:59:56: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:00:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 13:00:01: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 13:00:01: #1 total tags in treatment: 14254573 INFO @ Sat, 08 Sep 2018 13:00:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:00:01: #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 13:00:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 13:00:01: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 13:00:01: #1 total tags in treatment: 14254573 INFO @ Sat, 08 Sep 2018 13:00:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:00:01: #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 13:00:01: #1 tags after filtering in treatment: 12680273 INFO @ Sat, 08 Sep 2018 13:00:01: #1 tags after filtering in treatment: 12680273 INFO @ Sat, 08 Sep 2018 13:00:01: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Sep 2018 13:00:01: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Sep 2018 13:00:01: #1 finished! INFO @ Sat, 08 Sep 2018 13:00:01: #1 finished! INFO @ Sat, 08 Sep 2018 13:00:01: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:00:01: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:00:02: #2 number of paired peaks: 522 WARNING @ Sat, 08 Sep 2018 13:00:02: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 08 Sep 2018 13:00:02: start model_add_line... INFO @ Sat, 08 Sep 2018 13:00:02: #2 number of paired peaks: 522 WARNING @ Sat, 08 Sep 2018 13:00:02: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 08 Sep 2018 13:00:02: start model_add_line... INFO @ Sat, 08 Sep 2018 13:00:02: start X-correlation... INFO @ Sat, 08 Sep 2018 13:00:02: end of X-cor INFO @ Sat, 08 Sep 2018 13:00:02: #2 finished! INFO @ Sat, 08 Sep 2018 13:00:02: #2 predicted fragment length is 217 bps INFO @ Sat, 08 Sep 2018 13:00:02: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 08 Sep 2018 13:00:02: #2.2 Generate R script for model : SRX3058057.05_model.r INFO @ Sat, 08 Sep 2018 13:00:02: start X-correlation... INFO @ Sat, 08 Sep 2018 13:00:02: end of X-cor INFO @ Sat, 08 Sep 2018 13:00:02: #2 finished! INFO @ Sat, 08 Sep 2018 13:00:02: #2 predicted fragment length is 217 bps INFO @ Sat, 08 Sep 2018 13:00:02: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 08 Sep 2018 13:00:02: #2.2 Generate R script for model : SRX3058057.10_model.r WARNING @ Sat, 08 Sep 2018 13:00:03: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:00:03: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 08 Sep 2018 13:00:03: #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 13:00:03: #3 Call peaks... WARNING @ Sat, 08 Sep 2018 13:00:03: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:00:03: #2 You may need to consider one of the other alternative d(s): 217 INFO @ Sat, 08 Sep 2018 13:00:03: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 08 Sep 2018 13:00:03: #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 13:00:03: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:00:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:00:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:00:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:00:41: #4 Write output xls file... SRX3058057.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:41: #4 Write peak in narrowPeak format file... SRX3058057.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:41: #4 Write summits bed file... SRX3058057.20_summits.bed INFO @ Sat, 08 Sep 2018 13:00:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1792 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:00:48: #4 Write output xls file... SRX3058057.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:48: #4 Write peak in narrowPeak format file... SRX3058057.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:49: #4 Write summits bed file... SRX3058057.05_summits.bed INFO @ Sat, 08 Sep 2018 13:00:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4030 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:00:51: #4 Write output xls file... SRX3058057.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:51: #4 Write peak in narrowPeak format file... SRX3058057.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:51: #4 Write summits bed file... SRX3058057.10_summits.bed INFO @ Sat, 08 Sep 2018 13:00:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2851 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。