Job ID = 10714467 sra ファイルのダウンロード中... Completed: 1436869K bytes transferred in 24 seconds (471168K 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 23444682 spots for /home/okishinya/chipatlas/results/ce10/SRX4085383/SRR7167412.sra Written 23444682 spots for /home/okishinya/chipatlas/results/ce10/SRX4085383/SRR7167412.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: 00:22:07 23444682 reads; of these: 23444682 (100.00%) were paired; of these: 6400497 (27.30%) aligned concordantly 0 times 14448239 (61.63%) aligned concordantly exactly 1 time 2595946 (11.07%) aligned concordantly >1 times ---- 6400497 pairs aligned concordantly 0 times; of these: 349142 (5.45%) aligned discordantly 1 time ---- 6051355 pairs aligned 0 times concordantly or discordantly; of these: 12102710 mates make up the pairs; of these: 8841885 (73.06%) aligned 0 times 2767986 (22.87%) aligned exactly 1 time 492839 (4.07%) aligned >1 times 81.14% overall alignment rate Time searching: 00:22:07 Overall time: 00:22:07 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 16 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] 2185898 / 17267874 = 0.1266 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 @ Sun, 03 Jun 2018 13:16:00: # Command line: callpeak -t SRX4085383.bam -f BAM -g ce -n SRX4085383.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085383.20 # format = BAM # ChIP-seq file = ['SRX4085383.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 @ Sun, 03 Jun 2018 13:16:00: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:16:00: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:16:00: # Command line: callpeak -t SRX4085383.bam -f BAM -g ce -n SRX4085383.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085383.05 # format = BAM # ChIP-seq file = ['SRX4085383.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 @ Sun, 03 Jun 2018 13:16:00: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:16:00: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:16:00: # Command line: callpeak -t SRX4085383.bam -f BAM -g ce -n SRX4085383.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085383.10 # format = BAM # ChIP-seq file = ['SRX4085383.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 @ Sun, 03 Jun 2018 13:16:00: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:16:00: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:16:06: 1000000 INFO @ Sun, 03 Jun 2018 13:16:07: 1000000 INFO @ Sun, 03 Jun 2018 13:16:07: 1000000 INFO @ Sun, 03 Jun 2018 13:16:12: 2000000 INFO @ Sun, 03 Jun 2018 13:16:13: 2000000 INFO @ Sun, 03 Jun 2018 13:16:13: 2000000 INFO @ Sun, 03 Jun 2018 13:16:19: 3000000 INFO @ Sun, 03 Jun 2018 13:16:20: 3000000 INFO @ Sun, 03 Jun 2018 13:16:20: 3000000 INFO @ Sun, 03 Jun 2018 13:16:25: 4000000 INFO @ Sun, 03 Jun 2018 13:16:27: 4000000 INFO @ Sun, 03 Jun 2018 13:16:27: 4000000 INFO @ Sun, 03 Jun 2018 13:16:31: 5000000 INFO @ Sun, 03 Jun 2018 13:16:34: 5000000 INFO @ Sun, 03 Jun 2018 13:16:34: 5000000 INFO @ Sun, 03 Jun 2018 13:16:37: 6000000 INFO @ Sun, 03 Jun 2018 13:16:40: 6000000 INFO @ Sun, 03 Jun 2018 13:16:40: 6000000 INFO @ Sun, 03 Jun 2018 13:16:43: 7000000 INFO @ Sun, 03 Jun 2018 13:16:47: 7000000 INFO @ Sun, 03 Jun 2018 13:16:47: 7000000 INFO @ Sun, 03 Jun 2018 13:16:50: 8000000 INFO @ Sun, 03 Jun 2018 13:16:54: 8000000 INFO @ Sun, 03 Jun 2018 13:16:54: 8000000 INFO @ Sun, 03 Jun 2018 13:16:56: 9000000 INFO @ Sun, 03 Jun 2018 13:17:01: 9000000 INFO @ Sun, 03 Jun 2018 13:17:01: 9000000 INFO @ Sun, 03 Jun 2018 13:17:02: 10000000 INFO @ Sun, 03 Jun 2018 13:17:07: 10000000 INFO @ Sun, 03 Jun 2018 13:17:07: 10000000 INFO @ Sun, 03 Jun 2018 13:17:08: 11000000 INFO @ Sun, 03 Jun 2018 13:17:14: 11000000 INFO @ Sun, 03 Jun 2018 13:17:14: 11000000 INFO @ Sun, 03 Jun 2018 13:17:15: 12000000 INFO @ Sun, 03 Jun 2018 13:17:21: 13000000 INFO @ Sun, 03 Jun 2018 13:17:21: 12000000 INFO @ Sun, 03 Jun 2018 13:17:21: 12000000 INFO @ Sun, 03 Jun 2018 13:17:27: 14000000 INFO @ Sun, 03 Jun 2018 13:17:28: 13000000 INFO @ Sun, 03 Jun 2018 13:17:28: 13000000 INFO @ Sun, 03 Jun 2018 13:17:33: 15000000 INFO @ Sun, 03 Jun 2018 13:17:34: 14000000 INFO @ Sun, 03 Jun 2018 13:17:34: 14000000 INFO @ Sun, 03 Jun 2018 13:17:39: 16000000 INFO @ Sun, 03 Jun 2018 13:17:41: 15000000 INFO @ Sun, 03 Jun 2018 13:17:41: 15000000 INFO @ Sun, 03 Jun 2018 13:17:46: 17000000 INFO @ Sun, 03 Jun 2018 13:17:47: 16000000 INFO @ Sun, 03 Jun 2018 13:17:47: 16000000 INFO @ Sun, 03 Jun 2018 13:17:52: 18000000 INFO @ Sun, 03 Jun 2018 13:17:53: 17000000 INFO @ Sun, 03 Jun 2018 13:17:53: 17000000 INFO @ Sun, 03 Jun 2018 13:17:58: 19000000 INFO @ Sun, 03 Jun 2018 13:18:00: 18000000 INFO @ Sun, 03 Jun 2018 13:18:00: 18000000 INFO @ Sun, 03 Jun 2018 13:18:04: 20000000 INFO @ Sun, 03 Jun 2018 13:18:06: 19000000 INFO @ Sun, 03 Jun 2018 13:18:06: 19000000 INFO @ Sun, 03 Jun 2018 13:18:10: 21000000 INFO @ Sun, 03 Jun 2018 13:18:12: 20000000 INFO @ Sun, 03 Jun 2018 13:18:12: 20000000 INFO @ Sun, 03 Jun 2018 13:18:17: 22000000 INFO @ Sun, 03 Jun 2018 13:18:19: 21000000 INFO @ Sun, 03 Jun 2018 13:18:19: 21000000 INFO @ Sun, 03 Jun 2018 13:18:23: 23000000 INFO @ Sun, 03 Jun 2018 13:18:25: 22000000 INFO @ Sun, 03 Jun 2018 13:18:25: 22000000 INFO @ Sun, 03 Jun 2018 13:18:29: 24000000 INFO @ Sun, 03 Jun 2018 13:18:32: 23000000 INFO @ Sun, 03 Jun 2018 13:18:32: 23000000 INFO @ Sun, 03 Jun 2018 13:18:35: 25000000 INFO @ Sun, 03 Jun 2018 13:18:38: 24000000 INFO @ Sun, 03 Jun 2018 13:18:38: 24000000 INFO @ Sun, 03 Jun 2018 13:18:41: 26000000 INFO @ Sun, 03 Jun 2018 13:18:44: 25000000 INFO @ Sun, 03 Jun 2018 13:18:45: 25000000 INFO @ Sun, 03 Jun 2018 13:18:47: 27000000 INFO @ Sun, 03 Jun 2018 13:18:51: 26000000 INFO @ Sun, 03 Jun 2018 13:18:51: 26000000 INFO @ Sun, 03 Jun 2018 13:18:53: 28000000 INFO @ Sun, 03 Jun 2018 13:18:57: 27000000 INFO @ Sun, 03 Jun 2018 13:18:57: 27000000 INFO @ Sun, 03 Jun 2018 13:18:59: 29000000 INFO @ Sun, 03 Jun 2018 13:19:04: 28000000 INFO @ Sun, 03 Jun 2018 13:19:04: 28000000 INFO @ Sun, 03 Jun 2018 13:19:05: 30000000 INFO @ Sun, 03 Jun 2018 13:19:10: 29000000 INFO @ Sun, 03 Jun 2018 13:19:10: 29000000 INFO @ Sun, 03 Jun 2018 13:19:11: 31000000 INFO @ Sun, 03 Jun 2018 13:19:16: 30000000 INFO @ Sun, 03 Jun 2018 13:19:17: 30000000 INFO @ Sun, 03 Jun 2018 13:19:17: 32000000 INFO @ Sun, 03 Jun 2018 13:19:23: 31000000 INFO @ Sun, 03 Jun 2018 13:19:23: 31000000 INFO @ Sun, 03 Jun 2018 13:19:24: 33000000 INFO @ Sun, 03 Jun 2018 13:19:28: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:28: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:28: #1 total tags in treatment: 14889871 INFO @ Sun, 03 Jun 2018 13:19:28: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:19:28: #1 tags after filtering in treatment: 12900734 INFO @ Sun, 03 Jun 2018 13:19:28: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:19:28: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:28: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:29: #2 number of paired peaks: 296 WARNING @ Sun, 03 Jun 2018 13:19:29: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:29: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:29: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:29: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:29: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:29: #2 predicted fragment length is 98 bps INFO @ Sun, 03 Jun 2018 13:19:29: #2 alternative fragment length(s) may be 3,76,98,115 bps INFO @ Sun, 03 Jun 2018 13:19:29: #2.2 Generate R script for model : SRX4085383.20_model.r WARNING @ Sun, 03 Jun 2018 13:19:29: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:29: #2 You may need to consider one of the other alternative d(s): 3,76,98,115 WARNING @ Sun, 03 Jun 2018 13:19:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:19:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:30: 32000000 INFO @ Sun, 03 Jun 2018 13:19:30: 32000000 INFO @ Sun, 03 Jun 2018 13:19:36: 33000000 INFO @ Sun, 03 Jun 2018 13:19:36: 33000000 INFO @ Sun, 03 Jun 2018 13:19:40: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:40: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:40: #1 total tags in treatment: 14889871 INFO @ Sun, 03 Jun 2018 13:19:40: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:19:40: #1 tags after filtering in treatment: 12900734 INFO @ Sun, 03 Jun 2018 13:19:40: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:19:40: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:40: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:40: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:40: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:40: #1 total tags in treatment: 14889871 INFO @ Sun, 03 Jun 2018 13:19:40: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:19:41: #1 tags after filtering in treatment: 12900734 INFO @ Sun, 03 Jun 2018 13:19:41: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:19:41: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:41: #2 number of paired peaks: 296 WARNING @ Sun, 03 Jun 2018 13:19:41: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:41: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:41: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:41: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:41: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:41: #2 predicted fragment length is 98 bps INFO @ Sun, 03 Jun 2018 13:19:41: #2 alternative fragment length(s) may be 3,76,98,115 bps INFO @ Sun, 03 Jun 2018 13:19:41: #2.2 Generate R script for model : SRX4085383.05_model.r WARNING @ Sun, 03 Jun 2018 13:19:41: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:41: #2 You may need to consider one of the other alternative d(s): 3,76,98,115 WARNING @ Sun, 03 Jun 2018 13:19:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:19:41: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:41: #2 number of paired peaks: 296 WARNING @ Sun, 03 Jun 2018 13:19:41: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:41: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:42: #2 predicted fragment length is 98 bps INFO @ Sun, 03 Jun 2018 13:19:42: #2 alternative fragment length(s) may be 3,76,98,115 bps INFO @ Sun, 03 Jun 2018 13:19:42: #2.2 Generate R script for model : SRX4085383.10_model.r WARNING @ Sun, 03 Jun 2018 13:19:42: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:42: #2 You may need to consider one of the other alternative d(s): 3,76,98,115 WARNING @ Sun, 03 Jun 2018 13:19:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:19:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:10: #4 Write output xls file... SRX4085383.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:20:10: #4 Write peak in narrowPeak format file... SRX4085383.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:20:10: #4 Write summits bed file... SRX4085383.20_summits.bed INFO @ Sun, 03 Jun 2018 13:20:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (277 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:20:21: #4 Write output xls file... SRX4085383.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:20:21: #4 Write peak in narrowPeak format file... SRX4085383.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:20:21: #4 Write summits bed file... SRX4085383.10_summits.bed INFO @ Sun, 03 Jun 2018 13:20:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (607 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:20:22: #4 Write output xls file... SRX4085383.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:20:22: #4 Write peak in narrowPeak format file... SRX4085383.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:20:22: #4 Write summits bed file... SRX4085383.05_summits.bed INFO @ Sun, 03 Jun 2018 13:20:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1158 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。