Job ID = 10714524 sra ファイルのダウンロード中... Completed: 1386962K bytes transferred in 20 seconds (564069K 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 20859226 spots for /home/okishinya/chipatlas/results/ce10/SRX4085439/SRR7167468.sra Written 20859226 spots for /home/okishinya/chipatlas/results/ce10/SRX4085439/SRR7167468.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: 00:17:43 20859226 reads; of these: 20859226 (100.00%) were paired; of these: 8036549 (38.53%) aligned concordantly 0 times 10403629 (49.88%) aligned concordantly exactly 1 time 2419048 (11.60%) aligned concordantly >1 times ---- 8036549 pairs aligned concordantly 0 times; of these: 256836 (3.20%) aligned discordantly 1 time ---- 7779713 pairs aligned 0 times concordantly or discordantly; of these: 15559426 mates make up the pairs; of these: 11922105 (76.62%) aligned 0 times 3207407 (20.61%) aligned exactly 1 time 429914 (2.76%) aligned >1 times 71.42% overall alignment rate Time searching: 00:17:43 Overall time: 00:17:43 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] 1809229 / 12989991 = 0.1393 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 13:36:11: # Command line: callpeak -t SRX4085439.bam -f BAM -g ce -n SRX4085439.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085439.05 # format = BAM # ChIP-seq file = ['SRX4085439.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 13:36:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:11: # Command line: callpeak -t SRX4085439.bam -f BAM -g ce -n SRX4085439.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085439.20 # format = BAM # ChIP-seq file = ['SRX4085439.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 13:36:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:11: # Command line: callpeak -t SRX4085439.bam -f BAM -g ce -n SRX4085439.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085439.10 # format = BAM # ChIP-seq file = ['SRX4085439.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 13:36:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:17: 1000000 INFO @ Sun, 03 Jun 2018 13:36:18: 1000000 INFO @ Sun, 03 Jun 2018 13:36:18: 1000000 INFO @ Sun, 03 Jun 2018 13:36:24: 2000000 INFO @ Sun, 03 Jun 2018 13:36:24: 2000000 INFO @ Sun, 03 Jun 2018 13:36:24: 2000000 INFO @ Sun, 03 Jun 2018 13:36:30: 3000000 INFO @ Sun, 03 Jun 2018 13:36:31: 3000000 INFO @ Sun, 03 Jun 2018 13:36:31: 3000000 INFO @ Sun, 03 Jun 2018 13:36:37: 4000000 INFO @ Sun, 03 Jun 2018 13:36:37: 4000000 INFO @ Sun, 03 Jun 2018 13:36:37: 4000000 INFO @ Sun, 03 Jun 2018 13:36:43: 5000000 INFO @ Sun, 03 Jun 2018 13:36:43: 5000000 INFO @ Sun, 03 Jun 2018 13:36:43: 5000000 INFO @ Sun, 03 Jun 2018 13:36:49: 6000000 INFO @ Sun, 03 Jun 2018 13:36:50: 6000000 INFO @ Sun, 03 Jun 2018 13:36:50: 6000000 INFO @ Sun, 03 Jun 2018 13:36:56: 7000000 INFO @ Sun, 03 Jun 2018 13:36:56: 7000000 INFO @ Sun, 03 Jun 2018 13:36:56: 7000000 INFO @ Sun, 03 Jun 2018 13:37:02: 8000000 INFO @ Sun, 03 Jun 2018 13:37:03: 8000000 INFO @ Sun, 03 Jun 2018 13:37:03: 8000000 INFO @ Sun, 03 Jun 2018 13:37:08: 9000000 INFO @ Sun, 03 Jun 2018 13:37:09: 9000000 INFO @ Sun, 03 Jun 2018 13:37:09: 9000000 INFO @ Sun, 03 Jun 2018 13:37:15: 10000000 INFO @ Sun, 03 Jun 2018 13:37:16: 10000000 INFO @ Sun, 03 Jun 2018 13:37:16: 10000000 INFO @ Sun, 03 Jun 2018 13:37:21: 11000000 INFO @ Sun, 03 Jun 2018 13:37:22: 11000000 INFO @ Sun, 03 Jun 2018 13:37:22: 11000000 INFO @ Sun, 03 Jun 2018 13:37:27: 12000000 INFO @ Sun, 03 Jun 2018 13:37:29: 12000000 INFO @ Sun, 03 Jun 2018 13:37:29: 12000000 INFO @ Sun, 03 Jun 2018 13:37:34: 13000000 INFO @ Sun, 03 Jun 2018 13:37:35: 13000000 INFO @ Sun, 03 Jun 2018 13:37:35: 13000000 INFO @ Sun, 03 Jun 2018 13:37:41: 14000000 INFO @ Sun, 03 Jun 2018 13:37:41: 14000000 INFO @ Sun, 03 Jun 2018 13:37:42: 14000000 INFO @ Sun, 03 Jun 2018 13:37:47: 15000000 INFO @ Sun, 03 Jun 2018 13:37:48: 15000000 INFO @ Sun, 03 Jun 2018 13:37:49: 15000000 INFO @ Sun, 03 Jun 2018 13:37:54: 16000000 INFO @ Sun, 03 Jun 2018 13:37:54: 16000000 INFO @ Sun, 03 Jun 2018 13:37:56: 16000000 INFO @ Sun, 03 Jun 2018 13:38:00: 17000000 INFO @ Sun, 03 Jun 2018 13:38:01: 17000000 INFO @ Sun, 03 Jun 2018 13:38:03: 17000000 INFO @ Sun, 03 Jun 2018 13:38:06: 18000000 INFO @ Sun, 03 Jun 2018 13:38:08: 18000000 INFO @ Sun, 03 Jun 2018 13:38:10: 18000000 INFO @ Sun, 03 Jun 2018 13:38:13: 19000000 INFO @ Sun, 03 Jun 2018 13:38:14: 19000000 INFO @ Sun, 03 Jun 2018 13:38:17: 19000000 INFO @ Sun, 03 Jun 2018 13:38:20: 20000000 INFO @ Sun, 03 Jun 2018 13:38:20: 20000000 INFO @ Sun, 03 Jun 2018 13:38:24: 20000000 INFO @ Sun, 03 Jun 2018 13:38:27: 21000000 INFO @ Sun, 03 Jun 2018 13:38:27: 21000000 INFO @ Sun, 03 Jun 2018 13:38:31: 21000000 INFO @ Sun, 03 Jun 2018 13:38:33: 22000000 INFO @ Sun, 03 Jun 2018 13:38:33: 22000000 INFO @ Sun, 03 Jun 2018 13:38:37: 22000000 INFO @ Sun, 03 Jun 2018 13:38:40: 23000000 INFO @ Sun, 03 Jun 2018 13:38:40: 23000000 INFO @ Sun, 03 Jun 2018 13:38:44: 23000000 INFO @ Sun, 03 Jun 2018 13:38:46: 24000000 INFO @ Sun, 03 Jun 2018 13:38:47: 24000000 INFO @ Sun, 03 Jun 2018 13:38:50: 24000000 INFO @ Sun, 03 Jun 2018 13:38:52: 25000000 INFO @ Sun, 03 Jun 2018 13:38:53: 25000000 INFO @ Sun, 03 Jun 2018 13:38:56: 25000000 INFO @ Sun, 03 Jun 2018 13:38:58: 26000000 INFO @ Sun, 03 Jun 2018 13:38:59: 26000000 INFO @ Sun, 03 Jun 2018 13:38:59: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:38:59: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:38:59: #1 total tags in treatment: 11029983 INFO @ Sun, 03 Jun 2018 13:38:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:38:59: #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 13:38:59: #1 tags after filtering in treatment: 9106035 INFO @ Sun, 03 Jun 2018 13:38:59: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:38:59: #1 finished! INFO @ Sun, 03 Jun 2018 13:38:59: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:00: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:00: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:00: #1 total tags in treatment: 11029983 INFO @ Sun, 03 Jun 2018 13:39:00: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:00: #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 13:39:00: #1 tags after filtering in treatment: 9106035 INFO @ Sun, 03 Jun 2018 13:39:00: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:39:00: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:00: #2 number of paired peaks: 431 WARNING @ Sun, 03 Jun 2018 13:39:00: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:00: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:00: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:00: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:00: #2 predicted fragment length is 97 bps INFO @ Sun, 03 Jun 2018 13:39:00: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 03 Jun 2018 13:39:00: #2.2 Generate R script for model : SRX4085439.10_model.r WARNING @ Sun, 03 Jun 2018 13:39:00: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:39:00: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 03 Jun 2018 13:39:00: #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 13:39:00: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:00: #2 number of paired peaks: 431 WARNING @ Sun, 03 Jun 2018 13:39:00: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:01: #2 predicted fragment length is 97 bps INFO @ Sun, 03 Jun 2018 13:39:01: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 03 Jun 2018 13:39:01: #2.2 Generate R script for model : SRX4085439.05_model.r WARNING @ Sun, 03 Jun 2018 13:39:01: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:39:01: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 03 Jun 2018 13:39:01: #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 13:39:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:01: 26000000 INFO @ Sun, 03 Jun 2018 13:39:02: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:02: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:02: #1 total tags in treatment: 11029983 INFO @ Sun, 03 Jun 2018 13:39:02: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:02: #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 13:39:03: #1 tags after filtering in treatment: 9106035 INFO @ Sun, 03 Jun 2018 13:39:03: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:39:03: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:03: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:03: #2 number of paired peaks: 431 WARNING @ Sun, 03 Jun 2018 13:39:03: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:03: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:03: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:03: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:03: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:03: #2 predicted fragment length is 97 bps INFO @ Sun, 03 Jun 2018 13:39:03: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 03 Jun 2018 13:39:03: #2.2 Generate R script for model : SRX4085439.20_model.r WARNING @ Sun, 03 Jun 2018 13:39:03: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:39:03: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 03 Jun 2018 13:39:03: #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 13:39:03: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:32: #4 Write output xls file... SRX4085439.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:32: #4 Write peak in narrowPeak format file... SRX4085439.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:39:32: #4 Write summits bed file... SRX4085439.05_summits.bed INFO @ Sun, 03 Jun 2018 13:39:32: Done! INFO @ Sun, 03 Jun 2018 13:39:32: #4 Write output xls file... SRX4085439.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:32: #4 Write peak in narrowPeak format file... SRX4085439.10_peaks.narrowPeak pass1 - making usageList (7 chroms): 1 millis INFO @ Sun, 03 Jun 2018 13:39:32: #4 Write summits bed file... SRX4085439.10_summits.bed pass2 - checking and writing primary data (4523 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:39:32: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (2666 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:39:34: #4 Write output xls file... SRX4085439.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:34: #4 Write peak in narrowPeak format file... SRX4085439.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:39:34: #4 Write summits bed file... SRX4085439.20_summits.bed INFO @ Sun, 03 Jun 2018 13:39:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1229 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。