Job ID = 10845155 sra ファイルのダウンロード中... Completed: 1399045K bytes transferred in 91 seconds (125843K 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: SINGLE fastq に変換中... Read 27801818 spots for /home/okishinya/chipatlas/results/ce10/SRX2973395/SRR5786974.sra Written 27801818 spots for /home/okishinya/chipatlas/results/ce10/SRX2973395/SRR5786974.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: 00:15:20 27801818 reads; of these: 27801818 (100.00%) were unpaired; of these: 962121 (3.46%) aligned 0 times 22479986 (80.86%) aligned exactly 1 time 4359711 (15.68%) aligned >1 times 96.54% overall alignment rate Time searching: 00:15:20 Overall time: 00:15:20 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 12 files... [bam_rmdupse_core] 3122488 / 26839697 = 0.1163 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, 04 Jul 2018 09:53:27: # Command line: callpeak -t SRX2973395.bam -f BAM -g ce -n SRX2973395.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2973395.10 # format = BAM # ChIP-seq file = ['SRX2973395.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, 04 Jul 2018 09:53:27: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:53:27: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:53:27: # Command line: callpeak -t SRX2973395.bam -f BAM -g ce -n SRX2973395.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2973395.20 # format = BAM # ChIP-seq file = ['SRX2973395.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, 04 Jul 2018 09:53:27: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:53:27: # Command line: callpeak -t SRX2973395.bam -f BAM -g ce -n SRX2973395.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2973395.05 # format = BAM # ChIP-seq file = ['SRX2973395.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, 04 Jul 2018 09:53:27: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:53:27: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:53:27: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:53:37: 1000000 INFO @ Wed, 04 Jul 2018 09:53:37: 1000000 INFO @ Wed, 04 Jul 2018 09:53:37: 1000000 INFO @ Wed, 04 Jul 2018 09:53:46: 2000000 INFO @ Wed, 04 Jul 2018 09:53:46: 2000000 INFO @ Wed, 04 Jul 2018 09:53:46: 2000000 INFO @ Wed, 04 Jul 2018 09:53:55: 3000000 INFO @ Wed, 04 Jul 2018 09:53:55: 3000000 INFO @ Wed, 04 Jul 2018 09:53:55: 3000000 INFO @ Wed, 04 Jul 2018 09:54:04: 4000000 INFO @ Wed, 04 Jul 2018 09:54:05: 4000000 INFO @ Wed, 04 Jul 2018 09:54:05: 4000000 INFO @ Wed, 04 Jul 2018 09:54:13: 5000000 INFO @ Wed, 04 Jul 2018 09:54:14: 5000000 INFO @ Wed, 04 Jul 2018 09:54:14: 5000000 INFO @ Wed, 04 Jul 2018 09:54:23: 6000000 INFO @ Wed, 04 Jul 2018 09:54:23: 6000000 INFO @ Wed, 04 Jul 2018 09:54:23: 6000000 INFO @ Wed, 04 Jul 2018 09:54:32: 7000000 INFO @ Wed, 04 Jul 2018 09:54:32: 7000000 INFO @ Wed, 04 Jul 2018 09:54:32: 7000000 INFO @ Wed, 04 Jul 2018 09:54:41: 8000000 INFO @ Wed, 04 Jul 2018 09:54:42: 8000000 INFO @ Wed, 04 Jul 2018 09:54:42: 8000000 INFO @ Wed, 04 Jul 2018 09:54:50: 9000000 INFO @ Wed, 04 Jul 2018 09:54:51: 9000000 INFO @ Wed, 04 Jul 2018 09:54:51: 9000000 INFO @ Wed, 04 Jul 2018 09:54:59: 10000000 INFO @ Wed, 04 Jul 2018 09:55:00: 10000000 INFO @ Wed, 04 Jul 2018 09:55:00: 10000000 INFO @ Wed, 04 Jul 2018 09:55:08: 11000000 INFO @ Wed, 04 Jul 2018 09:55:09: 11000000 INFO @ Wed, 04 Jul 2018 09:55:09: 11000000 INFO @ Wed, 04 Jul 2018 09:55:17: 12000000 INFO @ Wed, 04 Jul 2018 09:55:18: 12000000 INFO @ Wed, 04 Jul 2018 09:55:19: 12000000 INFO @ Wed, 04 Jul 2018 09:55:26: 13000000 INFO @ Wed, 04 Jul 2018 09:55:28: 13000000 INFO @ Wed, 04 Jul 2018 09:55:28: 13000000 INFO @ Wed, 04 Jul 2018 09:55:35: 14000000 INFO @ Wed, 04 Jul 2018 09:55:37: 14000000 INFO @ Wed, 04 Jul 2018 09:55:37: 14000000 INFO @ Wed, 04 Jul 2018 09:55:44: 15000000 INFO @ Wed, 04 Jul 2018 09:55:46: 15000000 INFO @ Wed, 04 Jul 2018 09:55:47: 15000000 INFO @ Wed, 04 Jul 2018 09:55:53: 16000000 INFO @ Wed, 04 Jul 2018 09:55:56: 16000000 INFO @ Wed, 04 Jul 2018 09:55:56: 16000000 INFO @ Wed, 04 Jul 2018 09:56:02: 17000000 INFO @ Wed, 04 Jul 2018 09:56:05: 17000000 INFO @ Wed, 04 Jul 2018 09:56:05: 17000000 INFO @ Wed, 04 Jul 2018 09:56:11: 18000000 INFO @ Wed, 04 Jul 2018 09:56:14: 18000000 INFO @ Wed, 04 Jul 2018 09:56:14: 18000000 INFO @ Wed, 04 Jul 2018 09:56:20: 19000000 INFO @ Wed, 04 Jul 2018 09:56:23: 19000000 INFO @ Wed, 04 Jul 2018 09:56:23: 19000000 INFO @ Wed, 04 Jul 2018 09:56:29: 20000000 INFO @ Wed, 04 Jul 2018 09:56:33: 20000000 INFO @ Wed, 04 Jul 2018 09:56:33: 20000000 INFO @ Wed, 04 Jul 2018 09:56:38: 21000000 INFO @ Wed, 04 Jul 2018 09:56:42: 21000000 INFO @ Wed, 04 Jul 2018 09:56:42: 21000000 INFO @ Wed, 04 Jul 2018 09:56:47: 22000000 INFO @ Wed, 04 Jul 2018 09:56:52: 22000000 INFO @ Wed, 04 Jul 2018 09:56:52: 22000000 INFO @ Wed, 04 Jul 2018 09:56:56: 23000000 INFO @ Wed, 04 Jul 2018 09:57:01: 23000000 INFO @ Wed, 04 Jul 2018 09:57:01: 23000000 INFO @ Wed, 04 Jul 2018 09:57:02: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:57:02: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:57:02: #1 total tags in treatment: 23717209 INFO @ Wed, 04 Jul 2018 09:57:02: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:57:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:57:03: #1 tags after filtering in treatment: 23717209 INFO @ Wed, 04 Jul 2018 09:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:57:03: #1 finished! INFO @ Wed, 04 Jul 2018 09:57:03: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:57:04: #2 number of paired peaks: 118 WARNING @ Wed, 04 Jul 2018 09:57:04: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Wed, 04 Jul 2018 09:57:04: start model_add_line... INFO @ Wed, 04 Jul 2018 09:57:05: start X-correlation... INFO @ Wed, 04 Jul 2018 09:57:05: end of X-cor INFO @ Wed, 04 Jul 2018 09:57:05: #2 finished! INFO @ Wed, 04 Jul 2018 09:57:05: #2 predicted fragment length is 96 bps INFO @ Wed, 04 Jul 2018 09:57:05: #2 alternative fragment length(s) may be 2,40,75,96,577 bps INFO @ Wed, 04 Jul 2018 09:57:05: #2.2 Generate R script for model : SRX2973395.10_model.r WARNING @ Wed, 04 Jul 2018 09:57:05: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:57:05: #2 You may need to consider one of the other alternative d(s): 2,40,75,96,577 WARNING @ Wed, 04 Jul 2018 09:57:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:57:05: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:57:08: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:57:08: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:57:08: #1 total tags in treatment: 23717209 INFO @ Wed, 04 Jul 2018 09:57:08: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:57:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:57:08: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:57:08: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:57:08: #1 total tags in treatment: 23717209 INFO @ Wed, 04 Jul 2018 09:57:08: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:57:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:57:08: #1 tags after filtering in treatment: 23717209 INFO @ Wed, 04 Jul 2018 09:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:57:08: #1 finished! INFO @ Wed, 04 Jul 2018 09:57:08: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:57:08: #1 tags after filtering in treatment: 23717209 INFO @ Wed, 04 Jul 2018 09:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:57:08: #1 finished! INFO @ Wed, 04 Jul 2018 09:57:08: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:57:10: #2 number of paired peaks: 118 WARNING @ Wed, 04 Jul 2018 09:57:10: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Wed, 04 Jul 2018 09:57:10: start model_add_line... INFO @ Wed, 04 Jul 2018 09:57:10: #2 number of paired peaks: 118 WARNING @ Wed, 04 Jul 2018 09:57:10: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Wed, 04 Jul 2018 09:57:10: start model_add_line... INFO @ Wed, 04 Jul 2018 09:57:10: start X-correlation... INFO @ Wed, 04 Jul 2018 09:57:10: end of X-cor INFO @ Wed, 04 Jul 2018 09:57:10: #2 finished! INFO @ Wed, 04 Jul 2018 09:57:10: #2 predicted fragment length is 96 bps INFO @ Wed, 04 Jul 2018 09:57:10: #2 alternative fragment length(s) may be 2,40,75,96,577 bps INFO @ Wed, 04 Jul 2018 09:57:10: #2.2 Generate R script for model : SRX2973395.20_model.r WARNING @ Wed, 04 Jul 2018 09:57:10: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:57:10: #2 You may need to consider one of the other alternative d(s): 2,40,75,96,577 WARNING @ Wed, 04 Jul 2018 09:57:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:57:10: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:57:10: start X-correlation... INFO @ Wed, 04 Jul 2018 09:57:10: end of X-cor INFO @ Wed, 04 Jul 2018 09:57:10: #2 finished! INFO @ Wed, 04 Jul 2018 09:57:10: #2 predicted fragment length is 96 bps INFO @ Wed, 04 Jul 2018 09:57:10: #2 alternative fragment length(s) may be 2,40,75,96,577 bps INFO @ Wed, 04 Jul 2018 09:57:10: #2.2 Generate R script for model : SRX2973395.05_model.r WARNING @ Wed, 04 Jul 2018 09:57:10: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:57:10: #2 You may need to consider one of the other alternative d(s): 2,40,75,96,577 WARNING @ Wed, 04 Jul 2018 09:57:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:57:10: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:57:44: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:57:49: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:57:53: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:58:05: #4 Write output xls file... SRX2973395.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:58:05: #4 Write peak in narrowPeak format file... SRX2973395.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:58:05: #4 Write summits bed file... SRX2973395.10_summits.bed INFO @ Wed, 04 Jul 2018 09:58:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (416 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:58:10: #4 Write output xls file... SRX2973395.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:58:10: #4 Write peak in narrowPeak format file... SRX2973395.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:58:10: #4 Write summits bed file... SRX2973395.05_summits.bed INFO @ Wed, 04 Jul 2018 09:58:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (593 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:58:14: #4 Write output xls file... SRX2973395.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:58:14: #4 Write peak in narrowPeak format file... SRX2973395.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:58:14: #4 Write summits bed file... SRX2973395.20_summits.bed INFO @ Wed, 04 Jul 2018 09:58:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (242 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。