Job ID = 10714392 sra ファイルのダウンロード中... Completed: 398552K bytes transferred in 10 seconds (306657K 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 14054183 spots for /home/okishinya/chipatlas/results/ce10/SRX4082352/SRR7164170.sra Written 14054183 spots for /home/okishinya/chipatlas/results/ce10/SRX4082352/SRR7164170.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: 00:03:32 14054183 reads; of these: 14054183 (100.00%) were unpaired; of these: 231918 (1.65%) aligned 0 times 11969032 (85.16%) aligned exactly 1 time 1853233 (13.19%) aligned >1 times 98.35% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:33 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 8 files... [bam_rmdupse_core] 1519388 / 13822265 = 0.1099 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 12:35:47: # Command line: callpeak -t SRX4082352.bam -f BAM -g ce -n SRX4082352.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082352.20 # format = BAM # ChIP-seq file = ['SRX4082352.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 12:35:47: # Command line: callpeak -t SRX4082352.bam -f BAM -g ce -n SRX4082352.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082352.05 # format = BAM # ChIP-seq file = ['SRX4082352.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 12:35:47: # Command line: callpeak -t SRX4082352.bam -f BAM -g ce -n SRX4082352.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082352.10 # format = BAM # ChIP-seq file = ['SRX4082352.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 12:35:47: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:47: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:47: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:47: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:47: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:47: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:53: 1000000 INFO @ Sun, 03 Jun 2018 12:35:53: 1000000 INFO @ Sun, 03 Jun 2018 12:35:54: 1000000 INFO @ Sun, 03 Jun 2018 12:35:59: 2000000 INFO @ Sun, 03 Jun 2018 12:36:00: 2000000 INFO @ Sun, 03 Jun 2018 12:36:02: 2000000 INFO @ Sun, 03 Jun 2018 12:36:06: 3000000 INFO @ Sun, 03 Jun 2018 12:36:07: 3000000 INFO @ Sun, 03 Jun 2018 12:36:10: 3000000 INFO @ Sun, 03 Jun 2018 12:36:14: 4000000 INFO @ Sun, 03 Jun 2018 12:36:15: 4000000 INFO @ Sun, 03 Jun 2018 12:36:18: 4000000 INFO @ Sun, 03 Jun 2018 12:36:21: 5000000 INFO @ Sun, 03 Jun 2018 12:36:24: 5000000 INFO @ Sun, 03 Jun 2018 12:36:26: 5000000 INFO @ Sun, 03 Jun 2018 12:36:27: 6000000 INFO @ Sun, 03 Jun 2018 12:36:33: 6000000 INFO @ Sun, 03 Jun 2018 12:36:34: 6000000 INFO @ Sun, 03 Jun 2018 12:36:34: 7000000 INFO @ Sun, 03 Jun 2018 12:36:40: 8000000 INFO @ Sun, 03 Jun 2018 12:36:41: 7000000 INFO @ Sun, 03 Jun 2018 12:36:41: 7000000 INFO @ Sun, 03 Jun 2018 12:36:49: 9000000 INFO @ Sun, 03 Jun 2018 12:36:49: 8000000 INFO @ Sun, 03 Jun 2018 12:36:51: 8000000 INFO @ Sun, 03 Jun 2018 12:36:57: 9000000 INFO @ Sun, 03 Jun 2018 12:36:57: 10000000 INFO @ Sun, 03 Jun 2018 12:36:58: 9000000 INFO @ Sun, 03 Jun 2018 12:37:04: 10000000 INFO @ Sun, 03 Jun 2018 12:37:05: 11000000 INFO @ Sun, 03 Jun 2018 12:37:06: 10000000 INFO @ Sun, 03 Jun 2018 12:37:11: 11000000 INFO @ Sun, 03 Jun 2018 12:37:13: 12000000 INFO @ Sun, 03 Jun 2018 12:37:14: 11000000 INFO @ Sun, 03 Jun 2018 12:37:15: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:15: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:15: #1 total tags in treatment: 12302877 INFO @ Sun, 03 Jun 2018 12:37:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:15: #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 12:37:15: #1 tags after filtering in treatment: 12302877 INFO @ Sun, 03 Jun 2018 12:37:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:15: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:16: #2 number of paired peaks: 117 WARNING @ Sun, 03 Jun 2018 12:37:16: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sun, 03 Jun 2018 12:37:16: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:16: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:17: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:17: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:17: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:37:17: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 03 Jun 2018 12:37:17: #2.2 Generate R script for model : SRX4082352.05_model.r WARNING @ Sun, 03 Jun 2018 12:37:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:37:17: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 03 Jun 2018 12:37:17: #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 12:37:17: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:18: 12000000 INFO @ Sun, 03 Jun 2018 12:37:20: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:20: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:20: #1 total tags in treatment: 12302877 INFO @ Sun, 03 Jun 2018 12:37:20: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:20: #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 12:37:20: #1 tags after filtering in treatment: 12302877 INFO @ Sun, 03 Jun 2018 12:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:20: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:20: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:20: 12000000 INFO @ Sun, 03 Jun 2018 12:37:21: #2 number of paired peaks: 117 WARNING @ Sun, 03 Jun 2018 12:37:21: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sun, 03 Jun 2018 12:37:21: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:21: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:21: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:21: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:21: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:37:21: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 03 Jun 2018 12:37:21: #2.2 Generate R script for model : SRX4082352.20_model.r WARNING @ Sun, 03 Jun 2018 12:37:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:37:21: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 03 Jun 2018 12:37:21: #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 12:37:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:22: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:22: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:22: #1 total tags in treatment: 12302877 INFO @ Sun, 03 Jun 2018 12:37:22: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:22: #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 12:37:22: #1 tags after filtering in treatment: 12302877 INFO @ Sun, 03 Jun 2018 12:37:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:22: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:22: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:23: #2 number of paired peaks: 117 WARNING @ Sun, 03 Jun 2018 12:37:23: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sun, 03 Jun 2018 12:37:23: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:23: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:23: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:23: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:23: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:37:23: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 03 Jun 2018 12:37:23: #2.2 Generate R script for model : SRX4082352.10_model.r WARNING @ Sun, 03 Jun 2018 12:37:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:37:23: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 03 Jun 2018 12:37:23: #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 12:37:23: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:41: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:54: #4 Write output xls file... SRX4082352.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:54: #4 Write peak in narrowPeak format file... SRX4082352.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:54: #4 Write summits bed file... SRX4082352.05_summits.bed INFO @ Sun, 03 Jun 2018 12:37:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:59: #4 Write output xls file... SRX4082352.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:59: #4 Write peak in narrowPeak format file... SRX4082352.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:59: #4 Write summits bed file... SRX4082352.20_summits.bed INFO @ Sun, 03 Jun 2018 12:37:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:04: #4 Write output xls file... SRX4082352.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:04: #4 Write peak in narrowPeak format file... SRX4082352.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:04: #4 Write summits bed file... SRX4082352.10_summits.bed INFO @ Sun, 03 Jun 2018 12:38:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。