Job ID = 10320325 sra ファイルのダウンロード中... Completed: 428642K bytes transferred in 59 seconds (58596K 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... Written 12336907 spots for /home/okishinya/chipatlas/results/ce10/SRX3043416/SRR5875900.sra Written 12336907 spots total 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:27 12336907 reads; of these: 12336907 (100.00%) were unpaired; of these: 3504414 (28.41%) aligned 0 times 7604035 (61.64%) aligned exactly 1 time 1228458 (9.96%) aligned >1 times 71.59% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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_rmdupse_core] 952109 / 8832493 = 0.1078 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 @ Thu, 11 Jan 2018 02:11:59: # Command line: callpeak -t SRX3043416.bam -f BAM -g ce -n SRX3043416.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043416.05 # format = BAM # ChIP-seq file = ['SRX3043416.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 @ Thu, 11 Jan 2018 02:11:59: # Command line: callpeak -t SRX3043416.bam -f BAM -g ce -n SRX3043416.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043416.20 # format = BAM # ChIP-seq file = ['SRX3043416.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 @ Thu, 11 Jan 2018 02:11:59: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:11:59: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:11:59: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:11:59: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:11:59: # Command line: callpeak -t SRX3043416.bam -f BAM -g ce -n SRX3043416.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043416.10 # format = BAM # ChIP-seq file = ['SRX3043416.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 @ Thu, 11 Jan 2018 02:11:59: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:11:59: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:12:06: 1000000 INFO @ Thu, 11 Jan 2018 02:12:06: 1000000 INFO @ Thu, 11 Jan 2018 02:12:06: 1000000 INFO @ Thu, 11 Jan 2018 02:12:14: 2000000 INFO @ Thu, 11 Jan 2018 02:12:14: 2000000 INFO @ Thu, 11 Jan 2018 02:12:14: 2000000 INFO @ Thu, 11 Jan 2018 02:12:21: 3000000 INFO @ Thu, 11 Jan 2018 02:12:21: 3000000 INFO @ Thu, 11 Jan 2018 02:12:21: 3000000 INFO @ Thu, 11 Jan 2018 02:12:28: 4000000 INFO @ Thu, 11 Jan 2018 02:12:28: 4000000 INFO @ Thu, 11 Jan 2018 02:12:28: 4000000 INFO @ Thu, 11 Jan 2018 02:12:35: 5000000 INFO @ Thu, 11 Jan 2018 02:12:36: 5000000 INFO @ Thu, 11 Jan 2018 02:12:36: 5000000 INFO @ Thu, 11 Jan 2018 02:12:42: 6000000 INFO @ Thu, 11 Jan 2018 02:12:43: 6000000 INFO @ Thu, 11 Jan 2018 02:12:43: 6000000 INFO @ Thu, 11 Jan 2018 02:12:49: 7000000 INFO @ Thu, 11 Jan 2018 02:12:50: 7000000 INFO @ Thu, 11 Jan 2018 02:12:50: 7000000 INFO @ Thu, 11 Jan 2018 02:12:55: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:12:55: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:12:55: #1 total tags in treatment: 7880384 INFO @ Thu, 11 Jan 2018 02:12:55: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:12:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:12:55: #1 tags after filtering in treatment: 7880384 INFO @ Thu, 11 Jan 2018 02:12:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:12:55: #1 finished! INFO @ Thu, 11 Jan 2018 02:12:55: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:12:56: #2 number of paired peaks: 195 WARNING @ Thu, 11 Jan 2018 02:12:56: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Thu, 11 Jan 2018 02:12:56: start model_add_line... INFO @ Thu, 11 Jan 2018 02:12:56: start X-correlation... INFO @ Thu, 11 Jan 2018 02:12:56: end of X-cor INFO @ Thu, 11 Jan 2018 02:12:56: #2 finished! INFO @ Thu, 11 Jan 2018 02:12:56: #2 predicted fragment length is 53 bps INFO @ Thu, 11 Jan 2018 02:12:56: #2 alternative fragment length(s) may be 2,53,190,486,542,564 bps INFO @ Thu, 11 Jan 2018 02:12:56: #2.2 Generate R script for model : SRX3043416.20_model.r WARNING @ Thu, 11 Jan 2018 02:12:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:12:56: #2 You may need to consider one of the other alternative d(s): 2,53,190,486,542,564 WARNING @ Thu, 11 Jan 2018 02:12:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:12:56: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:12:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:12:57: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:12:57: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:12:57: #1 total tags in treatment: 7880384 INFO @ Thu, 11 Jan 2018 02:12:57: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:12:57: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:12:57: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:12:57: #1 total tags in treatment: 7880384 INFO @ Thu, 11 Jan 2018 02:12:57: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:12:57: #1 tags after filtering in treatment: 7880384 INFO @ Thu, 11 Jan 2018 02:12:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:12:57: #1 finished! INFO @ Thu, 11 Jan 2018 02:12:57: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:12:57: #1 tags after filtering in treatment: 7880384 INFO @ Thu, 11 Jan 2018 02:12:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:12:57: #1 finished! INFO @ Thu, 11 Jan 2018 02:12:57: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:12:57: #2 number of paired peaks: 195 WARNING @ Thu, 11 Jan 2018 02:12:57: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Thu, 11 Jan 2018 02:12:57: start model_add_line... INFO @ Thu, 11 Jan 2018 02:12:57: #2 number of paired peaks: 195 WARNING @ Thu, 11 Jan 2018 02:12:57: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Thu, 11 Jan 2018 02:12:57: start model_add_line... INFO @ Thu, 11 Jan 2018 02:12:57: start X-correlation... INFO @ Thu, 11 Jan 2018 02:12:57: start X-correlation... INFO @ Thu, 11 Jan 2018 02:12:57: end of X-cor INFO @ Thu, 11 Jan 2018 02:12:57: end of X-cor INFO @ Thu, 11 Jan 2018 02:12:57: #2 finished! INFO @ Thu, 11 Jan 2018 02:12:57: #2 finished! INFO @ Thu, 11 Jan 2018 02:12:57: #2 predicted fragment length is 53 bps INFO @ Thu, 11 Jan 2018 02:12:57: #2 predicted fragment length is 53 bps INFO @ Thu, 11 Jan 2018 02:12:57: #2 alternative fragment length(s) may be 2,53,190,486,542,564 bps INFO @ Thu, 11 Jan 2018 02:12:57: #2 alternative fragment length(s) may be 2,53,190,486,542,564 bps INFO @ Thu, 11 Jan 2018 02:12:57: #2.2 Generate R script for model : SRX3043416.05_model.r INFO @ Thu, 11 Jan 2018 02:12:57: #2.2 Generate R script for model : SRX3043416.10_model.r WARNING @ Thu, 11 Jan 2018 02:12:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:12:57: #2 You may need to consider one of the other alternative d(s): 2,53,190,486,542,564 WARNING @ Thu, 11 Jan 2018 02:12:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:12:57: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:12:57: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 11 Jan 2018 02:12:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:12:58: #2 You may need to consider one of the other alternative d(s): 2,53,190,486,542,564 WARNING @ Thu, 11 Jan 2018 02:12:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:12:58: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:13:13: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:13:14: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:13:16: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:13:22: #4 Write output xls file... SRX3043416.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:13:22: #4 Write peak in narrowPeak format file... SRX3043416.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:13:22: #4 Write summits bed file... SRX3043416.20_summits.bed INFO @ Thu, 11 Jan 2018 02:13:22: Done! INFO @ Thu, 11 Jan 2018 02:13:22: #4 Write output xls file... SRX3043416.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:13:22: #4 Write peak in narrowPeak format file... SRX3043416.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:13:22: #4 Write summits bed file... SRX3043416.05_summits.bed INFO @ Thu, 11 Jan 2018 02:13:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:13:24: #4 Write output xls file... SRX3043416.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:13:24: #4 Write peak in narrowPeak format file... SRX3043416.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:13:24: #4 Write summits bed file... SRX3043416.10_summits.bed INFO @ Thu, 11 Jan 2018 02:13:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (238 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。