Job ID = 11170874 sra ファイルのダウンロード中... Completed: 600436K bytes transferred in 51 seconds (94698K 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 21320060 spots for /home/okishinya/chipatlas/results/ce10/SRX3942555/SRR7010076.sra Written 21320060 spots for /home/okishinya/chipatlas/results/ce10/SRX3942555/SRR7010076.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: 00:07:41 21320060 reads; of these: 21320060 (100.00%) were unpaired; of these: 6002514 (28.15%) aligned 0 times 11425433 (53.59%) aligned exactly 1 time 3892113 (18.26%) aligned >1 times 71.85% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 10506413 / 15317546 = 0.6859 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 @ Sat, 08 Sep 2018 11:38:14: # Command line: callpeak -t SRX3942555.bam -f BAM -g ce -n SRX3942555.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3942555.10 # format = BAM # ChIP-seq file = ['SRX3942555.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 @ Sat, 08 Sep 2018 11:38:14: # Command line: callpeak -t SRX3942555.bam -f BAM -g ce -n SRX3942555.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3942555.20 # format = BAM # ChIP-seq file = ['SRX3942555.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 @ Sat, 08 Sep 2018 11:38:14: # Command line: callpeak -t SRX3942555.bam -f BAM -g ce -n SRX3942555.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3942555.05 # format = BAM # ChIP-seq file = ['SRX3942555.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 @ Sat, 08 Sep 2018 11:38:14: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:38:14: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:38:14: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:38:14: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:14: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:14: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:20: 1000000 INFO @ Sat, 08 Sep 2018 11:38:20: 1000000 INFO @ Sat, 08 Sep 2018 11:38:20: 1000000 INFO @ Sat, 08 Sep 2018 11:38:26: 2000000 INFO @ Sat, 08 Sep 2018 11:38:27: 2000000 INFO @ Sat, 08 Sep 2018 11:38:27: 2000000 INFO @ Sat, 08 Sep 2018 11:38:33: 3000000 INFO @ Sat, 08 Sep 2018 11:38:33: 3000000 INFO @ Sat, 08 Sep 2018 11:38:34: 3000000 INFO @ Sat, 08 Sep 2018 11:38:39: 4000000 INFO @ Sat, 08 Sep 2018 11:38:39: 4000000 INFO @ Sat, 08 Sep 2018 11:38:40: 4000000 INFO @ Sat, 08 Sep 2018 11:38:44: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:38:44: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:38:44: #1 total tags in treatment: 4811133 INFO @ Sat, 08 Sep 2018 11:38:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:38:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:38:44: #1 tags after filtering in treatment: 4811133 INFO @ Sat, 08 Sep 2018 11:38:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:38:44: #1 finished! INFO @ Sat, 08 Sep 2018 11:38:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:38:45: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:38:45: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:38:45: #1 total tags in treatment: 4811133 INFO @ Sat, 08 Sep 2018 11:38:45: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:38:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:38:45: #2 number of paired peaks: 2628 INFO @ Sat, 08 Sep 2018 11:38:45: start model_add_line... INFO @ Sat, 08 Sep 2018 11:38:45: #1 tags after filtering in treatment: 4811133 INFO @ Sat, 08 Sep 2018 11:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:38:45: #1 finished! INFO @ Sat, 08 Sep 2018 11:38:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:38:45: start X-correlation... INFO @ Sat, 08 Sep 2018 11:38:45: end of X-cor INFO @ Sat, 08 Sep 2018 11:38:45: #2 finished! INFO @ Sat, 08 Sep 2018 11:38:45: #2 predicted fragment length is 89 bps INFO @ Sat, 08 Sep 2018 11:38:45: #2 alternative fragment length(s) may be 3,85,89,598 bps INFO @ Sat, 08 Sep 2018 11:38:45: #2.2 Generate R script for model : SRX3942555.20_model.r WARNING @ Sat, 08 Sep 2018 11:38:45: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:38:45: #2 You may need to consider one of the other alternative d(s): 3,85,89,598 WARNING @ Sat, 08 Sep 2018 11:38:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:38:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:38:45: #2 number of paired peaks: 2628 INFO @ Sat, 08 Sep 2018 11:38:45: start model_add_line... INFO @ Sat, 08 Sep 2018 11:38:45: start X-correlation... INFO @ Sat, 08 Sep 2018 11:38:45: end of X-cor INFO @ Sat, 08 Sep 2018 11:38:45: #2 finished! INFO @ Sat, 08 Sep 2018 11:38:45: #2 predicted fragment length is 89 bps INFO @ Sat, 08 Sep 2018 11:38:45: #2 alternative fragment length(s) may be 3,85,89,598 bps INFO @ Sat, 08 Sep 2018 11:38:45: #2.2 Generate R script for model : SRX3942555.05_model.r WARNING @ Sat, 08 Sep 2018 11:38:45: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:38:45: #2 You may need to consider one of the other alternative d(s): 3,85,89,598 WARNING @ Sat, 08 Sep 2018 11:38:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:38:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:38:45: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:38:45: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:38:45: #1 total tags in treatment: 4811133 INFO @ Sat, 08 Sep 2018 11:38:45: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:38:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:38:45: #1 tags after filtering in treatment: 4811133 INFO @ Sat, 08 Sep 2018 11:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:38:45: #1 finished! INFO @ Sat, 08 Sep 2018 11:38:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:38:46: #2 number of paired peaks: 2628 INFO @ Sat, 08 Sep 2018 11:38:46: start model_add_line... INFO @ Sat, 08 Sep 2018 11:38:46: start X-correlation... INFO @ Sat, 08 Sep 2018 11:38:46: end of X-cor INFO @ Sat, 08 Sep 2018 11:38:46: #2 finished! INFO @ Sat, 08 Sep 2018 11:38:46: #2 predicted fragment length is 89 bps INFO @ Sat, 08 Sep 2018 11:38:46: #2 alternative fragment length(s) may be 3,85,89,598 bps INFO @ Sat, 08 Sep 2018 11:38:46: #2.2 Generate R script for model : SRX3942555.10_model.r WARNING @ Sat, 08 Sep 2018 11:38:46: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:38:46: #2 You may need to consider one of the other alternative d(s): 3,85,89,598 WARNING @ Sat, 08 Sep 2018 11:38:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:38:46: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:38:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:38:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:39:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:39:03: #4 Write output xls file... SRX3942555.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:39:03: #4 Write peak in narrowPeak format file... SRX3942555.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:39:03: #4 Write summits bed file... SRX3942555.20_summits.bed INFO @ Sat, 08 Sep 2018 11:39:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:39:04: #4 Write output xls file... SRX3942555.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:39:04: #4 Write peak in narrowPeak format file... SRX3942555.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:39:04: #4 Write summits bed file... SRX3942555.05_summits.bed INFO @ Sat, 08 Sep 2018 11:39:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1412 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:39:06: #4 Write output xls file... SRX3942555.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:39:06: #4 Write peak in narrowPeak format file... SRX3942555.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:39:06: #4 Write summits bed file... SRX3942555.10_summits.bed INFO @ Sat, 08 Sep 2018 11:39:06: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (707 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。