Job ID = 11240703 sra ファイルのダウンロード中... Completed: 222181K bytes transferred in 6 seconds (264262K 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 7849928 spots for /home/okishinya/chipatlas/results/ce10/SRX4456926/SRR7591867.sra Written 7849928 spots for /home/okishinya/chipatlas/results/ce10/SRX4456926/SRR7591867.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: 00:01:51 7849928 reads; of these: 7849928 (100.00%) were unpaired; of these: 1154169 (14.70%) aligned 0 times 5692938 (72.52%) aligned exactly 1 time 1002821 (12.77%) aligned >1 times 85.30% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 656333 / 6695759 = 0.0980 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, 07 Oct 2018 20:31:50: # Command line: callpeak -t SRX4456926.bam -f BAM -g ce -n SRX4456926.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4456926.10 # format = BAM # ChIP-seq file = ['SRX4456926.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, 07 Oct 2018 20:31:50: # Command line: callpeak -t SRX4456926.bam -f BAM -g ce -n SRX4456926.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4456926.20 # format = BAM # ChIP-seq file = ['SRX4456926.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, 07 Oct 2018 20:31:50: # Command line: callpeak -t SRX4456926.bam -f BAM -g ce -n SRX4456926.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4456926.05 # format = BAM # ChIP-seq file = ['SRX4456926.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, 07 Oct 2018 20:31:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:31:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:31:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:31:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:31:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:31:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:31:56: 1000000 INFO @ Sun, 07 Oct 2018 20:31:56: 1000000 INFO @ Sun, 07 Oct 2018 20:31:56: 1000000 INFO @ Sun, 07 Oct 2018 20:32:02: 2000000 INFO @ Sun, 07 Oct 2018 20:32:03: 2000000 INFO @ Sun, 07 Oct 2018 20:32:03: 2000000 INFO @ Sun, 07 Oct 2018 20:32:08: 3000000 INFO @ Sun, 07 Oct 2018 20:32:10: 3000000 INFO @ Sun, 07 Oct 2018 20:32:10: 3000000 INFO @ Sun, 07 Oct 2018 20:32:15: 4000000 INFO @ Sun, 07 Oct 2018 20:32:16: 4000000 INFO @ Sun, 07 Oct 2018 20:32:17: 4000000 INFO @ Sun, 07 Oct 2018 20:32:21: 5000000 INFO @ Sun, 07 Oct 2018 20:32:23: 5000000 INFO @ Sun, 07 Oct 2018 20:32:24: 5000000 INFO @ Sun, 07 Oct 2018 20:32:27: 6000000 INFO @ Sun, 07 Oct 2018 20:32:28: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:32:28: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:32:28: #1 total tags in treatment: 6039426 INFO @ Sun, 07 Oct 2018 20:32:28: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:32:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:32:28: #1 tags after filtering in treatment: 6039426 INFO @ Sun, 07 Oct 2018 20:32:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:32:28: #1 finished! INFO @ Sun, 07 Oct 2018 20:32:28: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:32:28: #2 number of paired peaks: 1004 INFO @ Sun, 07 Oct 2018 20:32:28: start model_add_line... INFO @ Sun, 07 Oct 2018 20:32:28: start X-correlation... INFO @ Sun, 07 Oct 2018 20:32:29: end of X-cor INFO @ Sun, 07 Oct 2018 20:32:29: #2 finished! INFO @ Sun, 07 Oct 2018 20:32:29: #2 predicted fragment length is 97 bps INFO @ Sun, 07 Oct 2018 20:32:29: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 07 Oct 2018 20:32:29: #2.2 Generate R script for model : SRX4456926.20_model.r WARNING @ Sun, 07 Oct 2018 20:32:29: #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, 07 Oct 2018 20:32:29: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Sun, 07 Oct 2018 20:32:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:32:29: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:32:29: 6000000 INFO @ Sun, 07 Oct 2018 20:32:29: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:32:29: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:32:29: #1 total tags in treatment: 6039426 INFO @ Sun, 07 Oct 2018 20:32:29: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:32:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:32:29: #1 tags after filtering in treatment: 6039426 INFO @ Sun, 07 Oct 2018 20:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:32:29: #1 finished! INFO @ Sun, 07 Oct 2018 20:32:29: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:32:30: #2 number of paired peaks: 1004 INFO @ Sun, 07 Oct 2018 20:32:30: start model_add_line... INFO @ Sun, 07 Oct 2018 20:32:30: start X-correlation... INFO @ Sun, 07 Oct 2018 20:32:30: end of X-cor INFO @ Sun, 07 Oct 2018 20:32:30: #2 finished! INFO @ Sun, 07 Oct 2018 20:32:30: #2 predicted fragment length is 97 bps INFO @ Sun, 07 Oct 2018 20:32:30: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 07 Oct 2018 20:32:30: #2.2 Generate R script for model : SRX4456926.10_model.r WARNING @ Sun, 07 Oct 2018 20:32:30: #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, 07 Oct 2018 20:32:30: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Sun, 07 Oct 2018 20:32:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:32:30: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:32:30: 6000000 INFO @ Sun, 07 Oct 2018 20:32:31: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:32:31: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:32:31: #1 total tags in treatment: 6039426 INFO @ Sun, 07 Oct 2018 20:32:31: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:32:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:32:31: #1 tags after filtering in treatment: 6039426 INFO @ Sun, 07 Oct 2018 20:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:32:31: #1 finished! INFO @ Sun, 07 Oct 2018 20:32:31: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:32:31: #2 number of paired peaks: 1004 INFO @ Sun, 07 Oct 2018 20:32:31: start model_add_line... INFO @ Sun, 07 Oct 2018 20:32:31: start X-correlation... INFO @ Sun, 07 Oct 2018 20:32:31: end of X-cor INFO @ Sun, 07 Oct 2018 20:32:31: #2 finished! INFO @ Sun, 07 Oct 2018 20:32:31: #2 predicted fragment length is 97 bps INFO @ Sun, 07 Oct 2018 20:32:31: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 07 Oct 2018 20:32:31: #2.2 Generate R script for model : SRX4456926.05_model.r WARNING @ Sun, 07 Oct 2018 20:32:31: #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, 07 Oct 2018 20:32:31: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Sun, 07 Oct 2018 20:32:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:32:31: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:32:43: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:32:44: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:32:47: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:32:50: #4 Write output xls file... SRX4456926.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:32:50: #4 Write peak in narrowPeak format file... SRX4456926.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:32:50: #4 Write summits bed file... SRX4456926.20_summits.bed INFO @ Sun, 07 Oct 2018 20:32:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:32:53: #4 Write output xls file... SRX4456926.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:32:53: #4 Write peak in narrowPeak format file... SRX4456926.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:32:53: #4 Write summits bed file... SRX4456926.10_summits.bed INFO @ Sun, 07 Oct 2018 20:32:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:32:54: #4 Write output xls file... SRX4456926.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:32:54: #4 Write peak in narrowPeak format file... SRX4456926.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:32:54: #4 Write summits bed file... SRX4456926.05_summits.bed INFO @ Sun, 07 Oct 2018 20:32:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1472 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。