Job ID = 1293679 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,886,975 reads read : 7,773,950 reads written : 3,886,975 reads 0-length : 3,886,975 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:03:24 3886975 reads; of these: 3886975 (100.00%) were unpaired; of these: 353832 (9.10%) aligned 0 times 3239898 (83.35%) aligned exactly 1 time 293245 (7.54%) aligned >1 times 90.90% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 666019 / 3533143 = 0.1885 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 @ Mon, 03 Jun 2019 01:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:42:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:42:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:42:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:42:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:42:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:42:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:42:22: 1000000 INFO @ Mon, 03 Jun 2019 01:42:26: 1000000 INFO @ Mon, 03 Jun 2019 01:42:26: 1000000 INFO @ Mon, 03 Jun 2019 01:42:34: 2000000 INFO @ Mon, 03 Jun 2019 01:42:41: 2000000 INFO @ Mon, 03 Jun 2019 01:42:43: 2000000 INFO @ Mon, 03 Jun 2019 01:42:44: #1 tag size is determined as 146 bps INFO @ Mon, 03 Jun 2019 01:42:44: #1 tag size = 146 INFO @ Mon, 03 Jun 2019 01:42:44: #1 total tags in treatment: 2867124 INFO @ Mon, 03 Jun 2019 01:42:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:42:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:42:44: #1 tags after filtering in treatment: 2867124 INFO @ Mon, 03 Jun 2019 01:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:42:44: #1 finished! INFO @ Mon, 03 Jun 2019 01:42:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:42:45: #2 number of paired peaks: 5139 INFO @ Mon, 03 Jun 2019 01:42:45: start model_add_line... INFO @ Mon, 03 Jun 2019 01:42:45: start X-correlation... INFO @ Mon, 03 Jun 2019 01:42:45: end of X-cor INFO @ Mon, 03 Jun 2019 01:42:45: #2 finished! INFO @ Mon, 03 Jun 2019 01:42:45: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 01:42:45: #2 alternative fragment length(s) may be 179 bps INFO @ Mon, 03 Jun 2019 01:42:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.20_model.r WARNING @ Mon, 03 Jun 2019 01:42:45: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:42:45: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Mon, 03 Jun 2019 01:42:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:42:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:42:54: #1 tag size is determined as 146 bps INFO @ Mon, 03 Jun 2019 01:42:54: #1 tag size = 146 INFO @ Mon, 03 Jun 2019 01:42:54: #1 total tags in treatment: 2867124 INFO @ Mon, 03 Jun 2019 01:42:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:42:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:42:54: #1 tags after filtering in treatment: 2867124 INFO @ Mon, 03 Jun 2019 01:42:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:42:54: #1 finished! INFO @ Mon, 03 Jun 2019 01:42:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:42:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:42:55: #2 number of paired peaks: 5139 INFO @ Mon, 03 Jun 2019 01:42:55: start model_add_line... INFO @ Mon, 03 Jun 2019 01:42:55: start X-correlation... INFO @ Mon, 03 Jun 2019 01:42:55: end of X-cor INFO @ Mon, 03 Jun 2019 01:42:55: #2 finished! INFO @ Mon, 03 Jun 2019 01:42:55: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 01:42:55: #2 alternative fragment length(s) may be 179 bps INFO @ Mon, 03 Jun 2019 01:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.10_model.r WARNING @ Mon, 03 Jun 2019 01:42:55: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:42:55: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Mon, 03 Jun 2019 01:42:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:42:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:42:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:42:57: #1 tag size is determined as 146 bps INFO @ Mon, 03 Jun 2019 01:42:57: #1 tag size = 146 INFO @ Mon, 03 Jun 2019 01:42:57: #1 total tags in treatment: 2867124 INFO @ Mon, 03 Jun 2019 01:42:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:42:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:42:57: #1 tags after filtering in treatment: 2867124 INFO @ Mon, 03 Jun 2019 01:42:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:42:57: #1 finished! INFO @ Mon, 03 Jun 2019 01:42:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:42:58: #2 number of paired peaks: 5139 INFO @ Mon, 03 Jun 2019 01:42:58: start model_add_line... INFO @ Mon, 03 Jun 2019 01:42:58: start X-correlation... INFO @ Mon, 03 Jun 2019 01:42:58: end of X-cor INFO @ Mon, 03 Jun 2019 01:42:58: #2 finished! INFO @ Mon, 03 Jun 2019 01:42:58: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 01:42:58: #2 alternative fragment length(s) may be 179 bps INFO @ Mon, 03 Jun 2019 01:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.05_model.r WARNING @ Mon, 03 Jun 2019 01:42:58: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:42:58: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Mon, 03 Jun 2019 01:42:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:42:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.20_summits.bed INFO @ Mon, 03 Jun 2019 01:43:01: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1927 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:43:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:43:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:43:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:43:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:43:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.10_summits.bed INFO @ Mon, 03 Jun 2019 01:43:11: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (4049 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 01:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091590/SRX1091590.05_summits.bed INFO @ Mon, 03 Jun 2019 01:43:13: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7490 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。