Job ID = 2589106 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,249,716 reads read : 9,249,716 reads written : 9,249,716 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:55 9249716 reads; of these: 9249716 (100.00%) were unpaired; of these: 860433 (9.30%) aligned 0 times 4998687 (54.04%) aligned exactly 1 time 3390596 (36.66%) aligned >1 times 90.70% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 3458610 / 8389283 = 0.4123 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, 12 Aug 2019 17:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.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 @ Mon, 12 Aug 2019 17:01:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:01:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.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 @ Mon, 12 Aug 2019 17:01:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:01:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.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 @ Mon, 12 Aug 2019 17:01:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:01:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:01:48: 1000000 INFO @ Mon, 12 Aug 2019 17:01:49: 1000000 INFO @ Mon, 12 Aug 2019 17:01:49: 1000000 INFO @ Mon, 12 Aug 2019 17:01:55: 2000000 INFO @ Mon, 12 Aug 2019 17:01:57: 2000000 INFO @ Mon, 12 Aug 2019 17:01:58: 2000000 INFO @ Mon, 12 Aug 2019 17:02:02: 3000000 INFO @ Mon, 12 Aug 2019 17:02:04: 3000000 INFO @ Mon, 12 Aug 2019 17:02:06: 3000000 INFO @ Mon, 12 Aug 2019 17:02:09: 4000000 INFO @ Mon, 12 Aug 2019 17:02:11: 4000000 INFO @ Mon, 12 Aug 2019 17:02:14: 4000000 INFO @ Mon, 12 Aug 2019 17:02:16: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 17:02:16: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 17:02:16: #1 total tags in treatment: 4930673 INFO @ Mon, 12 Aug 2019 17:02:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:02:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:02:16: #1 tags after filtering in treatment: 4930673 INFO @ Mon, 12 Aug 2019 17:02:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:02:16: #1 finished! INFO @ Mon, 12 Aug 2019 17:02:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:02:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:02:16: #2 number of paired peaks: 3769 INFO @ Mon, 12 Aug 2019 17:02:16: start model_add_line... INFO @ Mon, 12 Aug 2019 17:02:17: start X-correlation... INFO @ Mon, 12 Aug 2019 17:02:17: end of X-cor INFO @ Mon, 12 Aug 2019 17:02:17: #2 finished! INFO @ Mon, 12 Aug 2019 17:02:17: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 17:02:17: #2 alternative fragment length(s) may be 3,56,94,113 bps INFO @ Mon, 12 Aug 2019 17:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.10_model.r WARNING @ Mon, 12 Aug 2019 17:02:17: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:02:17: #2 You may need to consider one of the other alternative d(s): 3,56,94,113 WARNING @ Mon, 12 Aug 2019 17:02:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:02:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:02:18: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 17:02:18: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 17:02:18: #1 total tags in treatment: 4930673 INFO @ Mon, 12 Aug 2019 17:02:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:02:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:02:18: #1 tags after filtering in treatment: 4930673 INFO @ Mon, 12 Aug 2019 17:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:02:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:02:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:02:19: #2 number of paired peaks: 3769 INFO @ Mon, 12 Aug 2019 17:02:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:02:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:02:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:02:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:02:19: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 17:02:19: #2 alternative fragment length(s) may be 3,56,94,113 bps INFO @ Mon, 12 Aug 2019 17:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.20_model.r WARNING @ Mon, 12 Aug 2019 17:02:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:02:19: #2 You may need to consider one of the other alternative d(s): 3,56,94,113 WARNING @ Mon, 12 Aug 2019 17:02:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:02:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:02:22: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 17:02:22: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 17:02:22: #1 total tags in treatment: 4930673 INFO @ Mon, 12 Aug 2019 17:02:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:02:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:02:22: #1 tags after filtering in treatment: 4930673 INFO @ Mon, 12 Aug 2019 17:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:02:22: #1 finished! INFO @ Mon, 12 Aug 2019 17:02:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:02:23: #2 number of paired peaks: 3769 INFO @ Mon, 12 Aug 2019 17:02:23: start model_add_line... INFO @ Mon, 12 Aug 2019 17:02:23: start X-correlation... INFO @ Mon, 12 Aug 2019 17:02:23: end of X-cor INFO @ Mon, 12 Aug 2019 17:02:23: #2 finished! INFO @ Mon, 12 Aug 2019 17:02:23: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 17:02:23: #2 alternative fragment length(s) may be 3,56,94,113 bps INFO @ Mon, 12 Aug 2019 17:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.05_model.r WARNING @ Mon, 12 Aug 2019 17:02:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:02:23: #2 You may need to consider one of the other alternative d(s): 3,56,94,113 WARNING @ Mon, 12 Aug 2019 17:02:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:02:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:02:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:02:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:02:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.10_summits.bed INFO @ Mon, 12 Aug 2019 17:02:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.20_summits.bed INFO @ Mon, 12 Aug 2019 17:02:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:02:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:02:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:02:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999205/ERX1999205.05_summits.bed INFO @ Mon, 12 Aug 2019 17:02:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1075 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。