Job ID = 2589965 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,595,479 reads read : 5,595,479 reads written : 5,595,479 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: 00:01:28 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127681 (2.28%) aligned 0 times 4499706 (80.42%) aligned exactly 1 time 968092 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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] 319453 / 5467798 = 0.0584 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 18:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.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 18:58:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:58:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:58:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.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 18:58:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:58:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.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 18:58:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:58:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:58:24: 1000000 INFO @ Mon, 12 Aug 2019 18:58:25: 1000000 INFO @ Mon, 12 Aug 2019 18:58:27: 1000000 INFO @ Mon, 12 Aug 2019 18:58:32: 2000000 INFO @ Mon, 12 Aug 2019 18:58:33: 2000000 INFO @ Mon, 12 Aug 2019 18:58:35: 2000000 INFO @ Mon, 12 Aug 2019 18:58:39: 3000000 INFO @ Mon, 12 Aug 2019 18:58:40: 3000000 INFO @ Mon, 12 Aug 2019 18:58:42: 3000000 INFO @ Mon, 12 Aug 2019 18:58:46: 4000000 INFO @ Mon, 12 Aug 2019 18:58:47: 4000000 INFO @ Mon, 12 Aug 2019 18:58:50: 4000000 INFO @ Mon, 12 Aug 2019 18:58:53: 5000000 INFO @ Mon, 12 Aug 2019 18:58:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:58:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:58:55: #1 total tags in treatment: 5148345 INFO @ Mon, 12 Aug 2019 18:58:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:58:55: #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 18:58:55: #1 tags after filtering in treatment: 5148345 INFO @ Mon, 12 Aug 2019 18:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:58:55: #1 finished! INFO @ Mon, 12 Aug 2019 18:58:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:58:55: 5000000 INFO @ Mon, 12 Aug 2019 18:58:55: #2 number of paired peaks: 435 WARNING @ Mon, 12 Aug 2019 18:58:55: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Mon, 12 Aug 2019 18:58:55: start model_add_line... INFO @ Mon, 12 Aug 2019 18:58:55: start X-correlation... INFO @ Mon, 12 Aug 2019 18:58:55: end of X-cor INFO @ Mon, 12 Aug 2019 18:58:55: #2 finished! INFO @ Mon, 12 Aug 2019 18:58:55: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 18:58:55: #2 alternative fragment length(s) may be 48,504,596 bps INFO @ Mon, 12 Aug 2019 18:58:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.05_model.r WARNING @ Mon, 12 Aug 2019 18:58:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:58:55: #2 You may need to consider one of the other alternative d(s): 48,504,596 WARNING @ Mon, 12 Aug 2019 18:58:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:58:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:58:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:58:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:58:56: #1 total tags in treatment: 5148345 INFO @ Mon, 12 Aug 2019 18:58:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:58:56: #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 18:58:56: #1 tags after filtering in treatment: 5148345 INFO @ Mon, 12 Aug 2019 18:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:58:56: #1 finished! INFO @ Mon, 12 Aug 2019 18:58:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:58:56: #2 number of paired peaks: 435 WARNING @ Mon, 12 Aug 2019 18:58:56: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Mon, 12 Aug 2019 18:58:56: start model_add_line... INFO @ Mon, 12 Aug 2019 18:58:56: start X-correlation... INFO @ Mon, 12 Aug 2019 18:58:57: end of X-cor INFO @ Mon, 12 Aug 2019 18:58:57: #2 finished! INFO @ Mon, 12 Aug 2019 18:58:57: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 18:58:57: #2 alternative fragment length(s) may be 48,504,596 bps INFO @ Mon, 12 Aug 2019 18:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.10_model.r WARNING @ Mon, 12 Aug 2019 18:58:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:58:57: #2 You may need to consider one of the other alternative d(s): 48,504,596 WARNING @ Mon, 12 Aug 2019 18:58:57: #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 18:58:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:58:57: 5000000 INFO @ Mon, 12 Aug 2019 18:58:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:58:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:58:58: #1 total tags in treatment: 5148345 INFO @ Mon, 12 Aug 2019 18:58:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:58:58: #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 18:58:58: #1 tags after filtering in treatment: 5148345 INFO @ Mon, 12 Aug 2019 18:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:58:58: #1 finished! INFO @ Mon, 12 Aug 2019 18:58:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:58:59: #2 number of paired peaks: 435 WARNING @ Mon, 12 Aug 2019 18:58:59: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Mon, 12 Aug 2019 18:58:59: start model_add_line... INFO @ Mon, 12 Aug 2019 18:58:59: start X-correlation... INFO @ Mon, 12 Aug 2019 18:58:59: end of X-cor INFO @ Mon, 12 Aug 2019 18:58:59: #2 finished! INFO @ Mon, 12 Aug 2019 18:58:59: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 18:58:59: #2 alternative fragment length(s) may be 48,504,596 bps INFO @ Mon, 12 Aug 2019 18:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.20_model.r WARNING @ Mon, 12 Aug 2019 18:58:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:58:59: #2 You may need to consider one of the other alternative d(s): 48,504,596 WARNING @ Mon, 12 Aug 2019 18:58:59: #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 18:58:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:59:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:59:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:59:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.05_summits.bed INFO @ Mon, 12 Aug 2019 18:59:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.10_summits.bed INFO @ Mon, 12 Aug 2019 18:59:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (331 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466496/SRX466496.20_summits.bed INFO @ Mon, 12 Aug 2019 18:59:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 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。