Job ID = 2589752 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,219,334 reads read : 9,219,334 reads written : 9,219,334 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947358.sra.cache’: 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: 00:01:13 9219334 reads; of these: 9219334 (100.00%) were unpaired; of these: 3555254 (38.56%) aligned 0 times 4817061 (52.25%) aligned exactly 1 time 847019 (9.19%) aligned >1 times 61.44% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 495357 / 5664080 = 0.0875 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 18:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.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 18:25:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:25:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.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 18:25:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:25:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.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 18:25:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:25:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:25:44: 1000000 INFO @ Mon, 12 Aug 2019 18:25:45: 1000000 INFO @ Mon, 12 Aug 2019 18:25:46: 1000000 INFO @ Mon, 12 Aug 2019 18:25:51: 2000000 INFO @ Mon, 12 Aug 2019 18:25:53: 2000000 INFO @ Mon, 12 Aug 2019 18:25:53: 2000000 INFO @ Mon, 12 Aug 2019 18:25:59: 3000000 INFO @ Mon, 12 Aug 2019 18:26:01: 3000000 INFO @ Mon, 12 Aug 2019 18:26:01: 3000000 INFO @ Mon, 12 Aug 2019 18:26:06: 4000000 INFO @ Mon, 12 Aug 2019 18:26:09: 4000000 INFO @ Mon, 12 Aug 2019 18:26:09: 4000000 INFO @ Mon, 12 Aug 2019 18:26:14: 5000000 INFO @ Mon, 12 Aug 2019 18:26:15: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:15: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:15: #1 total tags in treatment: 5168723 INFO @ Mon, 12 Aug 2019 18:26:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:15: #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 18:26:15: #1 tags after filtering in treatment: 5168723 INFO @ Mon, 12 Aug 2019 18:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:15: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:16: #2 number of paired peaks: 396 WARNING @ Mon, 12 Aug 2019 18:26:16: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Mon, 12 Aug 2019 18:26:16: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:16: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:16: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:16: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:16: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 18:26:16: #2 alternative fragment length(s) may be 3,32,438,505,521,549,566,596 bps INFO @ Mon, 12 Aug 2019 18:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.05_model.r WARNING @ Mon, 12 Aug 2019 18:26:16: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:26:16: #2 You may need to consider one of the other alternative d(s): 3,32,438,505,521,549,566,596 WARNING @ Mon, 12 Aug 2019 18:26:16: #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 18:26:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:16: 5000000 INFO @ Mon, 12 Aug 2019 18:26:16: 5000000 INFO @ Mon, 12 Aug 2019 18:26:17: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:17: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:17: #1 total tags in treatment: 5168723 INFO @ Mon, 12 Aug 2019 18:26:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:17: #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 18:26:17: #1 tags after filtering in treatment: 5168723 INFO @ Mon, 12 Aug 2019 18:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:17: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:17: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:26:17: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:26:17: #1 total tags in treatment: 5168723 INFO @ Mon, 12 Aug 2019 18:26:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:26:17: #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 18:26:18: #1 tags after filtering in treatment: 5168723 INFO @ Mon, 12 Aug 2019 18:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:26:18: #1 finished! INFO @ Mon, 12 Aug 2019 18:26:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:26:18: #2 number of paired peaks: 396 WARNING @ Mon, 12 Aug 2019 18:26:18: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Mon, 12 Aug 2019 18:26:18: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:18: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:18: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:18: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:18: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 18:26:18: #2 alternative fragment length(s) may be 3,32,438,505,521,549,566,596 bps INFO @ Mon, 12 Aug 2019 18:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.10_model.r WARNING @ Mon, 12 Aug 2019 18:26:18: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:26:18: #2 You may need to consider one of the other alternative d(s): 3,32,438,505,521,549,566,596 WARNING @ Mon, 12 Aug 2019 18:26:18: #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 18:26:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:18: #2 number of paired peaks: 396 WARNING @ Mon, 12 Aug 2019 18:26:18: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Mon, 12 Aug 2019 18:26:18: start model_add_line... INFO @ Mon, 12 Aug 2019 18:26:18: start X-correlation... INFO @ Mon, 12 Aug 2019 18:26:18: end of X-cor INFO @ Mon, 12 Aug 2019 18:26:18: #2 finished! INFO @ Mon, 12 Aug 2019 18:26:18: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 18:26:18: #2 alternative fragment length(s) may be 3,32,438,505,521,549,566,596 bps INFO @ Mon, 12 Aug 2019 18:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.20_model.r WARNING @ Mon, 12 Aug 2019 18:26:18: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:26:18: #2 You may need to consider one of the other alternative d(s): 3,32,438,505,521,549,566,596 WARNING @ Mon, 12 Aug 2019 18:26:18: #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 18:26:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:26:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:26:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:26:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:26:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:26:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:26:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.05_summits.bed INFO @ Mon, 12 Aug 2019 18:26:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.10_summits.bed INFO @ Mon, 12 Aug 2019 18:26:41: Done! INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331127/SRX331127.20_summits.bed INFO @ Mon, 12 Aug 2019 18:26:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (38 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。