Job ID = 1292316 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,129,788 reads read : 13,129,788 reads written : 13,129,788 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: 00:03:32 13129788 reads; of these: 13129788 (100.00%) were unpaired; of these: 270389 (2.06%) aligned 0 times 10628305 (80.95%) aligned exactly 1 time 2231094 (16.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2050833 / 12859399 = 0.1595 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, 02 Jun 2019 17:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.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, 02 Jun 2019 17:58:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.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, 02 Jun 2019 17:58:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.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, 02 Jun 2019 17:58:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:39: 1000000 INFO @ Sun, 02 Jun 2019 17:58:41: 1000000 INFO @ Sun, 02 Jun 2019 17:58:43: 1000000 INFO @ Sun, 02 Jun 2019 17:58:47: 2000000 INFO @ Sun, 02 Jun 2019 17:58:50: 2000000 INFO @ Sun, 02 Jun 2019 17:58:54: 2000000 INFO @ Sun, 02 Jun 2019 17:58:55: 3000000 INFO @ Sun, 02 Jun 2019 17:58:59: 3000000 INFO @ Sun, 02 Jun 2019 17:59:03: 4000000 INFO @ Sun, 02 Jun 2019 17:59:04: 3000000 INFO @ Sun, 02 Jun 2019 17:59:08: 4000000 INFO @ Sun, 02 Jun 2019 17:59:10: 5000000 INFO @ Sun, 02 Jun 2019 17:59:15: 4000000 INFO @ Sun, 02 Jun 2019 17:59:17: 5000000 INFO @ Sun, 02 Jun 2019 17:59:18: 6000000 INFO @ Sun, 02 Jun 2019 17:59:25: 5000000 INFO @ Sun, 02 Jun 2019 17:59:26: 7000000 INFO @ Sun, 02 Jun 2019 17:59:26: 6000000 INFO @ Sun, 02 Jun 2019 17:59:34: 8000000 INFO @ Sun, 02 Jun 2019 17:59:36: 7000000 INFO @ Sun, 02 Jun 2019 17:59:36: 6000000 INFO @ Sun, 02 Jun 2019 17:59:42: 9000000 INFO @ Sun, 02 Jun 2019 17:59:45: 8000000 INFO @ Sun, 02 Jun 2019 17:59:47: 7000000 INFO @ Sun, 02 Jun 2019 17:59:50: 10000000 INFO @ Sun, 02 Jun 2019 17:59:54: 9000000 INFO @ Sun, 02 Jun 2019 17:59:56: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:59:56: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:59:56: #1 total tags in treatment: 10808566 INFO @ Sun, 02 Jun 2019 17:59:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:59:57: #1 tags after filtering in treatment: 10808566 INFO @ Sun, 02 Jun 2019 17:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:59:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:58: #2 number of paired peaks: 376 WARNING @ Sun, 02 Jun 2019 17:59:58: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Sun, 02 Jun 2019 17:59:58: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:58: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:58: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:58: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:58: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 17:59:58: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 17:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.10_model.r WARNING @ Sun, 02 Jun 2019 17:59:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:59:58: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 17:59:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:59:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:58: 8000000 INFO @ Sun, 02 Jun 2019 18:00:03: 10000000 INFO @ Sun, 02 Jun 2019 18:00:08: 9000000 INFO @ Sun, 02 Jun 2019 18:00:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:00:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:00:11: #1 total tags in treatment: 10808566 INFO @ Sun, 02 Jun 2019 18:00:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:00:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:00:11: #1 tags after filtering in treatment: 10808566 INFO @ Sun, 02 Jun 2019 18:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:00:11: #1 finished! INFO @ Sun, 02 Jun 2019 18:00:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:00:12: #2 number of paired peaks: 376 WARNING @ Sun, 02 Jun 2019 18:00:12: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Sun, 02 Jun 2019 18:00:12: start model_add_line... INFO @ Sun, 02 Jun 2019 18:00:12: start X-correlation... INFO @ Sun, 02 Jun 2019 18:00:12: end of X-cor INFO @ Sun, 02 Jun 2019 18:00:12: #2 finished! INFO @ Sun, 02 Jun 2019 18:00:12: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:00:12: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 18:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.20_model.r WARNING @ Sun, 02 Jun 2019 18:00:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:00:12: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 18:00:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:00:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:00:21: 10000000 INFO @ Sun, 02 Jun 2019 18:00:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:00:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:00:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:00:30: #1 total tags in treatment: 10808566 INFO @ Sun, 02 Jun 2019 18:00:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:00:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:00:30: #1 tags after filtering in treatment: 10808566 INFO @ Sun, 02 Jun 2019 18:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:00:30: #1 finished! INFO @ Sun, 02 Jun 2019 18:00:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:00:31: #2 number of paired peaks: 376 WARNING @ Sun, 02 Jun 2019 18:00:31: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Sun, 02 Jun 2019 18:00:31: start model_add_line... INFO @ Sun, 02 Jun 2019 18:00:31: start X-correlation... INFO @ Sun, 02 Jun 2019 18:00:31: end of X-cor INFO @ Sun, 02 Jun 2019 18:00:31: #2 finished! INFO @ Sun, 02 Jun 2019 18:00:31: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:00:31: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 18:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.05_model.r WARNING @ Sun, 02 Jun 2019 18:00:31: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:00:31: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 18:00:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:00:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.10_summits.bed INFO @ Sun, 02 Jun 2019 18:00:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:00:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:00:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:00:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:00:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.20_summits.bed INFO @ Sun, 02 Jun 2019 18:00:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:01:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:01:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:01:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:01:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331341/SRX331341.05_summits.bed INFO @ Sun, 02 Jun 2019 18:01:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (692 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。