Job ID = 1292419 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,699,445 reads read : 11,398,890 reads written : 5,699,445 reads 0-length : 5,699,445 spots read : 5,559,787 reads read : 11,119,574 reads written : 5,559,787 reads 0-length : 5,559,787 spots read : 5,697,305 reads read : 11,394,610 reads written : 5,697,305 reads 0-length : 5,697,305 spots read : 5,501,410 reads read : 11,002,820 reads written : 5,501,410 reads 0-length : 5,501,410 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: 00:11:08 22457947 reads; of these: 22457947 (100.00%) were unpaired; of these: 710716 (3.16%) aligned 0 times 18603647 (82.84%) aligned exactly 1 time 3143584 (14.00%) aligned >1 times 96.84% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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 12 files... [bam_rmdupse_core] 3506376 / 21747231 = 0.1612 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 18:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.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 18:55:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.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 18:55:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.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 18:55:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:40: 1000000 INFO @ Sun, 02 Jun 2019 18:55:41: 1000000 INFO @ Sun, 02 Jun 2019 18:55:42: 1000000 INFO @ Sun, 02 Jun 2019 18:55:52: 2000000 INFO @ Sun, 02 Jun 2019 18:55:54: 2000000 INFO @ Sun, 02 Jun 2019 18:55:56: 2000000 INFO @ Sun, 02 Jun 2019 18:56:05: 3000000 INFO @ Sun, 02 Jun 2019 18:56:07: 3000000 INFO @ Sun, 02 Jun 2019 18:56:09: 3000000 INFO @ Sun, 02 Jun 2019 18:56:17: 4000000 INFO @ Sun, 02 Jun 2019 18:56:21: 4000000 INFO @ Sun, 02 Jun 2019 18:56:22: 4000000 INFO @ Sun, 02 Jun 2019 18:56:28: 5000000 INFO @ Sun, 02 Jun 2019 18:56:33: 5000000 INFO @ Sun, 02 Jun 2019 18:56:35: 5000000 INFO @ Sun, 02 Jun 2019 18:56:40: 6000000 INFO @ Sun, 02 Jun 2019 18:56:46: 6000000 INFO @ Sun, 02 Jun 2019 18:56:48: 6000000 INFO @ Sun, 02 Jun 2019 18:56:52: 7000000 INFO @ Sun, 02 Jun 2019 18:56:59: 7000000 INFO @ Sun, 02 Jun 2019 18:57:01: 7000000 INFO @ Sun, 02 Jun 2019 18:57:04: 8000000 INFO @ Sun, 02 Jun 2019 18:57:12: 8000000 INFO @ Sun, 02 Jun 2019 18:57:14: 8000000 INFO @ Sun, 02 Jun 2019 18:57:16: 9000000 INFO @ Sun, 02 Jun 2019 18:57:26: 9000000 INFO @ Sun, 02 Jun 2019 18:57:27: 9000000 INFO @ Sun, 02 Jun 2019 18:57:28: 10000000 INFO @ Sun, 02 Jun 2019 18:57:39: 10000000 INFO @ Sun, 02 Jun 2019 18:57:41: 11000000 INFO @ Sun, 02 Jun 2019 18:57:41: 10000000 INFO @ Sun, 02 Jun 2019 18:57:53: 11000000 INFO @ Sun, 02 Jun 2019 18:57:53: 12000000 INFO @ Sun, 02 Jun 2019 18:57:54: 11000000 INFO @ Sun, 02 Jun 2019 18:58:05: 13000000 INFO @ Sun, 02 Jun 2019 18:58:06: 12000000 INFO @ Sun, 02 Jun 2019 18:58:08: 12000000 INFO @ Sun, 02 Jun 2019 18:58:16: 14000000 INFO @ Sun, 02 Jun 2019 18:58:19: 13000000 INFO @ Sun, 02 Jun 2019 18:58:21: 13000000 INFO @ Sun, 02 Jun 2019 18:58:28: 15000000 INFO @ Sun, 02 Jun 2019 18:58:32: 14000000 INFO @ Sun, 02 Jun 2019 18:58:34: 14000000 INFO @ Sun, 02 Jun 2019 18:58:40: 16000000 INFO @ Sun, 02 Jun 2019 18:58:45: 15000000 INFO @ Sun, 02 Jun 2019 18:58:47: 15000000 INFO @ Sun, 02 Jun 2019 18:58:54: 17000000 INFO @ Sun, 02 Jun 2019 18:59:01: 16000000 INFO @ Sun, 02 Jun 2019 18:59:01: 16000000 INFO @ Sun, 02 Jun 2019 18:59:09: 18000000 INFO @ Sun, 02 Jun 2019 18:59:12: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:59:12: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:59:12: #1 total tags in treatment: 18240855 INFO @ Sun, 02 Jun 2019 18:59:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:59:12: #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 18:59:13: #1 tags after filtering in treatment: 18240855 INFO @ Sun, 02 Jun 2019 18:59:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:59:13: #1 finished! INFO @ Sun, 02 Jun 2019 18:59:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:59:14: #2 number of paired peaks: 150 WARNING @ Sun, 02 Jun 2019 18:59:14: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sun, 02 Jun 2019 18:59:14: start model_add_line... INFO @ Sun, 02 Jun 2019 18:59:14: start X-correlation... INFO @ Sun, 02 Jun 2019 18:59:15: end of X-cor INFO @ Sun, 02 Jun 2019 18:59:15: #2 finished! INFO @ Sun, 02 Jun 2019 18:59:15: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 18:59:15: #2 alternative fragment length(s) may be 2,66,535,572 bps INFO @ Sun, 02 Jun 2019 18:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.05_model.r WARNING @ Sun, 02 Jun 2019 18:59:15: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:59:15: #2 You may need to consider one of the other alternative d(s): 2,66,535,572 WARNING @ Sun, 02 Jun 2019 18:59:15: #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 18:59:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:16: 17000000 INFO @ Sun, 02 Jun 2019 18:59:16: 17000000 INFO @ Sun, 02 Jun 2019 18:59:29: 18000000 INFO @ Sun, 02 Jun 2019 18:59:30: 18000000 INFO @ Sun, 02 Jun 2019 18:59:32: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:59:32: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:59:32: #1 total tags in treatment: 18240855 INFO @ Sun, 02 Jun 2019 18:59:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:59:32: #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 18:59:33: #1 tags after filtering in treatment: 18240855 INFO @ Sun, 02 Jun 2019 18:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:59:33: #1 finished! INFO @ Sun, 02 Jun 2019 18:59:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:59:33: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:59:33: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:59:33: #1 total tags in treatment: 18240855 INFO @ Sun, 02 Jun 2019 18:59:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:59:33: #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 18:59:34: #1 tags after filtering in treatment: 18240855 INFO @ Sun, 02 Jun 2019 18:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:59:34: #1 finished! INFO @ Sun, 02 Jun 2019 18:59:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:59:34: #2 number of paired peaks: 150 WARNING @ Sun, 02 Jun 2019 18:59:34: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sun, 02 Jun 2019 18:59:34: start model_add_line... INFO @ Sun, 02 Jun 2019 18:59:35: start X-correlation... INFO @ Sun, 02 Jun 2019 18:59:35: end of X-cor INFO @ Sun, 02 Jun 2019 18:59:35: #2 finished! INFO @ Sun, 02 Jun 2019 18:59:35: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 18:59:35: #2 alternative fragment length(s) may be 2,66,535,572 bps INFO @ Sun, 02 Jun 2019 18:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.20_model.r WARNING @ Sun, 02 Jun 2019 18:59:35: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:59:35: #2 You may need to consider one of the other alternative d(s): 2,66,535,572 WARNING @ Sun, 02 Jun 2019 18:59:35: #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 18:59:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:35: #2 number of paired peaks: 150 WARNING @ Sun, 02 Jun 2019 18:59:35: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sun, 02 Jun 2019 18:59:35: start model_add_line... INFO @ Sun, 02 Jun 2019 18:59:35: start X-correlation... INFO @ Sun, 02 Jun 2019 18:59:35: end of X-cor INFO @ Sun, 02 Jun 2019 18:59:35: #2 finished! INFO @ Sun, 02 Jun 2019 18:59:35: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 18:59:35: #2 alternative fragment length(s) may be 2,66,535,572 bps INFO @ Sun, 02 Jun 2019 18:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.10_model.r WARNING @ Sun, 02 Jun 2019 18:59:35: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:59:35: #2 You may need to consider one of the other alternative d(s): 2,66,535,572 WARNING @ Sun, 02 Jun 2019 18:59:35: #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 18:59:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.05_summits.bed INFO @ Sun, 02 Jun 2019 19:00:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1468 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.20_summits.bed INFO @ Sun, 02 Jun 2019 19:00:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194204/SRX4194204.10_summits.bed INFO @ Sun, 02 Jun 2019 19:00:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (536 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。