Job ID = 1292378 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,754,778 reads read : 21,509,556 reads written : 10,754,778 reads 0-length : 10,754,778 spots read : 20,858,613 reads read : 41,717,226 reads written : 20,858,613 reads 0-length : 20,858,613 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: 00:04:50 31613391 reads; of these: 31613391 (100.00%) were unpaired; of these: 18646920 (58.98%) aligned 0 times 10703925 (33.86%) aligned exactly 1 time 2262546 (7.16%) aligned >1 times 41.02% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 2150031 / 12966471 = 0.1658 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 18:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.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 18:29:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:29:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.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 18:29:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:29:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.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 18:29:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:29:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:29:09: 1000000 INFO @ Sun, 02 Jun 2019 18:29:09: 1000000 INFO @ Sun, 02 Jun 2019 18:29:10: 1000000 INFO @ Sun, 02 Jun 2019 18:29:15: 2000000 INFO @ Sun, 02 Jun 2019 18:29:17: 2000000 INFO @ Sun, 02 Jun 2019 18:29:18: 2000000 INFO @ Sun, 02 Jun 2019 18:29:22: 3000000 INFO @ Sun, 02 Jun 2019 18:29:24: 3000000 INFO @ Sun, 02 Jun 2019 18:29:26: 3000000 INFO @ Sun, 02 Jun 2019 18:29:29: 4000000 INFO @ Sun, 02 Jun 2019 18:29:31: 4000000 INFO @ Sun, 02 Jun 2019 18:29:35: 4000000 INFO @ Sun, 02 Jun 2019 18:29:36: 5000000 INFO @ Sun, 02 Jun 2019 18:29:38: 5000000 INFO @ Sun, 02 Jun 2019 18:29:43: 6000000 INFO @ Sun, 02 Jun 2019 18:29:43: 5000000 INFO @ Sun, 02 Jun 2019 18:29:46: 6000000 INFO @ Sun, 02 Jun 2019 18:29:49: 7000000 INFO @ Sun, 02 Jun 2019 18:29:51: 6000000 INFO @ Sun, 02 Jun 2019 18:29:53: 7000000 INFO @ Sun, 02 Jun 2019 18:29:56: 8000000 INFO @ Sun, 02 Jun 2019 18:29:59: 7000000 INFO @ Sun, 02 Jun 2019 18:30:00: 8000000 INFO @ Sun, 02 Jun 2019 18:30:02: 9000000 INFO @ Sun, 02 Jun 2019 18:30:07: 8000000 INFO @ Sun, 02 Jun 2019 18:30:07: 9000000 INFO @ Sun, 02 Jun 2019 18:30:09: 10000000 INFO @ Sun, 02 Jun 2019 18:30:14: 10000000 INFO @ Sun, 02 Jun 2019 18:30:14: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 18:30:14: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 18:30:14: #1 total tags in treatment: 10816440 INFO @ Sun, 02 Jun 2019 18:30:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:30:14: #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 18:30:14: #1 tags after filtering in treatment: 10816440 INFO @ Sun, 02 Jun 2019 18:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:30:14: #1 finished! INFO @ Sun, 02 Jun 2019 18:30:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:30:14: 9000000 INFO @ Sun, 02 Jun 2019 18:30:15: #2 number of paired peaks: 355 WARNING @ Sun, 02 Jun 2019 18:30:15: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Sun, 02 Jun 2019 18:30:15: start model_add_line... INFO @ Sun, 02 Jun 2019 18:30:15: start X-correlation... INFO @ Sun, 02 Jun 2019 18:30:15: end of X-cor INFO @ Sun, 02 Jun 2019 18:30:15: #2 finished! INFO @ Sun, 02 Jun 2019 18:30:15: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:30:15: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 02 Jun 2019 18:30:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.10_model.r WARNING @ Sun, 02 Jun 2019 18:30:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:30:16: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 02 Jun 2019 18:30:16: #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 18:30:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:30:20: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 18:30:20: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 18:30:20: #1 total tags in treatment: 10816440 INFO @ Sun, 02 Jun 2019 18:30:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:30:20: #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 18:30:20: #1 tags after filtering in treatment: 10816440 INFO @ Sun, 02 Jun 2019 18:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:30:20: #1 finished! INFO @ Sun, 02 Jun 2019 18:30:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:30:21: #2 number of paired peaks: 355 WARNING @ Sun, 02 Jun 2019 18:30:21: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Sun, 02 Jun 2019 18:30:21: start model_add_line... INFO @ Sun, 02 Jun 2019 18:30:21: start X-correlation... INFO @ Sun, 02 Jun 2019 18:30:21: end of X-cor INFO @ Sun, 02 Jun 2019 18:30:21: #2 finished! INFO @ Sun, 02 Jun 2019 18:30:21: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:30:21: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 02 Jun 2019 18:30:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.05_model.r WARNING @ Sun, 02 Jun 2019 18:30:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:30:21: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 02 Jun 2019 18:30:21: #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 18:30:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:30:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:30:22: 10000000 INFO @ Sun, 02 Jun 2019 18:30:29: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 18:30:29: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 18:30:29: #1 total tags in treatment: 10816440 INFO @ Sun, 02 Jun 2019 18:30:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:30:29: #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 18:30:29: #1 tags after filtering in treatment: 10816440 INFO @ Sun, 02 Jun 2019 18:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:30:29: #1 finished! INFO @ Sun, 02 Jun 2019 18:30:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:30:30: #2 number of paired peaks: 355 WARNING @ Sun, 02 Jun 2019 18:30:30: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Sun, 02 Jun 2019 18:30:30: start model_add_line... INFO @ Sun, 02 Jun 2019 18:30:30: start X-correlation... INFO @ Sun, 02 Jun 2019 18:30:30: end of X-cor INFO @ Sun, 02 Jun 2019 18:30:30: #2 finished! INFO @ Sun, 02 Jun 2019 18:30:30: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:30:30: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 02 Jun 2019 18:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.20_model.r WARNING @ Sun, 02 Jun 2019 18:30:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:30:30: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 02 Jun 2019 18:30:30: #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 18:30:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:30:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:30:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.10_summits.bed INFO @ Sun, 02 Jun 2019 18:30:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:30:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.05_summits.bed INFO @ Sun, 02 Jun 2019 18:31:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3883437/SRX3883437.20_summits.bed INFO @ Sun, 02 Jun 2019 18:31:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (231 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。