Job ID = 1293026 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,496,496 reads read : 22,992,992 reads written : 11,496,496 reads 0-length : 11,496,496 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: 00:02:56 11496496 reads; of these: 11496496 (100.00%) were unpaired; of these: 226503 (1.97%) aligned 0 times 9484871 (82.50%) aligned exactly 1 time 1785122 (15.53%) aligned >1 times 98.03% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 796383 / 11269993 = 0.0707 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 21:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.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 21:34:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:34:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.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 21:34:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:34:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.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 21:34:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:34:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:02: 1000000 INFO @ Sun, 02 Jun 2019 21:35:02: 1000000 INFO @ Sun, 02 Jun 2019 21:35:05: 1000000 INFO @ Sun, 02 Jun 2019 21:35:10: 2000000 INFO @ Sun, 02 Jun 2019 21:35:11: 2000000 INFO @ Sun, 02 Jun 2019 21:35:15: 2000000 INFO @ Sun, 02 Jun 2019 21:35:18: 3000000 INFO @ Sun, 02 Jun 2019 21:35:19: 3000000 INFO @ Sun, 02 Jun 2019 21:35:26: 3000000 INFO @ Sun, 02 Jun 2019 21:35:26: 4000000 INFO @ Sun, 02 Jun 2019 21:35:27: 4000000 INFO @ Sun, 02 Jun 2019 21:35:34: 5000000 INFO @ Sun, 02 Jun 2019 21:35:36: 4000000 INFO @ Sun, 02 Jun 2019 21:35:36: 5000000 INFO @ Sun, 02 Jun 2019 21:35:43: 6000000 INFO @ Sun, 02 Jun 2019 21:35:46: 6000000 INFO @ Sun, 02 Jun 2019 21:35:47: 5000000 INFO @ Sun, 02 Jun 2019 21:35:52: 7000000 INFO @ Sun, 02 Jun 2019 21:35:55: 7000000 INFO @ Sun, 02 Jun 2019 21:35:57: 6000000 INFO @ Sun, 02 Jun 2019 21:36:00: 8000000 INFO @ Sun, 02 Jun 2019 21:36:04: 8000000 INFO @ Sun, 02 Jun 2019 21:36:08: 7000000 INFO @ Sun, 02 Jun 2019 21:36:08: 9000000 INFO @ Sun, 02 Jun 2019 21:36:13: 9000000 INFO @ Sun, 02 Jun 2019 21:36:16: 10000000 INFO @ Sun, 02 Jun 2019 21:36:18: 8000000 INFO @ Sun, 02 Jun 2019 21:36:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:36:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:36:20: #1 total tags in treatment: 10473610 INFO @ Sun, 02 Jun 2019 21:36:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:20: #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 21:36:20: #1 tags after filtering in treatment: 10473610 INFO @ Sun, 02 Jun 2019 21:36:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:20: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:21: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 21:36:21: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:21: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:21: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:21: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:21: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:21: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 21:36:21: #2 alternative fragment length(s) may be 2,50,551 bps INFO @ Sun, 02 Jun 2019 21:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.20_model.r WARNING @ Sun, 02 Jun 2019 21:36:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:36:21: #2 You may need to consider one of the other alternative d(s): 2,50,551 WARNING @ Sun, 02 Jun 2019 21:36:21: #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 21:36:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:21: 10000000 INFO @ Sun, 02 Jun 2019 21:36:25: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:36:25: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:36:25: #1 total tags in treatment: 10473610 INFO @ Sun, 02 Jun 2019 21:36:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:25: #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 21:36:26: #1 tags after filtering in treatment: 10473610 INFO @ Sun, 02 Jun 2019 21:36:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:26: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:27: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 21:36:27: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:27: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:27: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:27: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:27: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:27: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 21:36:27: #2 alternative fragment length(s) may be 2,50,551 bps INFO @ Sun, 02 Jun 2019 21:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.10_model.r WARNING @ Sun, 02 Jun 2019 21:36:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:36:27: #2 You may need to consider one of the other alternative d(s): 2,50,551 WARNING @ Sun, 02 Jun 2019 21:36:27: #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 21:36:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:28: 9000000 INFO @ Sun, 02 Jun 2019 21:36:38: 10000000 INFO @ Sun, 02 Jun 2019 21:36:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:36:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:36:43: #1 total tags in treatment: 10473610 INFO @ Sun, 02 Jun 2019 21:36:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:43: #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 21:36:43: #1 tags after filtering in treatment: 10473610 INFO @ Sun, 02 Jun 2019 21:36:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:44: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 21:36:44: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:44: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:44: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:44: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:44: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:44: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 21:36:44: #2 alternative fragment length(s) may be 2,50,551 bps INFO @ Sun, 02 Jun 2019 21:36:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.05_model.r WARNING @ Sun, 02 Jun 2019 21:36:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:36:44: #2 You may need to consider one of the other alternative d(s): 2,50,551 WARNING @ Sun, 02 Jun 2019 21:36:44: #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 21:36:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:36:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.20_summits.bed INFO @ Sun, 02 Jun 2019 21:37:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.10_summits.bed INFO @ Sun, 02 Jun 2019 21:37:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020794/SRX5020794.05_summits.bed INFO @ Sun, 02 Jun 2019 21:37:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (630 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。