Job ID = 4178452 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,129,941 reads read : 36,259,882 reads written : 18,129,941 reads 0-length : 18,129,941 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:23 18129941 reads; of these: 18129941 (100.00%) were unpaired; of these: 1411310 (7.78%) aligned 0 times 14399140 (79.42%) aligned exactly 1 time 2319491 (12.79%) aligned >1 times 92.22% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6170121 / 16718631 = 0.3691 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:43:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:43:56: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:43:56: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:02: 1000000 INFO @ Thu, 05 Dec 2019 12:44:09: 2000000 INFO @ Thu, 05 Dec 2019 12:44:15: 3000000 INFO @ Thu, 05 Dec 2019 12:44:22: 4000000 INFO @ Thu, 05 Dec 2019 12:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:44:24: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:44:24: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:29: 5000000 INFO @ Thu, 05 Dec 2019 12:44:31: 1000000 INFO @ Thu, 05 Dec 2019 12:44:37: 6000000 INFO @ Thu, 05 Dec 2019 12:44:39: 2000000 INFO @ Thu, 05 Dec 2019 12:44:44: 7000000 INFO @ Thu, 05 Dec 2019 12:44:46: 3000000 INFO @ Thu, 05 Dec 2019 12:44:51: 8000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:44:54: 4000000 INFO @ Thu, 05 Dec 2019 12:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:44:54: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:44:54: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:59: 9000000 INFO @ Thu, 05 Dec 2019 12:45:02: 5000000 INFO @ Thu, 05 Dec 2019 12:45:02: 1000000 INFO @ Thu, 05 Dec 2019 12:45:08: 10000000 INFO @ Thu, 05 Dec 2019 12:45:10: 6000000 INFO @ Thu, 05 Dec 2019 12:45:10: 2000000 INFO @ Thu, 05 Dec 2019 12:45:12: #1 tag size is determined as 101 bps INFO @ Thu, 05 Dec 2019 12:45:12: #1 tag size = 101 INFO @ Thu, 05 Dec 2019 12:45:12: #1 total tags in treatment: 10548510 INFO @ Thu, 05 Dec 2019 12:45:12: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:45:12: #1 tags after filtering in treatment: 10548510 INFO @ Thu, 05 Dec 2019 12:45:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:12: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:12: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:13: #2 number of paired peaks: 175 WARNING @ Thu, 05 Dec 2019 12:45:13: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:13: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:13: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:13: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:13: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:13: #2 predicted fragment length is 186 bps INFO @ Thu, 05 Dec 2019 12:45:13: #2 alternative fragment length(s) may be 168,186 bps INFO @ Thu, 05 Dec 2019 12:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.05_model.r WARNING @ Thu, 05 Dec 2019 12:45:13: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:45:13: #2 You may need to consider one of the other alternative d(s): 168,186 WARNING @ Thu, 05 Dec 2019 12:45:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:45:13: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:18: 7000000 INFO @ Thu, 05 Dec 2019 12:45:18: 3000000 INFO @ Thu, 05 Dec 2019 12:45:26: 8000000 INFO @ Thu, 05 Dec 2019 12:45:26: 4000000 INFO @ Thu, 05 Dec 2019 12:45:34: 9000000 INFO @ Thu, 05 Dec 2019 12:45:34: 5000000 INFO @ Thu, 05 Dec 2019 12:45:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:45:42: 10000000 INFO @ Thu, 05 Dec 2019 12:45:42: 6000000 INFO @ Thu, 05 Dec 2019 12:45:46: #1 tag size is determined as 101 bps INFO @ Thu, 05 Dec 2019 12:45:46: #1 tag size = 101 INFO @ Thu, 05 Dec 2019 12:45:46: #1 total tags in treatment: 10548510 INFO @ Thu, 05 Dec 2019 12:45:46: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:45:46: #1 tags after filtering in treatment: 10548510 INFO @ Thu, 05 Dec 2019 12:45:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:46: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:46: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.05_summits.bed INFO @ Thu, 05 Dec 2019 12:45:47: Done! INFO @ Thu, 05 Dec 2019 12:45:47: #2 number of paired peaks: 175 WARNING @ Thu, 05 Dec 2019 12:45:47: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:47: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:47: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:47: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:47: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:47: #2 predicted fragment length is 186 bps INFO @ Thu, 05 Dec 2019 12:45:47: #2 alternative fragment length(s) may be 168,186 bps INFO @ Thu, 05 Dec 2019 12:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.10_model.r WARNING @ Thu, 05 Dec 2019 12:45:47: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:45:47: #2 You may need to consider one of the other alternative d(s): 168,186 WARNING @ Thu, 05 Dec 2019 12:45:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:45:47: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:47: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2888 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:45:50: 7000000 INFO @ Thu, 05 Dec 2019 12:45:57: 8000000 INFO @ Thu, 05 Dec 2019 12:46:05: 9000000 INFO @ Thu, 05 Dec 2019 12:46:08: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:46:13: 10000000 INFO @ Thu, 05 Dec 2019 12:46:17: #1 tag size is determined as 101 bps INFO @ Thu, 05 Dec 2019 12:46:17: #1 tag size = 101 INFO @ Thu, 05 Dec 2019 12:46:17: #1 total tags in treatment: 10548510 INFO @ Thu, 05 Dec 2019 12:46:17: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:46:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:46:17: #1 tags after filtering in treatment: 10548510 INFO @ Thu, 05 Dec 2019 12:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:46:17: #1 finished! INFO @ Thu, 05 Dec 2019 12:46:17: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:46:18: #2 number of paired peaks: 175 WARNING @ Thu, 05 Dec 2019 12:46:18: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 05 Dec 2019 12:46:18: start model_add_line... INFO @ Thu, 05 Dec 2019 12:46:18: start X-correlation... INFO @ Thu, 05 Dec 2019 12:46:18: end of X-cor INFO @ Thu, 05 Dec 2019 12:46:18: #2 finished! INFO @ Thu, 05 Dec 2019 12:46:18: #2 predicted fragment length is 186 bps INFO @ Thu, 05 Dec 2019 12:46:18: #2 alternative fragment length(s) may be 168,186 bps INFO @ Thu, 05 Dec 2019 12:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.20_model.r WARNING @ Thu, 05 Dec 2019 12:46:18: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:46:18: #2 You may need to consider one of the other alternative d(s): 168,186 WARNING @ Thu, 05 Dec 2019 12:46:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:46:18: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.10_summits.bed INFO @ Thu, 05 Dec 2019 12:46:21: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:46:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:46:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:46:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:46:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4510351/SRX4510351.20_summits.bed INFO @ Thu, 05 Dec 2019 12:46:51: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (311 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。