Job ID = 4178515 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,772,231 reads read : 20,772,231 reads written : 20,772,231 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: 00:08:20 20772231 reads; of these: 20772231 (100.00%) were unpaired; of these: 2383045 (11.47%) aligned 0 times 12596767 (60.64%) aligned exactly 1 time 5792419 (27.89%) aligned >1 times 88.53% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 4039241 / 18389186 = 0.2197 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.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 12:56:00: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:00: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:09: 1000000 INFO @ Thu, 05 Dec 2019 12:56:17: 2000000 INFO @ Thu, 05 Dec 2019 12:56:26: 3000000 INFO @ Thu, 05 Dec 2019 12:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.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 12:56:30: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:30: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:34: 4000000 INFO @ Thu, 05 Dec 2019 12:56:41: 1000000 INFO @ Thu, 05 Dec 2019 12:56:43: 5000000 INFO @ Thu, 05 Dec 2019 12:56:51: 6000000 INFO @ Thu, 05 Dec 2019 12:56:53: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.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 12:57:00: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:00: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:00: 7000000 INFO @ Thu, 05 Dec 2019 12:57:06: 3000000 INFO @ Thu, 05 Dec 2019 12:57:10: 8000000 INFO @ Thu, 05 Dec 2019 12:57:11: 1000000 INFO @ Thu, 05 Dec 2019 12:57:18: 9000000 INFO @ Thu, 05 Dec 2019 12:57:19: 4000000 INFO @ Thu, 05 Dec 2019 12:57:23: 2000000 INFO @ Thu, 05 Dec 2019 12:57:27: 10000000 INFO @ Thu, 05 Dec 2019 12:57:33: 5000000 INFO @ Thu, 05 Dec 2019 12:57:34: 3000000 INFO @ Thu, 05 Dec 2019 12:57:36: 11000000 INFO @ Thu, 05 Dec 2019 12:57:44: 12000000 INFO @ Thu, 05 Dec 2019 12:57:46: 6000000 INFO @ Thu, 05 Dec 2019 12:57:46: 4000000 INFO @ Thu, 05 Dec 2019 12:57:53: 13000000 INFO @ Thu, 05 Dec 2019 12:58:04: 5000000 INFO @ Thu, 05 Dec 2019 12:58:05: 7000000 INFO @ Thu, 05 Dec 2019 12:58:05: 14000000 INFO @ Thu, 05 Dec 2019 12:58:10: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:58:10: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:58:10: #1 total tags in treatment: 14349945 INFO @ Thu, 05 Dec 2019 12:58:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:58:10: #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 12:58:11: #1 tags after filtering in treatment: 14349945 INFO @ Thu, 05 Dec 2019 12:58:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:58:11: #1 finished! INFO @ Thu, 05 Dec 2019 12:58:11: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:58:14: #2 number of paired peaks: 110 WARNING @ Thu, 05 Dec 2019 12:58:14: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Thu, 05 Dec 2019 12:58:14: start model_add_line... INFO @ Thu, 05 Dec 2019 12:58:14: start X-correlation... INFO @ Thu, 05 Dec 2019 12:58:14: end of X-cor INFO @ Thu, 05 Dec 2019 12:58:14: #2 finished! INFO @ Thu, 05 Dec 2019 12:58:14: #2 predicted fragment length is 66 bps INFO @ Thu, 05 Dec 2019 12:58:14: #2 alternative fragment length(s) may be 40,66,103,131,180,193,218,263,305,380,387,408,448,501,531,570,593 bps INFO @ Thu, 05 Dec 2019 12:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.05_model.r WARNING @ Thu, 05 Dec 2019 12:58:14: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:58:14: #2 You may need to consider one of the other alternative d(s): 40,66,103,131,180,193,218,263,305,380,387,408,448,501,531,570,593 WARNING @ Thu, 05 Dec 2019 12:58:14: #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 12:58:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:58:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:58:20: 6000000 INFO @ Thu, 05 Dec 2019 12:58:22: 8000000 INFO @ Thu, 05 Dec 2019 12:58:30: 7000000 INFO @ Thu, 05 Dec 2019 12:58:33: 9000000 INFO @ Thu, 05 Dec 2019 12:58:40: 8000000 INFO @ Thu, 05 Dec 2019 12:58:43: 10000000 INFO @ Thu, 05 Dec 2019 12:58:49: 9000000 INFO @ Thu, 05 Dec 2019 12:58:55: 11000000 INFO @ Thu, 05 Dec 2019 12:58:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:58: 10000000 INFO @ Thu, 05 Dec 2019 12:59:08: 11000000 INFO @ Thu, 05 Dec 2019 12:59:08: 12000000 INFO @ Thu, 05 Dec 2019 12:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.05_summits.bed INFO @ Thu, 05 Dec 2019 12:59:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1670 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:59:17: 12000000 INFO @ Thu, 05 Dec 2019 12:59:21: 13000000 INFO @ Thu, 05 Dec 2019 12:59:26: 13000000 INFO @ Thu, 05 Dec 2019 12:59:34: 14000000 INFO @ Thu, 05 Dec 2019 12:59:35: 14000000 INFO @ Thu, 05 Dec 2019 12:59:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:38: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:38: #1 total tags in treatment: 14349945 INFO @ Thu, 05 Dec 2019 12:59:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:38: #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 12:59:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:38: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:38: #1 total tags in treatment: 14349945 INFO @ Thu, 05 Dec 2019 12:59:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:38: #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 12:59:38: #1 tags after filtering in treatment: 14349945 INFO @ Thu, 05 Dec 2019 12:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:38: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:38: #1 tags after filtering in treatment: 14349945 INFO @ Thu, 05 Dec 2019 12:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:38: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:39: #2 number of paired peaks: 110 WARNING @ Thu, 05 Dec 2019 12:59:39: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:39: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:40: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:40: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:40: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:40: #2 predicted fragment length is 66 bps INFO @ Thu, 05 Dec 2019 12:59:40: #2 alternative fragment length(s) may be 40,66,103,131,180,193,218,263,305,380,387,408,448,501,531,570,593 bps INFO @ Thu, 05 Dec 2019 12:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.10_model.r WARNING @ Thu, 05 Dec 2019 12:59:40: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:40: #2 You may need to consider one of the other alternative d(s): 40,66,103,131,180,193,218,263,305,380,387,408,448,501,531,570,593 WARNING @ Thu, 05 Dec 2019 12:59:40: #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 12:59:40: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:40: #2 number of paired peaks: 110 WARNING @ Thu, 05 Dec 2019 12:59:40: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:40: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:40: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:40: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:40: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:40: #2 predicted fragment length is 66 bps INFO @ Thu, 05 Dec 2019 12:59:40: #2 alternative fragment length(s) may be 40,66,103,131,180,193,218,263,305,380,387,408,448,501,531,570,593 bps INFO @ Thu, 05 Dec 2019 12:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.20_model.r WARNING @ Thu, 05 Dec 2019 12:59:40: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:40: #2 You may need to consider one of the other alternative d(s): 40,66,103,131,180,193,218,263,305,380,387,408,448,501,531,570,593 WARNING @ Thu, 05 Dec 2019 12:59:40: #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 12:59:40: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:00:25: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.20_summits.bed INFO @ Thu, 05 Dec 2019 13:00:45: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717037/SRX5717037.10_summits.bed INFO @ Thu, 05 Dec 2019 13:00:48: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (835 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。