Job ID = 2589361 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,516,788 reads read : 19,516,788 reads written : 19,516,788 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:15 19516788 reads; of these: 19516788 (100.00%) were unpaired; of these: 356991 (1.83%) aligned 0 times 15881327 (81.37%) aligned exactly 1 time 3278470 (16.80%) aligned >1 times 98.17% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 2283725 / 19159797 = 0.1192 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 @ Mon, 12 Aug 2019 17:51:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.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 @ Mon, 12 Aug 2019 17:51:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:51:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.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 @ Mon, 12 Aug 2019 17:51:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:51:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.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 @ Mon, 12 Aug 2019 17:51:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:51:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:51:43: 1000000 INFO @ Mon, 12 Aug 2019 17:51:45: 1000000 INFO @ Mon, 12 Aug 2019 17:51:49: 1000000 INFO @ Mon, 12 Aug 2019 17:51:50: 2000000 INFO @ Mon, 12 Aug 2019 17:51:54: 2000000 INFO @ Mon, 12 Aug 2019 17:51:58: 3000000 INFO @ Mon, 12 Aug 2019 17:52:00: 2000000 INFO @ Mon, 12 Aug 2019 17:52:03: 3000000 INFO @ Mon, 12 Aug 2019 17:52:06: 4000000 INFO @ Mon, 12 Aug 2019 17:52:12: 3000000 INFO @ Mon, 12 Aug 2019 17:52:12: 4000000 INFO @ Mon, 12 Aug 2019 17:52:13: 5000000 INFO @ Mon, 12 Aug 2019 17:52:21: 5000000 INFO @ Mon, 12 Aug 2019 17:52:21: 6000000 INFO @ Mon, 12 Aug 2019 17:52:23: 4000000 INFO @ Mon, 12 Aug 2019 17:52:28: 7000000 INFO @ Mon, 12 Aug 2019 17:52:29: 6000000 INFO @ Mon, 12 Aug 2019 17:52:33: 5000000 INFO @ Mon, 12 Aug 2019 17:52:36: 8000000 INFO @ Mon, 12 Aug 2019 17:52:38: 7000000 INFO @ Mon, 12 Aug 2019 17:52:43: 9000000 INFO @ Mon, 12 Aug 2019 17:52:44: 6000000 INFO @ Mon, 12 Aug 2019 17:52:47: 8000000 INFO @ Mon, 12 Aug 2019 17:52:51: 10000000 INFO @ Mon, 12 Aug 2019 17:52:54: 7000000 INFO @ Mon, 12 Aug 2019 17:52:56: 9000000 INFO @ Mon, 12 Aug 2019 17:52:59: 11000000 INFO @ Mon, 12 Aug 2019 17:53:05: 10000000 INFO @ Mon, 12 Aug 2019 17:53:05: 8000000 INFO @ Mon, 12 Aug 2019 17:53:08: 12000000 INFO @ Mon, 12 Aug 2019 17:53:14: 11000000 INFO @ Mon, 12 Aug 2019 17:53:16: 13000000 INFO @ Mon, 12 Aug 2019 17:53:17: 9000000 INFO @ Mon, 12 Aug 2019 17:53:23: 14000000 INFO @ Mon, 12 Aug 2019 17:53:24: 12000000 INFO @ Mon, 12 Aug 2019 17:53:27: 10000000 INFO @ Mon, 12 Aug 2019 17:53:32: 15000000 INFO @ Mon, 12 Aug 2019 17:53:32: 13000000 INFO @ Mon, 12 Aug 2019 17:53:39: 11000000 INFO @ Mon, 12 Aug 2019 17:53:40: 16000000 INFO @ Mon, 12 Aug 2019 17:53:41: 14000000 INFO @ Mon, 12 Aug 2019 17:53:47: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:53:47: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:53:47: #1 total tags in treatment: 16876072 INFO @ Mon, 12 Aug 2019 17:53:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:53:47: #1 tags after filtering in treatment: 16876072 INFO @ Mon, 12 Aug 2019 17:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:47: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:49: #2 number of paired peaks: 275 WARNING @ Mon, 12 Aug 2019 17:53:49: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Mon, 12 Aug 2019 17:53:49: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:49: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:49: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:49: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:49: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 17:53:49: #2 alternative fragment length(s) may be 1,48 bps INFO @ Mon, 12 Aug 2019 17:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.05_model.r WARNING @ Mon, 12 Aug 2019 17:53:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:53:49: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Mon, 12 Aug 2019 17:53:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:53:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:50: 12000000 INFO @ Mon, 12 Aug 2019 17:53:51: 15000000 INFO @ Mon, 12 Aug 2019 17:54:00: 16000000 INFO @ Mon, 12 Aug 2019 17:54:01: 13000000 INFO @ Mon, 12 Aug 2019 17:54:08: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:54:08: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:54:08: #1 total tags in treatment: 16876072 INFO @ Mon, 12 Aug 2019 17:54:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:54:08: #1 tags after filtering in treatment: 16876072 INFO @ Mon, 12 Aug 2019 17:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:08: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:10: #2 number of paired peaks: 275 WARNING @ Mon, 12 Aug 2019 17:54:10: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:10: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:10: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:10: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:10: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:10: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 17:54:10: #2 alternative fragment length(s) may be 1,48 bps INFO @ Mon, 12 Aug 2019 17:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.10_model.r WARNING @ Mon, 12 Aug 2019 17:54:10: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:10: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Mon, 12 Aug 2019 17:54:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:54:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:10: 14000000 INFO @ Mon, 12 Aug 2019 17:54:19: 15000000 INFO @ Mon, 12 Aug 2019 17:54:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:30: 16000000 INFO @ Mon, 12 Aug 2019 17:54:40: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:54:40: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:54:40: #1 total tags in treatment: 16876072 INFO @ Mon, 12 Aug 2019 17:54:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:54:40: #1 tags after filtering in treatment: 16876072 INFO @ Mon, 12 Aug 2019 17:54:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:40: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:41: #2 number of paired peaks: 275 WARNING @ Mon, 12 Aug 2019 17:54:41: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:41: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:42: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:42: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:42: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:42: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 17:54:42: #2 alternative fragment length(s) may be 1,48 bps INFO @ Mon, 12 Aug 2019 17:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.20_model.r WARNING @ Mon, 12 Aug 2019 17:54:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:42: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Mon, 12 Aug 2019 17:54:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:54:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.10_summits.bed INFO @ Mon, 12 Aug 2019 17:55:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:55:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078714/SRX1078714.20_summits.bed INFO @ Mon, 12 Aug 2019 17:55:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (196 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。