Job ID = 1292541 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 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: 00:05:48 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171821 (0.56%) aligned 0 times 25273572 (82.09%) aligned exactly 1 time 5342756 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 4710738 / 30616328 = 0.1539 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 19:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.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 19:47:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:47:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.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 19:47:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:47:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.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 19:47:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:47:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:47:57: 1000000 INFO @ Sun, 02 Jun 2019 19:47:57: 1000000 INFO @ Sun, 02 Jun 2019 19:47:59: 1000000 INFO @ Sun, 02 Jun 2019 19:48:04: 2000000 INFO @ Sun, 02 Jun 2019 19:48:05: 2000000 INFO @ Sun, 02 Jun 2019 19:48:08: 2000000 INFO @ Sun, 02 Jun 2019 19:48:11: 3000000 INFO @ Sun, 02 Jun 2019 19:48:12: 3000000 INFO @ Sun, 02 Jun 2019 19:48:16: 3000000 INFO @ Sun, 02 Jun 2019 19:48:18: 4000000 INFO @ Sun, 02 Jun 2019 19:48:20: 4000000 INFO @ Sun, 02 Jun 2019 19:48:24: 4000000 INFO @ Sun, 02 Jun 2019 19:48:25: 5000000 INFO @ Sun, 02 Jun 2019 19:48:27: 5000000 INFO @ Sun, 02 Jun 2019 19:48:32: 5000000 INFO @ Sun, 02 Jun 2019 19:48:32: 6000000 INFO @ Sun, 02 Jun 2019 19:48:34: 6000000 INFO @ Sun, 02 Jun 2019 19:48:40: 7000000 INFO @ Sun, 02 Jun 2019 19:48:40: 6000000 INFO @ Sun, 02 Jun 2019 19:48:42: 7000000 INFO @ Sun, 02 Jun 2019 19:48:47: 8000000 INFO @ Sun, 02 Jun 2019 19:48:49: 7000000 INFO @ Sun, 02 Jun 2019 19:48:51: 8000000 INFO @ Sun, 02 Jun 2019 19:48:54: 9000000 INFO @ Sun, 02 Jun 2019 19:48:58: 8000000 INFO @ Sun, 02 Jun 2019 19:48:58: 9000000 INFO @ Sun, 02 Jun 2019 19:49:01: 10000000 INFO @ Sun, 02 Jun 2019 19:49:05: 10000000 INFO @ Sun, 02 Jun 2019 19:49:06: 9000000 INFO @ Sun, 02 Jun 2019 19:49:08: 11000000 INFO @ Sun, 02 Jun 2019 19:49:12: 11000000 INFO @ Sun, 02 Jun 2019 19:49:15: 10000000 INFO @ Sun, 02 Jun 2019 19:49:16: 12000000 INFO @ Sun, 02 Jun 2019 19:49:20: 12000000 INFO @ Sun, 02 Jun 2019 19:49:23: 11000000 INFO @ Sun, 02 Jun 2019 19:49:23: 13000000 INFO @ Sun, 02 Jun 2019 19:49:27: 13000000 INFO @ Sun, 02 Jun 2019 19:49:31: 14000000 INFO @ Sun, 02 Jun 2019 19:49:31: 12000000 INFO @ Sun, 02 Jun 2019 19:49:34: 14000000 INFO @ Sun, 02 Jun 2019 19:49:38: 15000000 INFO @ Sun, 02 Jun 2019 19:49:40: 13000000 INFO @ Sun, 02 Jun 2019 19:49:41: 15000000 INFO @ Sun, 02 Jun 2019 19:49:46: 16000000 INFO @ Sun, 02 Jun 2019 19:49:48: 14000000 INFO @ Sun, 02 Jun 2019 19:49:48: 16000000 INFO @ Sun, 02 Jun 2019 19:49:53: 17000000 INFO @ Sun, 02 Jun 2019 19:49:55: 17000000 INFO @ Sun, 02 Jun 2019 19:49:56: 15000000 INFO @ Sun, 02 Jun 2019 19:50:00: 18000000 INFO @ Sun, 02 Jun 2019 19:50:02: 18000000 INFO @ Sun, 02 Jun 2019 19:50:04: 16000000 INFO @ Sun, 02 Jun 2019 19:50:07: 19000000 INFO @ Sun, 02 Jun 2019 19:50:09: 19000000 INFO @ Sun, 02 Jun 2019 19:50:12: 17000000 INFO @ Sun, 02 Jun 2019 19:50:14: 20000000 INFO @ Sun, 02 Jun 2019 19:50:16: 20000000 INFO @ Sun, 02 Jun 2019 19:50:21: 18000000 INFO @ Sun, 02 Jun 2019 19:50:21: 21000000 INFO @ Sun, 02 Jun 2019 19:50:23: 21000000 INFO @ Sun, 02 Jun 2019 19:50:28: 22000000 INFO @ Sun, 02 Jun 2019 19:50:29: 19000000 INFO @ Sun, 02 Jun 2019 19:50:31: 22000000 INFO @ Sun, 02 Jun 2019 19:50:36: 23000000 INFO @ Sun, 02 Jun 2019 19:50:37: 20000000 INFO @ Sun, 02 Jun 2019 19:50:38: 23000000 INFO @ Sun, 02 Jun 2019 19:50:42: 24000000 INFO @ Sun, 02 Jun 2019 19:50:45: 24000000 INFO @ Sun, 02 Jun 2019 19:50:45: 21000000 INFO @ Sun, 02 Jun 2019 19:50:49: 25000000 INFO @ Sun, 02 Jun 2019 19:50:52: 25000000 INFO @ Sun, 02 Jun 2019 19:50:53: 22000000 INFO @ Sun, 02 Jun 2019 19:50:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:50:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:50:56: #1 total tags in treatment: 25905590 INFO @ Sun, 02 Jun 2019 19:50:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:50:56: #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 19:50:56: #1 tags after filtering in treatment: 25905590 INFO @ Sun, 02 Jun 2019 19:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:50:56: #1 finished! INFO @ Sun, 02 Jun 2019 19:50:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:50:59: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:50:59: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:50:59: #1 total tags in treatment: 25905590 INFO @ Sun, 02 Jun 2019 19:50:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:50:59: #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 19:50:59: #2 number of paired peaks: 145 WARNING @ Sun, 02 Jun 2019 19:50:59: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sun, 02 Jun 2019 19:50:59: start model_add_line... INFO @ Sun, 02 Jun 2019 19:50:59: start X-correlation... INFO @ Sun, 02 Jun 2019 19:50:59: end of X-cor INFO @ Sun, 02 Jun 2019 19:50:59: #2 finished! INFO @ Sun, 02 Jun 2019 19:50:59: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:50:59: #2 alternative fragment length(s) may be 1,450,523,538,558,576 bps INFO @ Sun, 02 Jun 2019 19:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.05_model.r WARNING @ Sun, 02 Jun 2019 19:50:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:50:59: #2 You may need to consider one of the other alternative d(s): 1,450,523,538,558,576 WARNING @ Sun, 02 Jun 2019 19:50:59: #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 19:50:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:50:59: #1 tags after filtering in treatment: 25905590 INFO @ Sun, 02 Jun 2019 19:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:50:59: #1 finished! INFO @ Sun, 02 Jun 2019 19:50:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:51:01: #2 number of paired peaks: 145 WARNING @ Sun, 02 Jun 2019 19:51:01: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sun, 02 Jun 2019 19:51:01: start model_add_line... INFO @ Sun, 02 Jun 2019 19:51:01: start X-correlation... INFO @ Sun, 02 Jun 2019 19:51:01: end of X-cor INFO @ Sun, 02 Jun 2019 19:51:01: #2 finished! INFO @ Sun, 02 Jun 2019 19:51:01: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:51:01: #2 alternative fragment length(s) may be 1,450,523,538,558,576 bps INFO @ Sun, 02 Jun 2019 19:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.10_model.r WARNING @ Sun, 02 Jun 2019 19:51:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:51:01: #2 You may need to consider one of the other alternative d(s): 1,450,523,538,558,576 WARNING @ Sun, 02 Jun 2019 19:51:01: #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 19:51:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:51:02: 23000000 INFO @ Sun, 02 Jun 2019 19:51:10: 24000000 INFO @ Sun, 02 Jun 2019 19:51:18: 25000000 INFO @ Sun, 02 Jun 2019 19:51:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:51:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:51:25: #1 total tags in treatment: 25905590 INFO @ Sun, 02 Jun 2019 19:51:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:51:25: #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 19:51:26: #1 tags after filtering in treatment: 25905590 INFO @ Sun, 02 Jun 2019 19:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:51:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:51:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:51:28: #2 number of paired peaks: 145 WARNING @ Sun, 02 Jun 2019 19:51:28: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sun, 02 Jun 2019 19:51:28: start model_add_line... INFO @ Sun, 02 Jun 2019 19:51:28: start X-correlation... INFO @ Sun, 02 Jun 2019 19:51:28: end of X-cor INFO @ Sun, 02 Jun 2019 19:51:28: #2 finished! INFO @ Sun, 02 Jun 2019 19:51:28: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:51:28: #2 alternative fragment length(s) may be 1,450,523,538,558,576 bps INFO @ Sun, 02 Jun 2019 19:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.20_model.r WARNING @ Sun, 02 Jun 2019 19:51:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:51:28: #2 You may need to consider one of the other alternative d(s): 1,450,523,538,558,576 WARNING @ Sun, 02 Jun 2019 19:51:28: #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 19:51:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:51:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:51:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.05_summits.bed INFO @ Sun, 02 Jun 2019 19:52:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.10_summits.bed INFO @ Sun, 02 Jun 2019 19:52:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:52:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466555/SRX466555.20_summits.bed INFO @ Sun, 02 Jun 2019 19:52:42: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。