Job ID = 2590247 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,222,950 reads read : 30,222,950 reads written : 30,222,950 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: 00:11:00 30222950 reads; of these: 30222950 (100.00%) were unpaired; of these: 564977 (1.87%) aligned 0 times 24368073 (80.63%) aligned exactly 1 time 5289900 (17.50%) aligned >1 times 98.13% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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 16 files... [bam_rmdupse_core] 3793432 / 29657973 = 0.1279 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 20:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.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 20:52:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:52:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.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 20:52:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:52:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.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 20:52:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:52:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:27: 1000000 INFO @ Mon, 12 Aug 2019 20:52:28: 1000000 INFO @ Mon, 12 Aug 2019 20:52:29: 1000000 INFO @ Mon, 12 Aug 2019 20:52:35: 2000000 INFO @ Mon, 12 Aug 2019 20:52:36: 2000000 INFO @ Mon, 12 Aug 2019 20:52:37: 2000000 INFO @ Mon, 12 Aug 2019 20:52:42: 3000000 INFO @ Mon, 12 Aug 2019 20:52:43: 3000000 INFO @ Mon, 12 Aug 2019 20:52:44: 3000000 INFO @ Mon, 12 Aug 2019 20:52:50: 4000000 INFO @ Mon, 12 Aug 2019 20:52:51: 4000000 INFO @ Mon, 12 Aug 2019 20:52:52: 4000000 INFO @ Mon, 12 Aug 2019 20:52:58: 5000000 INFO @ Mon, 12 Aug 2019 20:52:59: 5000000 INFO @ Mon, 12 Aug 2019 20:53:00: 5000000 INFO @ Mon, 12 Aug 2019 20:53:06: 6000000 INFO @ Mon, 12 Aug 2019 20:53:06: 6000000 INFO @ Mon, 12 Aug 2019 20:53:08: 6000000 INFO @ Mon, 12 Aug 2019 20:53:13: 7000000 INFO @ Mon, 12 Aug 2019 20:53:14: 7000000 INFO @ Mon, 12 Aug 2019 20:53:15: 7000000 INFO @ Mon, 12 Aug 2019 20:53:21: 8000000 INFO @ Mon, 12 Aug 2019 20:53:22: 8000000 INFO @ Mon, 12 Aug 2019 20:53:23: 8000000 INFO @ Mon, 12 Aug 2019 20:53:29: 9000000 INFO @ Mon, 12 Aug 2019 20:53:29: 9000000 INFO @ Mon, 12 Aug 2019 20:53:31: 9000000 INFO @ Mon, 12 Aug 2019 20:53:36: 10000000 INFO @ Mon, 12 Aug 2019 20:53:37: 10000000 INFO @ Mon, 12 Aug 2019 20:53:38: 10000000 INFO @ Mon, 12 Aug 2019 20:53:44: 11000000 INFO @ Mon, 12 Aug 2019 20:53:44: 11000000 INFO @ Mon, 12 Aug 2019 20:53:46: 11000000 INFO @ Mon, 12 Aug 2019 20:53:52: 12000000 INFO @ Mon, 12 Aug 2019 20:53:52: 12000000 INFO @ Mon, 12 Aug 2019 20:53:54: 12000000 INFO @ Mon, 12 Aug 2019 20:53:59: 13000000 INFO @ Mon, 12 Aug 2019 20:54:00: 13000000 INFO @ Mon, 12 Aug 2019 20:54:01: 13000000 INFO @ Mon, 12 Aug 2019 20:54:07: 14000000 INFO @ Mon, 12 Aug 2019 20:54:07: 14000000 INFO @ Mon, 12 Aug 2019 20:54:09: 14000000 INFO @ Mon, 12 Aug 2019 20:54:15: 15000000 INFO @ Mon, 12 Aug 2019 20:54:15: 15000000 INFO @ Mon, 12 Aug 2019 20:54:17: 15000000 INFO @ Mon, 12 Aug 2019 20:54:22: 16000000 INFO @ Mon, 12 Aug 2019 20:54:23: 16000000 INFO @ Mon, 12 Aug 2019 20:54:24: 16000000 INFO @ Mon, 12 Aug 2019 20:54:30: 17000000 INFO @ Mon, 12 Aug 2019 20:54:30: 17000000 INFO @ Mon, 12 Aug 2019 20:54:32: 17000000 INFO @ Mon, 12 Aug 2019 20:54:38: 18000000 INFO @ Mon, 12 Aug 2019 20:54:38: 18000000 INFO @ Mon, 12 Aug 2019 20:54:39: 18000000 INFO @ Mon, 12 Aug 2019 20:54:46: 19000000 INFO @ Mon, 12 Aug 2019 20:54:46: 19000000 INFO @ Mon, 12 Aug 2019 20:54:47: 19000000 INFO @ Mon, 12 Aug 2019 20:54:53: 20000000 INFO @ Mon, 12 Aug 2019 20:54:53: 20000000 INFO @ Mon, 12 Aug 2019 20:54:55: 20000000 INFO @ Mon, 12 Aug 2019 20:55:01: 21000000 INFO @ Mon, 12 Aug 2019 20:55:01: 21000000 INFO @ Mon, 12 Aug 2019 20:55:02: 21000000 INFO @ Mon, 12 Aug 2019 20:55:09: 22000000 INFO @ Mon, 12 Aug 2019 20:55:09: 22000000 INFO @ Mon, 12 Aug 2019 20:55:10: 22000000 INFO @ Mon, 12 Aug 2019 20:55:16: 23000000 INFO @ Mon, 12 Aug 2019 20:55:16: 23000000 INFO @ Mon, 12 Aug 2019 20:55:18: 23000000 INFO @ Mon, 12 Aug 2019 20:55:24: 24000000 INFO @ Mon, 12 Aug 2019 20:55:24: 24000000 INFO @ Mon, 12 Aug 2019 20:55:25: 24000000 INFO @ Mon, 12 Aug 2019 20:55:32: 25000000 INFO @ Mon, 12 Aug 2019 20:55:32: 25000000 INFO @ Mon, 12 Aug 2019 20:55:33: 25000000 INFO @ Mon, 12 Aug 2019 20:55:38: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:55:38: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:55:38: #1 total tags in treatment: 25864541 INFO @ Mon, 12 Aug 2019 20:55:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:55:38: #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 20:55:39: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:55:39: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:55:39: #1 total tags in treatment: 25864541 INFO @ Mon, 12 Aug 2019 20:55:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:55:39: #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 20:55:39: #1 tags after filtering in treatment: 25864541 INFO @ Mon, 12 Aug 2019 20:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:55:39: #1 finished! INFO @ Mon, 12 Aug 2019 20:55:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:55:39: #1 tags after filtering in treatment: 25864541 INFO @ Mon, 12 Aug 2019 20:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:55:39: #1 finished! INFO @ Mon, 12 Aug 2019 20:55:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:55:40: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:55:40: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:55:40: #1 total tags in treatment: 25864541 INFO @ Mon, 12 Aug 2019 20:55:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:55:40: #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 20:55:40: #1 tags after filtering in treatment: 25864541 INFO @ Mon, 12 Aug 2019 20:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:55:40: #1 finished! INFO @ Mon, 12 Aug 2019 20:55:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:55:41: #2 number of paired peaks: 145 WARNING @ Mon, 12 Aug 2019 20:55:41: 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 @ Mon, 12 Aug 2019 20:55:41: start model_add_line... INFO @ Mon, 12 Aug 2019 20:55:41: #2 number of paired peaks: 145 WARNING @ Mon, 12 Aug 2019 20:55:41: 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 @ Mon, 12 Aug 2019 20:55:41: start model_add_line... INFO @ Mon, 12 Aug 2019 20:55:41: start X-correlation... INFO @ Mon, 12 Aug 2019 20:55:41: end of X-cor INFO @ Mon, 12 Aug 2019 20:55:41: #2 finished! INFO @ Mon, 12 Aug 2019 20:55:41: #2 predicted fragment length is 65 bps INFO @ Mon, 12 Aug 2019 20:55:41: #2 alternative fragment length(s) may be 2,44,65,559,598 bps INFO @ Mon, 12 Aug 2019 20:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.10_model.r WARNING @ Mon, 12 Aug 2019 20:55:41: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:55:41: #2 You may need to consider one of the other alternative d(s): 2,44,65,559,598 WARNING @ Mon, 12 Aug 2019 20:55:41: #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 20:55:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:55:42: start X-correlation... INFO @ Mon, 12 Aug 2019 20:55:42: end of X-cor INFO @ Mon, 12 Aug 2019 20:55:42: #2 finished! INFO @ Mon, 12 Aug 2019 20:55:42: #2 predicted fragment length is 65 bps INFO @ Mon, 12 Aug 2019 20:55:42: #2 alternative fragment length(s) may be 2,44,65,559,598 bps INFO @ Mon, 12 Aug 2019 20:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.05_model.r WARNING @ Mon, 12 Aug 2019 20:55:42: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:55:42: #2 You may need to consider one of the other alternative d(s): 2,44,65,559,598 WARNING @ Mon, 12 Aug 2019 20:55:42: #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 20:55:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:55:42: #2 number of paired peaks: 145 WARNING @ Mon, 12 Aug 2019 20:55:42: 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 @ Mon, 12 Aug 2019 20:55:42: start model_add_line... INFO @ Mon, 12 Aug 2019 20:55:43: start X-correlation... INFO @ Mon, 12 Aug 2019 20:55:43: end of X-cor INFO @ Mon, 12 Aug 2019 20:55:43: #2 finished! INFO @ Mon, 12 Aug 2019 20:55:43: #2 predicted fragment length is 65 bps INFO @ Mon, 12 Aug 2019 20:55:43: #2 alternative fragment length(s) may be 2,44,65,559,598 bps INFO @ Mon, 12 Aug 2019 20:55:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.20_model.r WARNING @ Mon, 12 Aug 2019 20:55:43: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:55:43: #2 You may need to consider one of the other alternative d(s): 2,44,65,559,598 WARNING @ Mon, 12 Aug 2019 20:55:43: #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 20:55:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:55:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:56:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:56:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:56:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.10_summits.bed INFO @ Mon, 12 Aug 2019 20:57:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.05_summits.bed INFO @ Mon, 12 Aug 2019 20:57:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985679/SRX5985679.20_summits.bed INFO @ Mon, 12 Aug 2019 20:57:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (244 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。