Job ID = 1292375 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 32,895,075 reads read : 65,790,150 reads written : 65,790,150 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: 00:50:39 32895075 reads; of these: 32895075 (100.00%) were paired; of these: 3218857 (9.79%) aligned concordantly 0 times 26403999 (80.27%) aligned concordantly exactly 1 time 3272219 (9.95%) aligned concordantly >1 times ---- 3218857 pairs aligned concordantly 0 times; of these: 1058699 (32.89%) aligned discordantly 1 time ---- 2160158 pairs aligned 0 times concordantly or discordantly; of these: 4320316 mates make up the pairs; of these: 3110785 (72.00%) aligned 0 times 747909 (17.31%) aligned exactly 1 time 461622 (10.68%) aligned >1 times 95.27% overall alignment rate Time searching: 00:50:39 Overall time: 00:50:39 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 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 13732289 / 30431254 = 0.4513 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 19:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.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 19:52:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:52:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.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 19:52:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:52:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.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 19:52:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:52:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:52:44: 1000000 INFO @ Sun, 02 Jun 2019 19:52:46: 1000000 INFO @ Sun, 02 Jun 2019 19:52:46: 1000000 INFO @ Sun, 02 Jun 2019 19:52:52: 2000000 INFO @ Sun, 02 Jun 2019 19:52:55: 2000000 INFO @ Sun, 02 Jun 2019 19:52:56: 2000000 INFO @ Sun, 02 Jun 2019 19:53:01: 3000000 INFO @ Sun, 02 Jun 2019 19:53:04: 3000000 INFO @ Sun, 02 Jun 2019 19:53:06: 3000000 INFO @ Sun, 02 Jun 2019 19:53:09: 4000000 INFO @ Sun, 02 Jun 2019 19:53:13: 4000000 INFO @ Sun, 02 Jun 2019 19:53:15: 4000000 INFO @ Sun, 02 Jun 2019 19:53:17: 5000000 INFO @ Sun, 02 Jun 2019 19:53:23: 5000000 INFO @ Sun, 02 Jun 2019 19:53:24: 5000000 INFO @ Sun, 02 Jun 2019 19:53:25: 6000000 INFO @ Sun, 02 Jun 2019 19:53:32: 6000000 INFO @ Sun, 02 Jun 2019 19:53:33: 7000000 INFO @ Sun, 02 Jun 2019 19:53:33: 6000000 INFO @ Sun, 02 Jun 2019 19:53:40: 8000000 INFO @ Sun, 02 Jun 2019 19:53:40: 7000000 INFO @ Sun, 02 Jun 2019 19:53:42: 7000000 INFO @ Sun, 02 Jun 2019 19:53:48: 9000000 INFO @ Sun, 02 Jun 2019 19:53:49: 8000000 INFO @ Sun, 02 Jun 2019 19:53:51: 8000000 INFO @ Sun, 02 Jun 2019 19:53:55: 10000000 INFO @ Sun, 02 Jun 2019 19:53:58: 9000000 INFO @ Sun, 02 Jun 2019 19:54:00: 9000000 INFO @ Sun, 02 Jun 2019 19:54:03: 11000000 INFO @ Sun, 02 Jun 2019 19:54:07: 10000000 INFO @ Sun, 02 Jun 2019 19:54:09: 10000000 INFO @ Sun, 02 Jun 2019 19:54:10: 12000000 INFO @ Sun, 02 Jun 2019 19:54:16: 11000000 INFO @ Sun, 02 Jun 2019 19:54:17: 11000000 INFO @ Sun, 02 Jun 2019 19:54:18: 13000000 INFO @ Sun, 02 Jun 2019 19:54:24: 12000000 INFO @ Sun, 02 Jun 2019 19:54:25: 14000000 INFO @ Sun, 02 Jun 2019 19:54:26: 12000000 INFO @ Sun, 02 Jun 2019 19:54:32: 15000000 INFO @ Sun, 02 Jun 2019 19:54:33: 13000000 INFO @ Sun, 02 Jun 2019 19:54:35: 13000000 INFO @ Sun, 02 Jun 2019 19:54:40: 16000000 INFO @ Sun, 02 Jun 2019 19:54:42: 14000000 INFO @ Sun, 02 Jun 2019 19:54:43: 14000000 INFO @ Sun, 02 Jun 2019 19:54:47: 17000000 INFO @ Sun, 02 Jun 2019 19:54:50: 15000000 INFO @ Sun, 02 Jun 2019 19:54:52: 15000000 INFO @ Sun, 02 Jun 2019 19:54:55: 18000000 INFO @ Sun, 02 Jun 2019 19:54:59: 16000000 INFO @ Sun, 02 Jun 2019 19:55:01: 16000000 INFO @ Sun, 02 Jun 2019 19:55:02: 19000000 INFO @ Sun, 02 Jun 2019 19:55:08: 17000000 INFO @ Sun, 02 Jun 2019 19:55:09: 17000000 INFO @ Sun, 02 Jun 2019 19:55:09: 20000000 INFO @ Sun, 02 Jun 2019 19:55:16: 18000000 INFO @ Sun, 02 Jun 2019 19:55:17: 21000000 INFO @ Sun, 02 Jun 2019 19:55:18: 18000000 INFO @ Sun, 02 Jun 2019 19:55:24: 22000000 INFO @ Sun, 02 Jun 2019 19:55:25: 19000000 INFO @ Sun, 02 Jun 2019 19:55:26: 19000000 INFO @ Sun, 02 Jun 2019 19:55:31: 23000000 INFO @ Sun, 02 Jun 2019 19:55:33: 20000000 INFO @ Sun, 02 Jun 2019 19:55:35: 20000000 INFO @ Sun, 02 Jun 2019 19:55:39: 24000000 INFO @ Sun, 02 Jun 2019 19:55:42: 21000000 INFO @ Sun, 02 Jun 2019 19:55:43: 21000000 INFO @ Sun, 02 Jun 2019 19:55:46: 25000000 INFO @ Sun, 02 Jun 2019 19:55:50: 22000000 INFO @ Sun, 02 Jun 2019 19:55:52: 22000000 INFO @ Sun, 02 Jun 2019 19:55:53: 26000000 INFO @ Sun, 02 Jun 2019 19:55:58: 23000000 INFO @ Sun, 02 Jun 2019 19:56:00: 27000000 INFO @ Sun, 02 Jun 2019 19:56:01: 23000000 INFO @ Sun, 02 Jun 2019 19:56:07: 24000000 INFO @ Sun, 02 Jun 2019 19:56:08: 28000000 INFO @ Sun, 02 Jun 2019 19:56:09: 24000000 INFO @ Sun, 02 Jun 2019 19:56:15: 29000000 INFO @ Sun, 02 Jun 2019 19:56:15: 25000000 INFO @ Sun, 02 Jun 2019 19:56:17: 25000000 INFO @ Sun, 02 Jun 2019 19:56:22: 30000000 INFO @ Sun, 02 Jun 2019 19:56:23: 26000000 INFO @ Sun, 02 Jun 2019 19:56:26: 26000000 INFO @ Sun, 02 Jun 2019 19:56:30: 31000000 INFO @ Sun, 02 Jun 2019 19:56:31: 27000000 INFO @ Sun, 02 Jun 2019 19:56:34: 27000000 INFO @ Sun, 02 Jun 2019 19:56:39: 32000000 INFO @ Sun, 02 Jun 2019 19:56:40: 28000000 INFO @ Sun, 02 Jun 2019 19:56:43: 28000000 INFO @ Sun, 02 Jun 2019 19:56:46: 33000000 INFO @ Sun, 02 Jun 2019 19:56:48: 29000000 INFO @ Sun, 02 Jun 2019 19:56:51: 29000000 INFO @ Sun, 02 Jun 2019 19:56:53: 34000000 INFO @ Sun, 02 Jun 2019 19:56:57: 30000000 INFO @ Sun, 02 Jun 2019 19:57:00: 30000000 INFO @ Sun, 02 Jun 2019 19:57:01: 35000000 INFO @ Sun, 02 Jun 2019 19:57:02: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:57:02: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:57:02: #1 total tags in treatment: 16208469 INFO @ Sun, 02 Jun 2019 19:57:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:57:02: #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 19:57:03: #1 tags after filtering in treatment: 13937661 INFO @ Sun, 02 Jun 2019 19:57:03: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 02 Jun 2019 19:57:03: #1 finished! INFO @ Sun, 02 Jun 2019 19:57:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:57:04: #2 number of paired peaks: 370 WARNING @ Sun, 02 Jun 2019 19:57:04: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sun, 02 Jun 2019 19:57:04: start model_add_line... INFO @ Sun, 02 Jun 2019 19:57:04: start X-correlation... INFO @ Sun, 02 Jun 2019 19:57:04: end of X-cor INFO @ Sun, 02 Jun 2019 19:57:04: #2 finished! INFO @ Sun, 02 Jun 2019 19:57:04: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 19:57:04: #2 alternative fragment length(s) may be 4,139,160 bps INFO @ Sun, 02 Jun 2019 19:57:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.20_model.r WARNING @ Sun, 02 Jun 2019 19:57:04: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:57:04: #2 You may need to consider one of the other alternative d(s): 4,139,160 WARNING @ Sun, 02 Jun 2019 19:57:04: #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 19:57:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:57:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:57:05: 31000000 INFO @ Sun, 02 Jun 2019 19:57:08: 31000000 INFO @ Sun, 02 Jun 2019 19:57:14: 32000000 INFO @ Sun, 02 Jun 2019 19:57:16: 32000000 INFO @ Sun, 02 Jun 2019 19:57:22: 33000000 INFO @ Sun, 02 Jun 2019 19:57:25: 33000000 INFO @ Sun, 02 Jun 2019 19:57:30: 34000000 INFO @ Sun, 02 Jun 2019 19:57:33: 34000000 INFO @ Sun, 02 Jun 2019 19:57:39: 35000000 INFO @ Sun, 02 Jun 2019 19:57:41: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:57:41: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:57:41: #1 total tags in treatment: 16208469 INFO @ Sun, 02 Jun 2019 19:57:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:57:41: #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 19:57:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:57:41: #1 tags after filtering in treatment: 13937661 INFO @ Sun, 02 Jun 2019 19:57:41: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 02 Jun 2019 19:57:41: #1 finished! INFO @ Sun, 02 Jun 2019 19:57:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:57:42: #2 number of paired peaks: 370 WARNING @ Sun, 02 Jun 2019 19:57:42: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sun, 02 Jun 2019 19:57:42: start model_add_line... INFO @ Sun, 02 Jun 2019 19:57:43: 35000000 INFO @ Sun, 02 Jun 2019 19:57:43: start X-correlation... INFO @ Sun, 02 Jun 2019 19:57:43: end of X-cor INFO @ Sun, 02 Jun 2019 19:57:43: #2 finished! INFO @ Sun, 02 Jun 2019 19:57:43: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 19:57:43: #2 alternative fragment length(s) may be 4,139,160 bps INFO @ Sun, 02 Jun 2019 19:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.05_model.r WARNING @ Sun, 02 Jun 2019 19:57:43: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:57:43: #2 You may need to consider one of the other alternative d(s): 4,139,160 WARNING @ Sun, 02 Jun 2019 19:57:43: #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 19:57:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:57:45: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:57:45: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:57:45: #1 total tags in treatment: 16208469 INFO @ Sun, 02 Jun 2019 19:57:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:57:45: #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 19:57:45: #1 tags after filtering in treatment: 13937661 INFO @ Sun, 02 Jun 2019 19:57:45: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 02 Jun 2019 19:57:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:57:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:57:46: #2 number of paired peaks: 370 WARNING @ Sun, 02 Jun 2019 19:57:46: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sun, 02 Jun 2019 19:57:46: start model_add_line... INFO @ Sun, 02 Jun 2019 19:57:46: start X-correlation... INFO @ Sun, 02 Jun 2019 19:57:46: end of X-cor INFO @ Sun, 02 Jun 2019 19:57:46: #2 finished! INFO @ Sun, 02 Jun 2019 19:57:46: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 19:57:46: #2 alternative fragment length(s) may be 4,139,160 bps INFO @ Sun, 02 Jun 2019 19:57:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.10_model.r WARNING @ Sun, 02 Jun 2019 19:57:46: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:57:46: #2 You may need to consider one of the other alternative d(s): 4,139,160 WARNING @ Sun, 02 Jun 2019 19:57:46: #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 19:57:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:57:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.20_summits.bed INFO @ Sun, 02 Jun 2019 19:57:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (244 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:58:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:58:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.05_summits.bed INFO @ Sun, 02 Jun 2019 19:58:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733162/SRX3733162.10_summits.bed INFO @ Sun, 02 Jun 2019 19:58:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (385 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。