Job ID = 1293405 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 30,361,136 reads read : 60,722,272 reads written : 60,722,272 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: 01:13:58 30361136 reads; of these: 30361136 (100.00%) were paired; of these: 5415071 (17.84%) aligned concordantly 0 times 19530799 (64.33%) aligned concordantly exactly 1 time 5415266 (17.84%) aligned concordantly >1 times ---- 5415071 pairs aligned concordantly 0 times; of these: 335305 (6.19%) aligned discordantly 1 time ---- 5079766 pairs aligned 0 times concordantly or discordantly; of these: 10159532 mates make up the pairs; of these: 9115929 (89.73%) aligned 0 times 697269 (6.86%) aligned exactly 1 time 346334 (3.41%) aligned >1 times 84.99% overall alignment rate Time searching: 01:13:58 Overall time: 01:13:58 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 24 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 8343096 / 25243229 = 0.3305 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, 03 Jun 2019 01:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.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 @ Mon, 03 Jun 2019 01:28:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:28:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.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 @ Mon, 03 Jun 2019 01:28:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:28:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.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 @ Mon, 03 Jun 2019 01:28:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:28:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:29:08: 1000000 INFO @ Mon, 03 Jun 2019 01:29:10: 1000000 INFO @ Mon, 03 Jun 2019 01:29:11: 1000000 INFO @ Mon, 03 Jun 2019 01:29:16: 2000000 INFO @ Mon, 03 Jun 2019 01:29:22: 2000000 INFO @ Mon, 03 Jun 2019 01:29:23: 2000000 INFO @ Mon, 03 Jun 2019 01:29:25: 3000000 INFO @ Mon, 03 Jun 2019 01:29:34: 4000000 INFO @ Mon, 03 Jun 2019 01:29:34: 3000000 INFO @ Mon, 03 Jun 2019 01:29:36: 3000000 INFO @ Mon, 03 Jun 2019 01:29:42: 5000000 INFO @ Mon, 03 Jun 2019 01:29:46: 4000000 INFO @ Mon, 03 Jun 2019 01:29:48: 4000000 INFO @ Mon, 03 Jun 2019 01:29:51: 6000000 INFO @ Mon, 03 Jun 2019 01:29:58: 5000000 INFO @ Mon, 03 Jun 2019 01:29:59: 5000000 INFO @ Mon, 03 Jun 2019 01:30:00: 7000000 INFO @ Mon, 03 Jun 2019 01:30:08: 8000000 INFO @ Mon, 03 Jun 2019 01:30:10: 6000000 INFO @ Mon, 03 Jun 2019 01:30:11: 6000000 INFO @ Mon, 03 Jun 2019 01:30:17: 9000000 INFO @ Mon, 03 Jun 2019 01:30:22: 7000000 INFO @ Mon, 03 Jun 2019 01:30:24: 7000000 INFO @ Mon, 03 Jun 2019 01:30:25: 10000000 INFO @ Mon, 03 Jun 2019 01:30:34: 11000000 INFO @ Mon, 03 Jun 2019 01:30:35: 8000000 INFO @ Mon, 03 Jun 2019 01:30:36: 8000000 INFO @ Mon, 03 Jun 2019 01:30:43: 12000000 INFO @ Mon, 03 Jun 2019 01:30:47: 9000000 INFO @ Mon, 03 Jun 2019 01:30:48: 9000000 INFO @ Mon, 03 Jun 2019 01:30:53: 13000000 INFO @ Mon, 03 Jun 2019 01:30:59: 10000000 INFO @ Mon, 03 Jun 2019 01:31:00: 10000000 INFO @ Mon, 03 Jun 2019 01:31:02: 14000000 INFO @ Mon, 03 Jun 2019 01:31:10: 15000000 INFO @ Mon, 03 Jun 2019 01:31:12: 11000000 INFO @ Mon, 03 Jun 2019 01:31:12: 11000000 INFO @ Mon, 03 Jun 2019 01:31:19: 16000000 INFO @ Mon, 03 Jun 2019 01:31:23: 12000000 INFO @ Mon, 03 Jun 2019 01:31:24: 12000000 INFO @ Mon, 03 Jun 2019 01:31:28: 17000000 INFO @ Mon, 03 Jun 2019 01:31:34: 13000000 INFO @ Mon, 03 Jun 2019 01:31:35: 13000000 INFO @ Mon, 03 Jun 2019 01:31:36: 18000000 INFO @ Mon, 03 Jun 2019 01:31:45: 19000000 INFO @ Mon, 03 Jun 2019 01:31:45: 14000000 INFO @ Mon, 03 Jun 2019 01:31:47: 14000000 INFO @ Mon, 03 Jun 2019 01:31:54: 20000000 INFO @ Mon, 03 Jun 2019 01:31:57: 15000000 INFO @ Mon, 03 Jun 2019 01:31:59: 15000000 INFO @ Mon, 03 Jun 2019 01:32:05: 21000000 INFO @ Mon, 03 Jun 2019 01:32:10: 16000000 INFO @ Mon, 03 Jun 2019 01:32:12: 16000000 INFO @ Mon, 03 Jun 2019 01:32:14: 22000000 INFO @ Mon, 03 Jun 2019 01:32:22: 17000000 INFO @ Mon, 03 Jun 2019 01:32:23: 23000000 INFO @ Mon, 03 Jun 2019 01:32:24: 17000000 INFO @ Mon, 03 Jun 2019 01:32:32: 24000000 INFO @ Mon, 03 Jun 2019 01:32:35: 18000000 INFO @ Mon, 03 Jun 2019 01:32:36: 18000000 INFO @ Mon, 03 Jun 2019 01:32:40: 25000000 INFO @ Mon, 03 Jun 2019 01:32:47: 19000000 INFO @ Mon, 03 Jun 2019 01:32:48: 19000000 INFO @ Mon, 03 Jun 2019 01:32:49: 26000000 INFO @ Mon, 03 Jun 2019 01:32:58: 27000000 INFO @ Mon, 03 Jun 2019 01:32:59: 20000000 INFO @ Mon, 03 Jun 2019 01:33:00: 20000000 INFO @ Mon, 03 Jun 2019 01:33:07: 28000000 INFO @ Mon, 03 Jun 2019 01:33:10: 21000000 INFO @ Mon, 03 Jun 2019 01:33:11: 21000000 INFO @ Mon, 03 Jun 2019 01:33:15: 29000000 INFO @ Mon, 03 Jun 2019 01:33:22: 22000000 INFO @ Mon, 03 Jun 2019 01:33:23: 22000000 INFO @ Mon, 03 Jun 2019 01:33:24: 30000000 INFO @ Mon, 03 Jun 2019 01:33:33: 31000000 INFO @ Mon, 03 Jun 2019 01:33:34: 23000000 INFO @ Mon, 03 Jun 2019 01:33:35: 23000000 INFO @ Mon, 03 Jun 2019 01:33:42: 32000000 INFO @ Mon, 03 Jun 2019 01:33:46: 24000000 INFO @ Mon, 03 Jun 2019 01:33:47: 24000000 INFO @ Mon, 03 Jun 2019 01:33:50: 33000000 INFO @ Mon, 03 Jun 2019 01:33:59: 25000000 INFO @ Mon, 03 Jun 2019 01:33:59: 34000000 INFO @ Mon, 03 Jun 2019 01:33:59: 25000000 INFO @ Mon, 03 Jun 2019 01:34:07: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:34:07: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:34:07: #1 total tags in treatment: 16683787 INFO @ Mon, 03 Jun 2019 01:34:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:34:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:34:07: #1 tags after filtering in treatment: 15583034 INFO @ Mon, 03 Jun 2019 01:34:07: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 01:34:07: #1 finished! INFO @ Mon, 03 Jun 2019 01:34:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:34:09: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 01:34:09: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 01:34:09: start model_add_line... INFO @ Mon, 03 Jun 2019 01:34:09: start X-correlation... INFO @ Mon, 03 Jun 2019 01:34:09: end of X-cor INFO @ Mon, 03 Jun 2019 01:34:09: #2 finished! INFO @ Mon, 03 Jun 2019 01:34:09: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 01:34:09: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 01:34:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.10_model.r WARNING @ Mon, 03 Jun 2019 01:34:09: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:34:09: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Mon, 03 Jun 2019 01:34:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:34:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:34:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:34:12: 26000000 INFO @ Mon, 03 Jun 2019 01:34:12: 26000000 INFO @ Mon, 03 Jun 2019 01:34:24: 27000000 INFO @ Mon, 03 Jun 2019 01:34:25: 27000000 INFO @ Mon, 03 Jun 2019 01:34:37: 28000000 INFO @ Mon, 03 Jun 2019 01:34:37: 28000000 INFO @ Mon, 03 Jun 2019 01:34:49: 29000000 INFO @ Mon, 03 Jun 2019 01:34:49: 29000000 INFO @ Mon, 03 Jun 2019 01:34:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:35:01: 30000000 INFO @ Mon, 03 Jun 2019 01:35:01: 30000000 INFO @ Mon, 03 Jun 2019 01:35:13: 31000000 INFO @ Mon, 03 Jun 2019 01:35:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.10_summits.bed INFO @ Mon, 03 Jun 2019 01:35:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1312 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:35:13: 31000000 INFO @ Mon, 03 Jun 2019 01:35:26: 32000000 INFO @ Mon, 03 Jun 2019 01:35:26: 32000000 INFO @ Mon, 03 Jun 2019 01:35:38: 33000000 INFO @ Mon, 03 Jun 2019 01:35:39: 33000000 INFO @ Mon, 03 Jun 2019 01:35:50: 34000000 INFO @ Mon, 03 Jun 2019 01:35:51: 34000000 INFO @ Mon, 03 Jun 2019 01:36:01: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:36:01: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:36:01: #1 total tags in treatment: 16683787 INFO @ Mon, 03 Jun 2019 01:36:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:36:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:36:01: #1 tags after filtering in treatment: 15583034 INFO @ Mon, 03 Jun 2019 01:36:01: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 01:36:01: #1 finished! INFO @ Mon, 03 Jun 2019 01:36:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:36:01: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:36:01: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:36:01: #1 total tags in treatment: 16683787 INFO @ Mon, 03 Jun 2019 01:36:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:36:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:36:02: #1 tags after filtering in treatment: 15583034 INFO @ Mon, 03 Jun 2019 01:36:02: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 01:36:02: #1 finished! INFO @ Mon, 03 Jun 2019 01:36:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:36:03: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 01:36:03: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 01:36:03: start model_add_line... INFO @ Mon, 03 Jun 2019 01:36:03: start X-correlation... INFO @ Mon, 03 Jun 2019 01:36:03: end of X-cor INFO @ Mon, 03 Jun 2019 01:36:03: #2 finished! INFO @ Mon, 03 Jun 2019 01:36:03: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 01:36:03: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 01:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.05_model.r WARNING @ Mon, 03 Jun 2019 01:36:03: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:36:03: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Mon, 03 Jun 2019 01:36:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:36:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:36:03: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 01:36:03: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 01:36:03: start model_add_line... INFO @ Mon, 03 Jun 2019 01:36:03: start X-correlation... INFO @ Mon, 03 Jun 2019 01:36:03: end of X-cor INFO @ Mon, 03 Jun 2019 01:36:03: #2 finished! INFO @ Mon, 03 Jun 2019 01:36:03: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 01:36:03: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 01:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.20_model.r WARNING @ Mon, 03 Jun 2019 01:36:03: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:36:03: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Mon, 03 Jun 2019 01:36:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:36:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:36:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:36:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.20_summits.bed INFO @ Mon, 03 Jun 2019 01:37:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075300/ERX2075300.05_summits.bed INFO @ Mon, 03 Jun 2019 01:37:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2848 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。