Job ID = 1295858 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,785,819 reads read : 33,571,638 reads written : 33,571,638 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: 00:44:36 16785819 reads; of these: 16785819 (100.00%) were paired; of these: 1721048 (10.25%) aligned concordantly 0 times 10088939 (60.10%) aligned concordantly exactly 1 time 4975832 (29.64%) aligned concordantly >1 times ---- 1721048 pairs aligned concordantly 0 times; of these: 30606 (1.78%) aligned discordantly 1 time ---- 1690442 pairs aligned 0 times concordantly or discordantly; of these: 3380884 mates make up the pairs; of these: 2785987 (82.40%) aligned 0 times 394903 (11.68%) aligned exactly 1 time 199994 (5.92%) aligned >1 times 91.70% overall alignment rate Time searching: 00:44:36 Overall time: 00:44:36 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 16 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] 1371587 / 15080808 = 0.0909 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 16:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.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 16:53:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:53:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.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 16:53:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:53:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.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 16:53:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:53:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:53:22: 1000000 INFO @ Mon, 03 Jun 2019 16:53:22: 1000000 INFO @ Mon, 03 Jun 2019 16:53:23: 1000000 INFO @ Mon, 03 Jun 2019 16:53:31: 2000000 INFO @ Mon, 03 Jun 2019 16:53:31: 2000000 INFO @ Mon, 03 Jun 2019 16:53:33: 2000000 INFO @ Mon, 03 Jun 2019 16:53:39: 3000000 INFO @ Mon, 03 Jun 2019 16:53:40: 3000000 INFO @ Mon, 03 Jun 2019 16:53:44: 3000000 INFO @ Mon, 03 Jun 2019 16:53:48: 4000000 INFO @ Mon, 03 Jun 2019 16:53:48: 4000000 INFO @ Mon, 03 Jun 2019 16:53:54: 4000000 INFO @ Mon, 03 Jun 2019 16:53:57: 5000000 INFO @ Mon, 03 Jun 2019 16:53:58: 5000000 INFO @ Mon, 03 Jun 2019 16:54:04: 5000000 INFO @ Mon, 03 Jun 2019 16:54:06: 6000000 INFO @ Mon, 03 Jun 2019 16:54:07: 6000000 INFO @ Mon, 03 Jun 2019 16:54:14: 6000000 INFO @ Mon, 03 Jun 2019 16:54:15: 7000000 INFO @ Mon, 03 Jun 2019 16:54:16: 7000000 INFO @ Mon, 03 Jun 2019 16:54:23: 8000000 INFO @ Mon, 03 Jun 2019 16:54:24: 8000000 INFO @ Mon, 03 Jun 2019 16:54:24: 7000000 INFO @ Mon, 03 Jun 2019 16:54:31: 9000000 INFO @ Mon, 03 Jun 2019 16:54:33: 9000000 INFO @ Mon, 03 Jun 2019 16:54:34: 8000000 INFO @ Mon, 03 Jun 2019 16:54:40: 10000000 INFO @ Mon, 03 Jun 2019 16:54:41: 10000000 INFO @ Mon, 03 Jun 2019 16:54:44: 9000000 INFO @ Mon, 03 Jun 2019 16:54:49: 11000000 INFO @ Mon, 03 Jun 2019 16:54:49: 11000000 INFO @ Mon, 03 Jun 2019 16:54:55: 10000000 INFO @ Mon, 03 Jun 2019 16:54:57: 12000000 INFO @ Mon, 03 Jun 2019 16:54:58: 12000000 INFO @ Mon, 03 Jun 2019 16:55:05: 11000000 INFO @ Mon, 03 Jun 2019 16:55:06: 13000000 INFO @ Mon, 03 Jun 2019 16:55:06: 13000000 INFO @ Mon, 03 Jun 2019 16:55:14: 14000000 INFO @ Mon, 03 Jun 2019 16:55:15: 12000000 INFO @ Mon, 03 Jun 2019 16:55:15: 14000000 INFO @ Mon, 03 Jun 2019 16:55:23: 15000000 INFO @ Mon, 03 Jun 2019 16:55:24: 15000000 INFO @ Mon, 03 Jun 2019 16:55:25: 13000000 INFO @ Mon, 03 Jun 2019 16:55:32: 16000000 INFO @ Mon, 03 Jun 2019 16:55:32: 16000000 INFO @ Mon, 03 Jun 2019 16:55:35: 14000000 INFO @ Mon, 03 Jun 2019 16:55:41: 17000000 INFO @ Mon, 03 Jun 2019 16:55:41: 17000000 INFO @ Mon, 03 Jun 2019 16:55:46: 15000000 INFO @ Mon, 03 Jun 2019 16:55:49: 18000000 INFO @ Mon, 03 Jun 2019 16:55:50: 18000000 INFO @ Mon, 03 Jun 2019 16:55:56: 16000000 INFO @ Mon, 03 Jun 2019 16:55:58: 19000000 INFO @ Mon, 03 Jun 2019 16:55:58: 19000000 INFO @ Mon, 03 Jun 2019 16:56:06: 17000000 INFO @ Mon, 03 Jun 2019 16:56:07: 20000000 INFO @ Mon, 03 Jun 2019 16:56:07: 20000000 INFO @ Mon, 03 Jun 2019 16:56:16: 21000000 INFO @ Mon, 03 Jun 2019 16:56:16: 21000000 INFO @ Mon, 03 Jun 2019 16:56:16: 18000000 INFO @ Mon, 03 Jun 2019 16:56:24: 22000000 INFO @ Mon, 03 Jun 2019 16:56:25: 22000000 INFO @ Mon, 03 Jun 2019 16:56:26: 19000000 INFO @ Mon, 03 Jun 2019 16:56:33: 23000000 INFO @ Mon, 03 Jun 2019 16:56:33: 23000000 INFO @ Mon, 03 Jun 2019 16:56:37: 20000000 INFO @ Mon, 03 Jun 2019 16:56:41: 24000000 INFO @ Mon, 03 Jun 2019 16:56:42: 24000000 INFO @ Mon, 03 Jun 2019 16:56:47: 21000000 INFO @ Mon, 03 Jun 2019 16:56:50: 25000000 INFO @ Mon, 03 Jun 2019 16:56:50: 25000000 INFO @ Mon, 03 Jun 2019 16:56:57: 22000000 INFO @ Mon, 03 Jun 2019 16:56:58: 26000000 INFO @ Mon, 03 Jun 2019 16:56:59: 26000000 INFO @ Mon, 03 Jun 2019 16:57:07: 23000000 INFO @ Mon, 03 Jun 2019 16:57:07: 27000000 INFO @ Mon, 03 Jun 2019 16:57:08: 27000000 INFO @ Mon, 03 Jun 2019 16:57:15: 28000000 INFO @ Mon, 03 Jun 2019 16:57:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:57:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:57:16: #1 total tags in treatment: 13694111 INFO @ Mon, 03 Jun 2019 16:57:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:57:16: #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 16:57:16: #1 tags after filtering in treatment: 12811618 INFO @ Mon, 03 Jun 2019 16:57:16: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 16:57:16: #1 finished! INFO @ Mon, 03 Jun 2019 16:57:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:57:16: 28000000 INFO @ Mon, 03 Jun 2019 16:57:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:57:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:57:17: #1 total tags in treatment: 13694111 INFO @ Mon, 03 Jun 2019 16:57:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:57:17: #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 16:57:17: #1 tags after filtering in treatment: 12811618 INFO @ Mon, 03 Jun 2019 16:57:17: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 16:57:17: #1 finished! INFO @ Mon, 03 Jun 2019 16:57:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:57:17: #2 number of paired peaks: 571 WARNING @ Mon, 03 Jun 2019 16:57:17: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 03 Jun 2019 16:57:17: start model_add_line... INFO @ Mon, 03 Jun 2019 16:57:17: start X-correlation... INFO @ Mon, 03 Jun 2019 16:57:18: end of X-cor INFO @ Mon, 03 Jun 2019 16:57:18: #2 finished! INFO @ Mon, 03 Jun 2019 16:57:18: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 16:57:18: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 16:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.10_model.r INFO @ Mon, 03 Jun 2019 16:57:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:57:18: 24000000 INFO @ Mon, 03 Jun 2019 16:57:18: #2 number of paired peaks: 571 WARNING @ Mon, 03 Jun 2019 16:57:18: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 03 Jun 2019 16:57:18: start model_add_line... INFO @ Mon, 03 Jun 2019 16:57:18: start X-correlation... INFO @ Mon, 03 Jun 2019 16:57:18: end of X-cor INFO @ Mon, 03 Jun 2019 16:57:18: #2 finished! INFO @ Mon, 03 Jun 2019 16:57:18: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 16:57:18: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 16:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.05_model.r INFO @ Mon, 03 Jun 2019 16:57:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:57:29: 25000000 INFO @ Mon, 03 Jun 2019 16:57:39: 26000000 INFO @ Mon, 03 Jun 2019 16:57:48: 27000000 INFO @ Mon, 03 Jun 2019 16:57:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:57:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:57:57: 28000000 INFO @ Mon, 03 Jun 2019 16:57:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:57:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:57:58: #1 total tags in treatment: 13694111 INFO @ Mon, 03 Jun 2019 16:57:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:57:58: #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 16:57:58: #1 tags after filtering in treatment: 12811618 INFO @ Mon, 03 Jun 2019 16:57:58: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 16:57:58: #1 finished! INFO @ Mon, 03 Jun 2019 16:57:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:57:59: #2 number of paired peaks: 571 WARNING @ Mon, 03 Jun 2019 16:57:59: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 03 Jun 2019 16:57:59: start model_add_line... INFO @ Mon, 03 Jun 2019 16:57:59: start X-correlation... INFO @ Mon, 03 Jun 2019 16:57:59: end of X-cor INFO @ Mon, 03 Jun 2019 16:57:59: #2 finished! INFO @ Mon, 03 Jun 2019 16:57:59: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 16:57:59: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 16:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.20_model.r INFO @ Mon, 03 Jun 2019 16:57:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.10_summits.bed INFO @ Mon, 03 Jun 2019 16:58:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1890 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.05_summits.bed INFO @ Mon, 03 Jun 2019 16:58:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3930 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:58:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577943/SRX4577943.20_summits.bed INFO @ Mon, 03 Jun 2019 16:58:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (907 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。