Job ID = 1294343 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 26,805,047 reads read : 53,610,094 reads written : 53,610,094 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: 00:43:07 26805047 reads; of these: 26805047 (100.00%) were paired; of these: 4780077 (17.83%) aligned concordantly 0 times 18664698 (69.63%) aligned concordantly exactly 1 time 3360272 (12.54%) aligned concordantly >1 times ---- 4780077 pairs aligned concordantly 0 times; of these: 398673 (8.34%) aligned discordantly 1 time ---- 4381404 pairs aligned 0 times concordantly or discordantly; of these: 8762808 mates make up the pairs; of these: 5182832 (59.15%) aligned 0 times 2666852 (30.43%) aligned exactly 1 time 913124 (10.42%) aligned >1 times 90.33% overall alignment rate Time searching: 00:43:07 Overall time: 00:43:07 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 20 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] 1803876 / 22347205 = 0.0807 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 08:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.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 08:01:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:01:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.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 08:01:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:01:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.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 08:01:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:01:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:01:41: 1000000 INFO @ Mon, 03 Jun 2019 08:01:42: 1000000 INFO @ Mon, 03 Jun 2019 08:01:44: 1000000 INFO @ Mon, 03 Jun 2019 08:01:48: 2000000 INFO @ Mon, 03 Jun 2019 08:01:50: 2000000 INFO @ Mon, 03 Jun 2019 08:01:54: 2000000 INFO @ Mon, 03 Jun 2019 08:01:55: 3000000 INFO @ Mon, 03 Jun 2019 08:01:57: 3000000 INFO @ Mon, 03 Jun 2019 08:02:02: 4000000 INFO @ Mon, 03 Jun 2019 08:02:04: 3000000 INFO @ Mon, 03 Jun 2019 08:02:05: 4000000 INFO @ Mon, 03 Jun 2019 08:02:10: 5000000 INFO @ Mon, 03 Jun 2019 08:02:14: 5000000 INFO @ Mon, 03 Jun 2019 08:02:14: 4000000 INFO @ Mon, 03 Jun 2019 08:02:17: 6000000 INFO @ Mon, 03 Jun 2019 08:02:21: 6000000 INFO @ Mon, 03 Jun 2019 08:02:24: 5000000 INFO @ Mon, 03 Jun 2019 08:02:24: 7000000 INFO @ Mon, 03 Jun 2019 08:02:29: 7000000 INFO @ Mon, 03 Jun 2019 08:02:31: 8000000 INFO @ Mon, 03 Jun 2019 08:02:34: 6000000 INFO @ Mon, 03 Jun 2019 08:02:36: 8000000 INFO @ Mon, 03 Jun 2019 08:02:38: 9000000 INFO @ Mon, 03 Jun 2019 08:02:44: 7000000 INFO @ Mon, 03 Jun 2019 08:02:44: 9000000 INFO @ Mon, 03 Jun 2019 08:02:45: 10000000 INFO @ Mon, 03 Jun 2019 08:02:52: 10000000 INFO @ Mon, 03 Jun 2019 08:02:53: 11000000 INFO @ Mon, 03 Jun 2019 08:02:53: 8000000 INFO @ Mon, 03 Jun 2019 08:02:59: 11000000 INFO @ Mon, 03 Jun 2019 08:03:00: 12000000 INFO @ Mon, 03 Jun 2019 08:03:03: 9000000 INFO @ Mon, 03 Jun 2019 08:03:06: 12000000 INFO @ Mon, 03 Jun 2019 08:03:07: 13000000 INFO @ Mon, 03 Jun 2019 08:03:13: 10000000 INFO @ Mon, 03 Jun 2019 08:03:14: 13000000 INFO @ Mon, 03 Jun 2019 08:03:14: 14000000 INFO @ Mon, 03 Jun 2019 08:03:22: 14000000 INFO @ Mon, 03 Jun 2019 08:03:22: 15000000 INFO @ Mon, 03 Jun 2019 08:03:23: 11000000 INFO @ Mon, 03 Jun 2019 08:03:30: 16000000 INFO @ Mon, 03 Jun 2019 08:03:30: 15000000 INFO @ Mon, 03 Jun 2019 08:03:32: 12000000 INFO @ Mon, 03 Jun 2019 08:03:36: 17000000 INFO @ Mon, 03 Jun 2019 08:03:37: 16000000 INFO @ Mon, 03 Jun 2019 08:03:41: 13000000 INFO @ Mon, 03 Jun 2019 08:03:43: 18000000 INFO @ Mon, 03 Jun 2019 08:03:45: 17000000 INFO @ Mon, 03 Jun 2019 08:03:50: 14000000 INFO @ Mon, 03 Jun 2019 08:03:51: 19000000 INFO @ Mon, 03 Jun 2019 08:03:53: 18000000 INFO @ Mon, 03 Jun 2019 08:03:59: 15000000 INFO @ Mon, 03 Jun 2019 08:03:59: 20000000 INFO @ Mon, 03 Jun 2019 08:04:00: 19000000 INFO @ Mon, 03 Jun 2019 08:04:07: 21000000 INFO @ Mon, 03 Jun 2019 08:04:08: 16000000 INFO @ Mon, 03 Jun 2019 08:04:08: 20000000 INFO @ Mon, 03 Jun 2019 08:04:14: 22000000 INFO @ Mon, 03 Jun 2019 08:04:15: 21000000 INFO @ Mon, 03 Jun 2019 08:04:17: 17000000 INFO @ Mon, 03 Jun 2019 08:04:22: 23000000 INFO @ Mon, 03 Jun 2019 08:04:23: 22000000 INFO @ Mon, 03 Jun 2019 08:04:25: 18000000 INFO @ Mon, 03 Jun 2019 08:04:29: 24000000 INFO @ Mon, 03 Jun 2019 08:04:31: 23000000 INFO @ Mon, 03 Jun 2019 08:04:34: 19000000 INFO @ Mon, 03 Jun 2019 08:04:38: 25000000 INFO @ Mon, 03 Jun 2019 08:04:39: 24000000 INFO @ Mon, 03 Jun 2019 08:04:46: 20000000 INFO @ Mon, 03 Jun 2019 08:04:48: 25000000 INFO @ Mon, 03 Jun 2019 08:04:48: 26000000 INFO @ Mon, 03 Jun 2019 08:04:55: 26000000 INFO @ Mon, 03 Jun 2019 08:04:55: 27000000 INFO @ Mon, 03 Jun 2019 08:04:56: 21000000 INFO @ Mon, 03 Jun 2019 08:05:03: 28000000 INFO @ Mon, 03 Jun 2019 08:05:03: 27000000 INFO @ Mon, 03 Jun 2019 08:05:05: 22000000 INFO @ Mon, 03 Jun 2019 08:05:11: 28000000 INFO @ Mon, 03 Jun 2019 08:05:11: 29000000 INFO @ Mon, 03 Jun 2019 08:05:14: 23000000 INFO @ Mon, 03 Jun 2019 08:05:18: 29000000 INFO @ Mon, 03 Jun 2019 08:05:20: 30000000 INFO @ Mon, 03 Jun 2019 08:05:23: 24000000 INFO @ Mon, 03 Jun 2019 08:05:27: 30000000 INFO @ Mon, 03 Jun 2019 08:05:28: 31000000 INFO @ Mon, 03 Jun 2019 08:05:33: 25000000 INFO @ Mon, 03 Jun 2019 08:05:34: 31000000 INFO @ Mon, 03 Jun 2019 08:05:35: 32000000 INFO @ Mon, 03 Jun 2019 08:05:42: 32000000 INFO @ Mon, 03 Jun 2019 08:05:43: 33000000 INFO @ Mon, 03 Jun 2019 08:05:43: 26000000 INFO @ Mon, 03 Jun 2019 08:05:50: 33000000 INFO @ Mon, 03 Jun 2019 08:05:50: 34000000 INFO @ Mon, 03 Jun 2019 08:05:53: 27000000 INFO @ Mon, 03 Jun 2019 08:05:58: 34000000 INFO @ Mon, 03 Jun 2019 08:06:00: 35000000 INFO @ Mon, 03 Jun 2019 08:06:03: 28000000 INFO @ Mon, 03 Jun 2019 08:06:06: 35000000 INFO @ Mon, 03 Jun 2019 08:06:09: 36000000 INFO @ Mon, 03 Jun 2019 08:06:14: 36000000 INFO @ Mon, 03 Jun 2019 08:06:14: 29000000 INFO @ Mon, 03 Jun 2019 08:06:16: 37000000 INFO @ Mon, 03 Jun 2019 08:06:22: 37000000 INFO @ Mon, 03 Jun 2019 08:06:23: 30000000 INFO @ Mon, 03 Jun 2019 08:06:23: 38000000 INFO @ Mon, 03 Jun 2019 08:06:29: 38000000 INFO @ Mon, 03 Jun 2019 08:06:32: 39000000 INFO @ Mon, 03 Jun 2019 08:06:33: 31000000 INFO @ Mon, 03 Jun 2019 08:06:37: 39000000 INFO @ Mon, 03 Jun 2019 08:06:40: 40000000 INFO @ Mon, 03 Jun 2019 08:06:43: 32000000 INFO @ Mon, 03 Jun 2019 08:06:45: 40000000 INFO @ Mon, 03 Jun 2019 08:06:48: 41000000 INFO @ Mon, 03 Jun 2019 08:06:52: 41000000 INFO @ Mon, 03 Jun 2019 08:06:53: 33000000 INFO @ Mon, 03 Jun 2019 08:06:56: 42000000 INFO @ Mon, 03 Jun 2019 08:07:00: 42000000 INFO @ Mon, 03 Jun 2019 08:07:02: 34000000 INFO @ Mon, 03 Jun 2019 08:07:03: 43000000 INFO @ Mon, 03 Jun 2019 08:07:07: 43000000 INFO @ Mon, 03 Jun 2019 08:07:10: 44000000 INFO @ Mon, 03 Jun 2019 08:07:11: 35000000 INFO @ Mon, 03 Jun 2019 08:07:16: 44000000 INFO @ Mon, 03 Jun 2019 08:07:16: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 08:07:16: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 08:07:16: #1 total tags in treatment: 20232522 INFO @ Mon, 03 Jun 2019 08:07:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:16: #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 08:07:17: #1 tags after filtering in treatment: 13652127 INFO @ Mon, 03 Jun 2019 08:07:17: #1 Redundant rate of treatment: 0.33 INFO @ Mon, 03 Jun 2019 08:07:17: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:20: #2 number of paired peaks: 14448 INFO @ Mon, 03 Jun 2019 08:07:20: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:20: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:20: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:20: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:20: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 08:07:20: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 08:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.10_model.r INFO @ Mon, 03 Jun 2019 08:07:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:20: 36000000 INFO @ Mon, 03 Jun 2019 08:07:22: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 08:07:22: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 08:07:22: #1 total tags in treatment: 20232522 INFO @ Mon, 03 Jun 2019 08:07:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:22: #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 08:07:23: #1 tags after filtering in treatment: 13652127 INFO @ Mon, 03 Jun 2019 08:07:23: #1 Redundant rate of treatment: 0.33 INFO @ Mon, 03 Jun 2019 08:07:23: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:26: #2 number of paired peaks: 14448 INFO @ Mon, 03 Jun 2019 08:07:26: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:26: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:26: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:26: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:26: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 08:07:26: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 08:07:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.05_model.r INFO @ Mon, 03 Jun 2019 08:07:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:30: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 08:07:38: 38000000 INFO @ Mon, 03 Jun 2019 08:07:47: 39000000 INFO @ Mon, 03 Jun 2019 08:07:56: 40000000 INFO @ Mon, 03 Jun 2019 08:08:04: 41000000 INFO @ Mon, 03 Jun 2019 08:08:13: 42000000 BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 08:08:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:22: 43000000 INFO @ Mon, 03 Jun 2019 08:08:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:32: 44000000 INFO @ Mon, 03 Jun 2019 08:08:40: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 08:08:40: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 08:08:40: #1 total tags in treatment: 20232522 INFO @ Mon, 03 Jun 2019 08:08:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:08:40: #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 08:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.10_summits.bed INFO @ Mon, 03 Jun 2019 08:08:40: Done! INFO @ Mon, 03 Jun 2019 08:08:40: #1 tags after filtering in treatment: 13652127 INFO @ Mon, 03 Jun 2019 08:08:40: #1 Redundant rate of treatment: 0.33 INFO @ Mon, 03 Jun 2019 08:08:40: #1 finished! INFO @ Mon, 03 Jun 2019 08:08:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:08:40: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (10710 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:08:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.05_summits.bed INFO @ Mon, 03 Jun 2019 08:08:43: Done! INFO @ Mon, 03 Jun 2019 08:08:43: #2 number of paired peaks: 14448 INFO @ Mon, 03 Jun 2019 08:08:43: start model_add_line... INFO @ Mon, 03 Jun 2019 08:08:44: start X-correlation... INFO @ Mon, 03 Jun 2019 08:08:44: end of X-cor INFO @ Mon, 03 Jun 2019 08:08:44: #2 finished! INFO @ Mon, 03 Jun 2019 08:08:44: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 08:08:44: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 08:08:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.20_model.r INFO @ Mon, 03 Jun 2019 08:08:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:08:44: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (12046 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:09:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:10:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612508/SRX2612508.20_summits.bed INFO @ Mon, 03 Jun 2019 08:10:01: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8606 records, 4 fields): 14 millis CompletedMACS2peakCalling