Job ID = 1295438 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,522,145 reads read : 43,044,290 reads written : 43,044,290 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: 00:50:52 21522145 reads; of these: 21522145 (100.00%) were paired; of these: 4059539 (18.86%) aligned concordantly 0 times 12851092 (59.71%) aligned concordantly exactly 1 time 4611514 (21.43%) aligned concordantly >1 times ---- 4059539 pairs aligned concordantly 0 times; of these: 108452 (2.67%) aligned discordantly 1 time ---- 3951087 pairs aligned 0 times concordantly or discordantly; of these: 7902174 mates make up the pairs; of these: 6496234 (82.21%) aligned 0 times 617856 (7.82%) aligned exactly 1 time 788084 (9.97%) aligned >1 times 84.91% overall alignment rate Time searching: 00:50:52 Overall time: 00:50:52 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] 1593837 / 17558554 = 0.0908 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 14:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.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 14:55:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:55:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.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 14:55:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:55:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.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 14:55:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:55:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:55:10: 1000000 INFO @ Mon, 03 Jun 2019 14:55:10: 1000000 INFO @ Mon, 03 Jun 2019 14:55:11: 1000000 INFO @ Mon, 03 Jun 2019 14:55:18: 2000000 INFO @ Mon, 03 Jun 2019 14:55:18: 2000000 INFO @ Mon, 03 Jun 2019 14:55:19: 2000000 INFO @ Mon, 03 Jun 2019 14:55:25: 3000000 INFO @ Mon, 03 Jun 2019 14:55:25: 3000000 INFO @ Mon, 03 Jun 2019 14:55:27: 3000000 INFO @ Mon, 03 Jun 2019 14:55:32: 4000000 INFO @ Mon, 03 Jun 2019 14:55:32: 4000000 INFO @ Mon, 03 Jun 2019 14:55:35: 4000000 INFO @ Mon, 03 Jun 2019 14:55:39: 5000000 INFO @ Mon, 03 Jun 2019 14:55:39: 5000000 INFO @ Mon, 03 Jun 2019 14:55:43: 5000000 INFO @ Mon, 03 Jun 2019 14:55:46: 6000000 INFO @ Mon, 03 Jun 2019 14:55:46: 6000000 INFO @ Mon, 03 Jun 2019 14:55:51: 6000000 INFO @ Mon, 03 Jun 2019 14:55:53: 7000000 INFO @ Mon, 03 Jun 2019 14:55:54: 7000000 INFO @ Mon, 03 Jun 2019 14:55:59: 7000000 INFO @ Mon, 03 Jun 2019 14:56:00: 8000000 INFO @ Mon, 03 Jun 2019 14:56:01: 8000000 INFO @ Mon, 03 Jun 2019 14:56:07: 8000000 INFO @ Mon, 03 Jun 2019 14:56:08: 9000000 INFO @ Mon, 03 Jun 2019 14:56:08: 9000000 INFO @ Mon, 03 Jun 2019 14:56:15: 10000000 INFO @ Mon, 03 Jun 2019 14:56:15: 9000000 INFO @ Mon, 03 Jun 2019 14:56:15: 10000000 INFO @ Mon, 03 Jun 2019 14:56:22: 11000000 INFO @ Mon, 03 Jun 2019 14:56:22: 11000000 INFO @ Mon, 03 Jun 2019 14:56:23: 10000000 INFO @ Mon, 03 Jun 2019 14:56:29: 12000000 INFO @ Mon, 03 Jun 2019 14:56:29: 12000000 INFO @ Mon, 03 Jun 2019 14:56:31: 11000000 INFO @ Mon, 03 Jun 2019 14:56:36: 13000000 INFO @ Mon, 03 Jun 2019 14:56:36: 13000000 INFO @ Mon, 03 Jun 2019 14:56:39: 12000000 INFO @ Mon, 03 Jun 2019 14:56:43: 14000000 INFO @ Mon, 03 Jun 2019 14:56:43: 14000000 INFO @ Mon, 03 Jun 2019 14:56:46: 13000000 INFO @ Mon, 03 Jun 2019 14:56:50: 15000000 INFO @ Mon, 03 Jun 2019 14:56:50: 15000000 INFO @ Mon, 03 Jun 2019 14:56:54: 14000000 INFO @ Mon, 03 Jun 2019 14:56:57: 16000000 INFO @ Mon, 03 Jun 2019 14:56:57: 16000000 INFO @ Mon, 03 Jun 2019 14:57:02: 15000000 INFO @ Mon, 03 Jun 2019 14:57:04: 17000000 INFO @ Mon, 03 Jun 2019 14:57:04: 17000000 INFO @ Mon, 03 Jun 2019 14:57:09: 16000000 INFO @ Mon, 03 Jun 2019 14:57:11: 18000000 INFO @ Mon, 03 Jun 2019 14:57:11: 18000000 INFO @ Mon, 03 Jun 2019 14:57:17: 17000000 INFO @ Mon, 03 Jun 2019 14:57:17: 19000000 INFO @ Mon, 03 Jun 2019 14:57:18: 19000000 INFO @ Mon, 03 Jun 2019 14:57:24: 20000000 INFO @ Mon, 03 Jun 2019 14:57:25: 20000000 INFO @ Mon, 03 Jun 2019 14:57:25: 18000000 INFO @ Mon, 03 Jun 2019 14:57:31: 21000000 INFO @ Mon, 03 Jun 2019 14:57:32: 21000000 INFO @ Mon, 03 Jun 2019 14:57:33: 19000000 INFO @ Mon, 03 Jun 2019 14:57:38: 22000000 INFO @ Mon, 03 Jun 2019 14:57:39: 22000000 INFO @ Mon, 03 Jun 2019 14:57:41: 20000000 INFO @ Mon, 03 Jun 2019 14:57:44: 23000000 INFO @ Mon, 03 Jun 2019 14:57:45: 23000000 INFO @ Mon, 03 Jun 2019 14:57:48: 21000000 INFO @ Mon, 03 Jun 2019 14:57:51: 24000000 INFO @ Mon, 03 Jun 2019 14:57:52: 24000000 INFO @ Mon, 03 Jun 2019 14:57:56: 22000000 INFO @ Mon, 03 Jun 2019 14:57:58: 25000000 INFO @ Mon, 03 Jun 2019 14:57:59: 25000000 INFO @ Mon, 03 Jun 2019 14:58:03: 23000000 INFO @ Mon, 03 Jun 2019 14:58:05: 26000000 INFO @ Mon, 03 Jun 2019 14:58:06: 26000000 INFO @ Mon, 03 Jun 2019 14:58:11: 24000000 INFO @ Mon, 03 Jun 2019 14:58:11: 27000000 INFO @ Mon, 03 Jun 2019 14:58:12: 27000000 INFO @ Mon, 03 Jun 2019 14:58:18: 28000000 INFO @ Mon, 03 Jun 2019 14:58:19: 25000000 INFO @ Mon, 03 Jun 2019 14:58:19: 28000000 INFO @ Mon, 03 Jun 2019 14:58:24: 29000000 INFO @ Mon, 03 Jun 2019 14:58:26: 29000000 INFO @ Mon, 03 Jun 2019 14:58:26: 26000000 INFO @ Mon, 03 Jun 2019 14:58:31: 30000000 INFO @ Mon, 03 Jun 2019 14:58:32: 30000000 INFO @ Mon, 03 Jun 2019 14:58:34: 27000000 INFO @ Mon, 03 Jun 2019 14:58:38: 31000000 INFO @ Mon, 03 Jun 2019 14:58:39: 31000000 INFO @ Mon, 03 Jun 2019 14:58:41: 28000000 INFO @ Mon, 03 Jun 2019 14:58:44: 32000000 INFO @ Mon, 03 Jun 2019 14:58:46: 32000000 INFO @ Mon, 03 Jun 2019 14:58:49: 29000000 INFO @ Mon, 03 Jun 2019 14:58:51: 33000000 INFO @ Mon, 03 Jun 2019 14:58:52: 33000000 INFO @ Mon, 03 Jun 2019 14:58:54: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:58:54: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:58:54: #1 total tags in treatment: 15871942 INFO @ Mon, 03 Jun 2019 14:58:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:58:54: #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 14:58:54: #1 tags after filtering in treatment: 8441134 INFO @ Mon, 03 Jun 2019 14:58:54: #1 Redundant rate of treatment: 0.47 INFO @ Mon, 03 Jun 2019 14:58:54: #1 finished! INFO @ Mon, 03 Jun 2019 14:58:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:58:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:58:55: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:58:55: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:58:55: #1 total tags in treatment: 15871942 INFO @ Mon, 03 Jun 2019 14:58:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:58:55: #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 14:58:55: #1 tags after filtering in treatment: 8441134 INFO @ Mon, 03 Jun 2019 14:58:55: #1 Redundant rate of treatment: 0.47 INFO @ Mon, 03 Jun 2019 14:58:55: #1 finished! INFO @ Mon, 03 Jun 2019 14:58:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:58:56: #2 number of paired peaks: 9953 INFO @ Mon, 03 Jun 2019 14:58:56: start model_add_line... INFO @ Mon, 03 Jun 2019 14:58:56: start X-correlation... INFO @ Mon, 03 Jun 2019 14:58:56: end of X-cor INFO @ Mon, 03 Jun 2019 14:58:56: #2 finished! INFO @ Mon, 03 Jun 2019 14:58:56: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 14:58:56: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 14:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.05_model.r INFO @ Mon, 03 Jun 2019 14:58:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:58:57: 30000000 INFO @ Mon, 03 Jun 2019 14:58:57: #2 number of paired peaks: 9953 INFO @ Mon, 03 Jun 2019 14:58:57: start model_add_line... INFO @ Mon, 03 Jun 2019 14:58:57: start X-correlation... INFO @ Mon, 03 Jun 2019 14:58:57: end of X-cor INFO @ Mon, 03 Jun 2019 14:58:57: #2 finished! INFO @ Mon, 03 Jun 2019 14:58:57: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 14:58:57: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 14:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.20_model.r INFO @ Mon, 03 Jun 2019 14:58:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:59:04: 31000000 INFO @ Mon, 03 Jun 2019 14:59:11: 32000000 INFO @ Mon, 03 Jun 2019 14:59:18: 33000000 INFO @ Mon, 03 Jun 2019 14:59:21: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:59:21: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:59:21: #1 total tags in treatment: 15871942 INFO @ Mon, 03 Jun 2019 14:59:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:59:21: #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 14:59:21: #1 tags after filtering in treatment: 8441134 INFO @ Mon, 03 Jun 2019 14:59:21: #1 Redundant rate of treatment: 0.47 INFO @ Mon, 03 Jun 2019 14:59:21: #1 finished! INFO @ Mon, 03 Jun 2019 14:59:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:59:23: #2 number of paired peaks: 9953 INFO @ Mon, 03 Jun 2019 14:59:23: start model_add_line... INFO @ Mon, 03 Jun 2019 14:59:23: start X-correlation... INFO @ Mon, 03 Jun 2019 14:59:23: end of X-cor INFO @ Mon, 03 Jun 2019 14:59:23: #2 finished! INFO @ Mon, 03 Jun 2019 14:59:23: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 14:59:23: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 14:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.10_model.r INFO @ Mon, 03 Jun 2019 14:59:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:59:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:59:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:59:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.05_summits.bed INFO @ Mon, 03 Jun 2019 14:59:43: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10189 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:59:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:59:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:59:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.20_summits.bed INFO @ Mon, 03 Jun 2019 14:59:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8083 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 14:59:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393653/SRX3393653.10_summits.bed INFO @ Mon, 03 Jun 2019 15:00:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9250 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。