Job ID = 1295439 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,559,224 reads read : 51,118,448 reads written : 51,118,448 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: 01:00:35 25559224 reads; of these: 25559224 (100.00%) were paired; of these: 4771446 (18.67%) aligned concordantly 0 times 15287856 (59.81%) aligned concordantly exactly 1 time 5499922 (21.52%) aligned concordantly >1 times ---- 4771446 pairs aligned concordantly 0 times; of these: 117841 (2.47%) aligned discordantly 1 time ---- 4653605 pairs aligned 0 times concordantly or discordantly; of these: 9307210 mates make up the pairs; of these: 7740405 (83.17%) aligned 0 times 696346 (7.48%) aligned exactly 1 time 870459 (9.35%) aligned >1 times 84.86% overall alignment rate Time searching: 01:00:35 Overall time: 01:00:35 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] 2137774 / 20890950 = 0.1023 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 15:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.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 15:09:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.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 15:09:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.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 15:09:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:54: 1000000 INFO @ Mon, 03 Jun 2019 15:09:55: 1000000 INFO @ Mon, 03 Jun 2019 15:09:55: 1000000 INFO @ Mon, 03 Jun 2019 15:10:01: 2000000 INFO @ Mon, 03 Jun 2019 15:10:02: 2000000 INFO @ Mon, 03 Jun 2019 15:10:04: 2000000 INFO @ Mon, 03 Jun 2019 15:10:09: 3000000 INFO @ Mon, 03 Jun 2019 15:10:10: 3000000 INFO @ Mon, 03 Jun 2019 15:10:12: 3000000 INFO @ Mon, 03 Jun 2019 15:10:16: 4000000 INFO @ Mon, 03 Jun 2019 15:10:17: 4000000 INFO @ Mon, 03 Jun 2019 15:10:21: 4000000 INFO @ Mon, 03 Jun 2019 15:10:23: 5000000 INFO @ Mon, 03 Jun 2019 15:10:25: 5000000 INFO @ Mon, 03 Jun 2019 15:10:29: 5000000 INFO @ Mon, 03 Jun 2019 15:10:30: 6000000 INFO @ Mon, 03 Jun 2019 15:10:32: 6000000 INFO @ Mon, 03 Jun 2019 15:10:37: 7000000 INFO @ Mon, 03 Jun 2019 15:10:37: 6000000 INFO @ Mon, 03 Jun 2019 15:10:39: 7000000 INFO @ Mon, 03 Jun 2019 15:10:44: 8000000 INFO @ Mon, 03 Jun 2019 15:10:46: 7000000 INFO @ Mon, 03 Jun 2019 15:10:47: 8000000 INFO @ Mon, 03 Jun 2019 15:10:51: 9000000 INFO @ Mon, 03 Jun 2019 15:10:54: 9000000 INFO @ Mon, 03 Jun 2019 15:10:54: 8000000 INFO @ Mon, 03 Jun 2019 15:10:58: 10000000 INFO @ Mon, 03 Jun 2019 15:11:01: 10000000 INFO @ Mon, 03 Jun 2019 15:11:02: 9000000 INFO @ Mon, 03 Jun 2019 15:11:05: 11000000 INFO @ Mon, 03 Jun 2019 15:11:09: 11000000 INFO @ Mon, 03 Jun 2019 15:11:11: 10000000 INFO @ Mon, 03 Jun 2019 15:11:12: 12000000 INFO @ Mon, 03 Jun 2019 15:11:16: 12000000 INFO @ Mon, 03 Jun 2019 15:11:19: 13000000 INFO @ Mon, 03 Jun 2019 15:11:19: 11000000 INFO @ Mon, 03 Jun 2019 15:11:23: 13000000 INFO @ Mon, 03 Jun 2019 15:11:26: 14000000 INFO @ Mon, 03 Jun 2019 15:11:28: 12000000 INFO @ Mon, 03 Jun 2019 15:11:31: 14000000 INFO @ Mon, 03 Jun 2019 15:11:33: 15000000 INFO @ Mon, 03 Jun 2019 15:11:36: 13000000 INFO @ Mon, 03 Jun 2019 15:11:38: 15000000 INFO @ Mon, 03 Jun 2019 15:11:40: 16000000 INFO @ Mon, 03 Jun 2019 15:11:44: 14000000 INFO @ Mon, 03 Jun 2019 15:11:45: 16000000 INFO @ Mon, 03 Jun 2019 15:11:47: 17000000 INFO @ Mon, 03 Jun 2019 15:11:52: 17000000 INFO @ Mon, 03 Jun 2019 15:11:53: 15000000 INFO @ Mon, 03 Jun 2019 15:11:54: 18000000 INFO @ Mon, 03 Jun 2019 15:11:59: 18000000 INFO @ Mon, 03 Jun 2019 15:12:01: 19000000 INFO @ Mon, 03 Jun 2019 15:12:01: 16000000 INFO @ Mon, 03 Jun 2019 15:12:06: 19000000 INFO @ Mon, 03 Jun 2019 15:12:08: 20000000 INFO @ Mon, 03 Jun 2019 15:12:09: 17000000 INFO @ Mon, 03 Jun 2019 15:12:14: 20000000 INFO @ Mon, 03 Jun 2019 15:12:16: 21000000 INFO @ Mon, 03 Jun 2019 15:12:18: 18000000 INFO @ Mon, 03 Jun 2019 15:12:21: 21000000 INFO @ Mon, 03 Jun 2019 15:12:23: 22000000 INFO @ Mon, 03 Jun 2019 15:12:27: 19000000 INFO @ Mon, 03 Jun 2019 15:12:28: 22000000 INFO @ Mon, 03 Jun 2019 15:12:30: 23000000 INFO @ Mon, 03 Jun 2019 15:12:35: 23000000 INFO @ Mon, 03 Jun 2019 15:12:35: 20000000 INFO @ Mon, 03 Jun 2019 15:12:37: 24000000 INFO @ Mon, 03 Jun 2019 15:12:42: 24000000 INFO @ Mon, 03 Jun 2019 15:12:43: 21000000 INFO @ Mon, 03 Jun 2019 15:12:44: 25000000 INFO @ Mon, 03 Jun 2019 15:12:50: 25000000 INFO @ Mon, 03 Jun 2019 15:12:51: 26000000 INFO @ Mon, 03 Jun 2019 15:12:52: 22000000 INFO @ Mon, 03 Jun 2019 15:12:57: 26000000 INFO @ Mon, 03 Jun 2019 15:12:58: 27000000 INFO @ Mon, 03 Jun 2019 15:13:00: 23000000 INFO @ Mon, 03 Jun 2019 15:13:04: 27000000 INFO @ Mon, 03 Jun 2019 15:13:05: 28000000 INFO @ Mon, 03 Jun 2019 15:13:09: 24000000 INFO @ Mon, 03 Jun 2019 15:13:12: 28000000 INFO @ Mon, 03 Jun 2019 15:13:13: 29000000 INFO @ Mon, 03 Jun 2019 15:13:18: 25000000 INFO @ Mon, 03 Jun 2019 15:13:20: 29000000 INFO @ Mon, 03 Jun 2019 15:13:20: 30000000 INFO @ Mon, 03 Jun 2019 15:13:26: 26000000 INFO @ Mon, 03 Jun 2019 15:13:27: 30000000 INFO @ Mon, 03 Jun 2019 15:13:27: 31000000 INFO @ Mon, 03 Jun 2019 15:13:34: 32000000 INFO @ Mon, 03 Jun 2019 15:13:34: 27000000 INFO @ Mon, 03 Jun 2019 15:13:35: 31000000 INFO @ Mon, 03 Jun 2019 15:13:42: 33000000 INFO @ Mon, 03 Jun 2019 15:13:42: 32000000 INFO @ Mon, 03 Jun 2019 15:13:43: 28000000 INFO @ Mon, 03 Jun 2019 15:13:49: 34000000 INFO @ Mon, 03 Jun 2019 15:13:49: 33000000 INFO @ Mon, 03 Jun 2019 15:13:51: 29000000 INFO @ Mon, 03 Jun 2019 15:13:56: 35000000 INFO @ Mon, 03 Jun 2019 15:13:57: 34000000 INFO @ Mon, 03 Jun 2019 15:14:00: 30000000 INFO @ Mon, 03 Jun 2019 15:14:04: 36000000 INFO @ Mon, 03 Jun 2019 15:14:04: 35000000 INFO @ Mon, 03 Jun 2019 15:14:08: 31000000 INFO @ Mon, 03 Jun 2019 15:14:11: 37000000 INFO @ Mon, 03 Jun 2019 15:14:11: 36000000 INFO @ Mon, 03 Jun 2019 15:14:16: 32000000 INFO @ Mon, 03 Jun 2019 15:14:18: 38000000 INFO @ Mon, 03 Jun 2019 15:14:19: 37000000 INFO @ Mon, 03 Jun 2019 15:14:25: 33000000 INFO @ Mon, 03 Jun 2019 15:14:26: 39000000 INFO @ Mon, 03 Jun 2019 15:14:26: 38000000 INFO @ Mon, 03 Jun 2019 15:14:27: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:14:27: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:14:27: #1 total tags in treatment: 18653648 INFO @ Mon, 03 Jun 2019 15:14:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:14:27: #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 15:14:27: #1 tags after filtering in treatment: 9465142 INFO @ Mon, 03 Jun 2019 15:14:27: #1 Redundant rate of treatment: 0.49 INFO @ Mon, 03 Jun 2019 15:14:27: #1 finished! INFO @ Mon, 03 Jun 2019 15:14:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:14:29: #2 number of paired peaks: 10345 INFO @ Mon, 03 Jun 2019 15:14:29: start model_add_line... INFO @ Mon, 03 Jun 2019 15:14:29: start X-correlation... INFO @ Mon, 03 Jun 2019 15:14:29: end of X-cor INFO @ Mon, 03 Jun 2019 15:14:29: #2 finished! INFO @ Mon, 03 Jun 2019 15:14:29: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 15:14:29: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 15:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.10_model.r INFO @ Mon, 03 Jun 2019 15:14:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:14:33: 39000000 INFO @ Mon, 03 Jun 2019 15:14:33: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:14:33: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:14:33: #1 total tags in treatment: 18653648 INFO @ Mon, 03 Jun 2019 15:14:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:14:33: #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 15:14:34: 34000000 INFO @ Mon, 03 Jun 2019 15:14:34: #1 tags after filtering in treatment: 9465142 INFO @ Mon, 03 Jun 2019 15:14:34: #1 Redundant rate of treatment: 0.49 INFO @ Mon, 03 Jun 2019 15:14:34: #1 finished! INFO @ Mon, 03 Jun 2019 15:14:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:14:36: #2 number of paired peaks: 10345 INFO @ Mon, 03 Jun 2019 15:14:36: start model_add_line... INFO @ Mon, 03 Jun 2019 15:14:36: start X-correlation... INFO @ Mon, 03 Jun 2019 15:14:36: end of X-cor INFO @ Mon, 03 Jun 2019 15:14:36: #2 finished! INFO @ Mon, 03 Jun 2019 15:14:36: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 15:14:36: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 15:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.20_model.r INFO @ Mon, 03 Jun 2019 15:14:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:14:42: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:14:50: 36000000 INFO @ Mon, 03 Jun 2019 15:14:58: 37000000 INFO @ Mon, 03 Jun 2019 15:15:05: 38000000 INFO @ Mon, 03 Jun 2019 15:15:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:13: 39000000 INFO @ Mon, 03 Jun 2019 15:15:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:14: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:15:14: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:15:14: #1 total tags in treatment: 18653648 INFO @ Mon, 03 Jun 2019 15:15:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:14: #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 15:15:15: #1 tags after filtering in treatment: 9465142 INFO @ Mon, 03 Jun 2019 15:15:15: #1 Redundant rate of treatment: 0.49 INFO @ Mon, 03 Jun 2019 15:15:15: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:17: #2 number of paired peaks: 10345 INFO @ Mon, 03 Jun 2019 15:15:17: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:17: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:17: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:17: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:17: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 15:15:17: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 15:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.05_model.r INFO @ Mon, 03 Jun 2019 15:15:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.10_summits.bed INFO @ Mon, 03 Jun 2019 15:15:22: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9612 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 15:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.20_summits.bed INFO @ Mon, 03 Jun 2019 15:15:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8437 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:15:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393654/SRX3393654.05_summits.bed INFO @ Mon, 03 Jun 2019 15:16:10: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10701 records, 4 fields): 16 millis CompletedMACS2peakCalling