Job ID = 1293342 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 106,243,017 reads read : 212,486,034 reads written : 212,486,034 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: 03:50:25 106243017 reads; of these: 106243017 (100.00%) were paired; of these: 24614530 (23.17%) aligned concordantly 0 times 57674608 (54.29%) aligned concordantly exactly 1 time 23953879 (22.55%) aligned concordantly >1 times ---- 24614530 pairs aligned concordantly 0 times; of these: 737213 (3.00%) aligned discordantly 1 time ---- 23877317 pairs aligned 0 times concordantly or discordantly; of these: 47754634 mates make up the pairs; of these: 44682795 (93.57%) aligned 0 times 1944400 (4.07%) aligned exactly 1 time 1127439 (2.36%) aligned >1 times 78.97% overall alignment rate Time searching: 03:50:25 Overall time: 03:50:25 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 72 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] 60422132 / 82295021 = 0.7342 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 04:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.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 04:39:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.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 04:39:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:39:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:39:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.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 04:39:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:39:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:39:33: 1000000 INFO @ Mon, 03 Jun 2019 04:39:34: 1000000 INFO @ Mon, 03 Jun 2019 04:39:34: 1000000 INFO @ Mon, 03 Jun 2019 04:39:40: 2000000 INFO @ Mon, 03 Jun 2019 04:39:41: 2000000 INFO @ Mon, 03 Jun 2019 04:39:41: 2000000 INFO @ Mon, 03 Jun 2019 04:39:46: 3000000 INFO @ Mon, 03 Jun 2019 04:39:48: 3000000 INFO @ Mon, 03 Jun 2019 04:39:48: 3000000 INFO @ Mon, 03 Jun 2019 04:39:51: 4000000 INFO @ Mon, 03 Jun 2019 04:39:55: 4000000 INFO @ Mon, 03 Jun 2019 04:39:55: 4000000 INFO @ Mon, 03 Jun 2019 04:39:57: 5000000 INFO @ Mon, 03 Jun 2019 04:40:02: 5000000 INFO @ Mon, 03 Jun 2019 04:40:02: 5000000 INFO @ Mon, 03 Jun 2019 04:40:03: 6000000 INFO @ Mon, 03 Jun 2019 04:40:08: 6000000 INFO @ Mon, 03 Jun 2019 04:40:08: 6000000 INFO @ Mon, 03 Jun 2019 04:40:09: 7000000 INFO @ Mon, 03 Jun 2019 04:40:15: 7000000 INFO @ Mon, 03 Jun 2019 04:40:15: 7000000 INFO @ Mon, 03 Jun 2019 04:40:15: 8000000 INFO @ Mon, 03 Jun 2019 04:40:22: 9000000 INFO @ Mon, 03 Jun 2019 04:40:22: 8000000 INFO @ Mon, 03 Jun 2019 04:40:22: 8000000 INFO @ Mon, 03 Jun 2019 04:40:28: 10000000 INFO @ Mon, 03 Jun 2019 04:40:30: 9000000 INFO @ Mon, 03 Jun 2019 04:40:30: 9000000 INFO @ Mon, 03 Jun 2019 04:40:34: 11000000 INFO @ Mon, 03 Jun 2019 04:40:37: 10000000 INFO @ Mon, 03 Jun 2019 04:40:37: 10000000 INFO @ Mon, 03 Jun 2019 04:40:40: 12000000 INFO @ Mon, 03 Jun 2019 04:40:44: 11000000 INFO @ Mon, 03 Jun 2019 04:40:44: 11000000 INFO @ Mon, 03 Jun 2019 04:40:46: 13000000 INFO @ Mon, 03 Jun 2019 04:40:51: 12000000 INFO @ Mon, 03 Jun 2019 04:40:51: 12000000 INFO @ Mon, 03 Jun 2019 04:40:52: 14000000 INFO @ Mon, 03 Jun 2019 04:40:58: 15000000 INFO @ Mon, 03 Jun 2019 04:40:58: 13000000 INFO @ Mon, 03 Jun 2019 04:40:59: 13000000 INFO @ Mon, 03 Jun 2019 04:41:04: 16000000 INFO @ Mon, 03 Jun 2019 04:41:06: 14000000 INFO @ Mon, 03 Jun 2019 04:41:06: 14000000 INFO @ Mon, 03 Jun 2019 04:41:10: 17000000 INFO @ Mon, 03 Jun 2019 04:41:13: 15000000 INFO @ Mon, 03 Jun 2019 04:41:13: 15000000 INFO @ Mon, 03 Jun 2019 04:41:16: 18000000 INFO @ Mon, 03 Jun 2019 04:41:20: 16000000 INFO @ Mon, 03 Jun 2019 04:41:20: 16000000 INFO @ Mon, 03 Jun 2019 04:41:22: 19000000 INFO @ Mon, 03 Jun 2019 04:41:27: 17000000 INFO @ Mon, 03 Jun 2019 04:41:27: 17000000 INFO @ Mon, 03 Jun 2019 04:41:28: 20000000 INFO @ Mon, 03 Jun 2019 04:41:34: 21000000 INFO @ Mon, 03 Jun 2019 04:41:34: 18000000 INFO @ Mon, 03 Jun 2019 04:41:34: 18000000 INFO @ Mon, 03 Jun 2019 04:41:40: 22000000 INFO @ Mon, 03 Jun 2019 04:41:41: 19000000 INFO @ Mon, 03 Jun 2019 04:41:41: 19000000 INFO @ Mon, 03 Jun 2019 04:41:46: 23000000 INFO @ Mon, 03 Jun 2019 04:41:48: 20000000 INFO @ Mon, 03 Jun 2019 04:41:48: 20000000 INFO @ Mon, 03 Jun 2019 04:41:52: 24000000 INFO @ Mon, 03 Jun 2019 04:41:54: 21000000 INFO @ Mon, 03 Jun 2019 04:41:55: 21000000 INFO @ Mon, 03 Jun 2019 04:41:58: 25000000 INFO @ Mon, 03 Jun 2019 04:42:01: 22000000 INFO @ Mon, 03 Jun 2019 04:42:01: 22000000 INFO @ Mon, 03 Jun 2019 04:42:04: 26000000 INFO @ Mon, 03 Jun 2019 04:42:07: 23000000 INFO @ Mon, 03 Jun 2019 04:42:08: 23000000 INFO @ Mon, 03 Jun 2019 04:42:10: 27000000 INFO @ Mon, 03 Jun 2019 04:42:14: 24000000 INFO @ Mon, 03 Jun 2019 04:42:15: 24000000 INFO @ Mon, 03 Jun 2019 04:42:16: 28000000 INFO @ Mon, 03 Jun 2019 04:42:21: 25000000 INFO @ Mon, 03 Jun 2019 04:42:21: 25000000 INFO @ Mon, 03 Jun 2019 04:42:22: 29000000 INFO @ Mon, 03 Jun 2019 04:42:27: 26000000 INFO @ Mon, 03 Jun 2019 04:42:28: 26000000 INFO @ Mon, 03 Jun 2019 04:42:29: 30000000 INFO @ Mon, 03 Jun 2019 04:42:34: 27000000 INFO @ Mon, 03 Jun 2019 04:42:35: 27000000 INFO @ Mon, 03 Jun 2019 04:42:36: 31000000 INFO @ Mon, 03 Jun 2019 04:42:41: 28000000 INFO @ Mon, 03 Jun 2019 04:42:41: 28000000 INFO @ Mon, 03 Jun 2019 04:42:42: 32000000 INFO @ Mon, 03 Jun 2019 04:42:47: 29000000 INFO @ Mon, 03 Jun 2019 04:42:48: 33000000 INFO @ Mon, 03 Jun 2019 04:42:48: 29000000 INFO @ Mon, 03 Jun 2019 04:42:54: 34000000 INFO @ Mon, 03 Jun 2019 04:42:54: 30000000 INFO @ Mon, 03 Jun 2019 04:42:55: 30000000 INFO @ Mon, 03 Jun 2019 04:43:00: 35000000 INFO @ Mon, 03 Jun 2019 04:43:02: 31000000 INFO @ Mon, 03 Jun 2019 04:43:02: 31000000 INFO @ Mon, 03 Jun 2019 04:43:06: 36000000 INFO @ Mon, 03 Jun 2019 04:43:08: 32000000 INFO @ Mon, 03 Jun 2019 04:43:09: 32000000 INFO @ Mon, 03 Jun 2019 04:43:12: 37000000 INFO @ Mon, 03 Jun 2019 04:43:15: 33000000 INFO @ Mon, 03 Jun 2019 04:43:16: 33000000 INFO @ Mon, 03 Jun 2019 04:43:19: 38000000 INFO @ Mon, 03 Jun 2019 04:43:22: 34000000 INFO @ Mon, 03 Jun 2019 04:43:23: 34000000 INFO @ Mon, 03 Jun 2019 04:43:25: 39000000 INFO @ Mon, 03 Jun 2019 04:43:28: 35000000 INFO @ Mon, 03 Jun 2019 04:43:29: 35000000 INFO @ Mon, 03 Jun 2019 04:43:31: 40000000 INFO @ Mon, 03 Jun 2019 04:43:35: 36000000 INFO @ Mon, 03 Jun 2019 04:43:36: 36000000 INFO @ Mon, 03 Jun 2019 04:43:37: 41000000 INFO @ Mon, 03 Jun 2019 04:43:42: 37000000 INFO @ Mon, 03 Jun 2019 04:43:43: 37000000 INFO @ Mon, 03 Jun 2019 04:43:43: 42000000 INFO @ Mon, 03 Jun 2019 04:43:49: 38000000 INFO @ Mon, 03 Jun 2019 04:43:50: 38000000 INFO @ Mon, 03 Jun 2019 04:43:50: 43000000 INFO @ Mon, 03 Jun 2019 04:43:55: 39000000 INFO @ Mon, 03 Jun 2019 04:43:56: 44000000 INFO @ Mon, 03 Jun 2019 04:43:57: 39000000 INFO @ Mon, 03 Jun 2019 04:44:02: 45000000 INFO @ Mon, 03 Jun 2019 04:44:02: 40000000 INFO @ Mon, 03 Jun 2019 04:44:04: 40000000 INFO @ Mon, 03 Jun 2019 04:44:08: 46000000 INFO @ Mon, 03 Jun 2019 04:44:09: 41000000 INFO @ Mon, 03 Jun 2019 04:44:10: 41000000 INFO @ Mon, 03 Jun 2019 04:44:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:44:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:44:14: #1 total tags in treatment: 21684083 INFO @ Mon, 03 Jun 2019 04:44:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:44:14: #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 04:44:15: #1 tags after filtering in treatment: 18860171 INFO @ Mon, 03 Jun 2019 04:44:15: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 03 Jun 2019 04:44:15: #1 finished! INFO @ Mon, 03 Jun 2019 04:44:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:44:16: 42000000 INFO @ Mon, 03 Jun 2019 04:44:16: #2 number of paired peaks: 775 WARNING @ Mon, 03 Jun 2019 04:44:16: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Mon, 03 Jun 2019 04:44:16: start model_add_line... INFO @ Mon, 03 Jun 2019 04:44:17: start X-correlation... INFO @ Mon, 03 Jun 2019 04:44:17: end of X-cor INFO @ Mon, 03 Jun 2019 04:44:17: #2 finished! INFO @ Mon, 03 Jun 2019 04:44:17: #2 predicted fragment length is 166 bps INFO @ Mon, 03 Jun 2019 04:44:17: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 03 Jun 2019 04:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.05_model.r INFO @ Mon, 03 Jun 2019 04:44:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:44:17: 42000000 INFO @ Mon, 03 Jun 2019 04:44:23: 43000000 INFO @ Mon, 03 Jun 2019 04:44:24: 43000000 INFO @ Mon, 03 Jun 2019 04:44:30: 44000000 INFO @ Mon, 03 Jun 2019 04:44:31: 44000000 INFO @ Mon, 03 Jun 2019 04:44:36: 45000000 INFO @ Mon, 03 Jun 2019 04:44:37: 45000000 INFO @ Mon, 03 Jun 2019 04:44:43: 46000000 INFO @ Mon, 03 Jun 2019 04:44:44: 46000000 INFO @ Mon, 03 Jun 2019 04:44:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:44:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:44:49: #1 total tags in treatment: 21684083 INFO @ Mon, 03 Jun 2019 04:44:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:44:49: #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 04:44:50: #1 tags after filtering in treatment: 18860171 INFO @ Mon, 03 Jun 2019 04:44:50: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 03 Jun 2019 04:44:50: #1 finished! INFO @ Mon, 03 Jun 2019 04:44:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:44:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:44:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:44:51: #1 total tags in treatment: 21684083 INFO @ Mon, 03 Jun 2019 04:44:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:44:51: #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 04:44:51: #1 tags after filtering in treatment: 18860171 INFO @ Mon, 03 Jun 2019 04:44:51: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 03 Jun 2019 04:44:51: #1 finished! INFO @ Mon, 03 Jun 2019 04:44:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:44:52: #2 number of paired peaks: 775 WARNING @ Mon, 03 Jun 2019 04:44:52: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Mon, 03 Jun 2019 04:44:52: start model_add_line... INFO @ Mon, 03 Jun 2019 04:44:52: start X-correlation... INFO @ Mon, 03 Jun 2019 04:44:52: end of X-cor INFO @ Mon, 03 Jun 2019 04:44:52: #2 finished! INFO @ Mon, 03 Jun 2019 04:44:52: #2 predicted fragment length is 166 bps INFO @ Mon, 03 Jun 2019 04:44:52: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 03 Jun 2019 04:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.20_model.r INFO @ Mon, 03 Jun 2019 04:44:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:44:53: #2 number of paired peaks: 775 WARNING @ Mon, 03 Jun 2019 04:44:53: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Mon, 03 Jun 2019 04:44:53: start model_add_line... INFO @ Mon, 03 Jun 2019 04:44:53: start X-correlation... INFO @ Mon, 03 Jun 2019 04:44:53: end of X-cor INFO @ Mon, 03 Jun 2019 04:44:53: #2 finished! INFO @ Mon, 03 Jun 2019 04:44:53: #2 predicted fragment length is 166 bps INFO @ Mon, 03 Jun 2019 04:44:53: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 03 Jun 2019 04:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.10_model.r INFO @ Mon, 03 Jun 2019 04:44:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:45:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:45:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:45:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:45:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.05_summits.bed INFO @ Mon, 03 Jun 2019 04:45:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14798 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:45:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:45:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.20_summits.bed INFO @ Mon, 03 Jun 2019 04:46:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3959 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818269/ERX1818269.10_summits.bed INFO @ Mon, 03 Jun 2019 04:46:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9020 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。