Job ID = 11597727 sra ファイルのダウンロード中... Completed: 1419476K bytes transferred in 15 seconds (734265K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 37099100 spots for /home/okishinya/chipatlas/results/dm3/ERX012711/ERR034185.sra Written 37099100 spots for /home/okishinya/chipatlas/results/dm3/ERX012711/ERR034185.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 01:15:30 37099100 reads; of these: 37099100 (100.00%) were paired; of these: 5615026 (15.14%) aligned concordantly 0 times 22694082 (61.17%) aligned concordantly exactly 1 time 8789992 (23.69%) aligned concordantly >1 times ---- 5615026 pairs aligned concordantly 0 times; of these: 345316 (6.15%) aligned discordantly 1 time ---- 5269710 pairs aligned 0 times concordantly or discordantly; of these: 10539420 mates make up the pairs; of these: 8316443 (78.91%) aligned 0 times 1278582 (12.13%) aligned exactly 1 time 944395 (8.96%) aligned >1 times 88.79% overall alignment rate Time searching: 01:15:30 Overall time: 01:15:30 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] 14118694 / 31626172 = 0.4464 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 @ Wed, 30 Jan 2019 15:57:32: # Command line: callpeak -t ERX012711.bam -f BAM -g dm -n ERX012711.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX012711.20 # format = BAM # ChIP-seq file = ['ERX012711.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 @ Wed, 30 Jan 2019 15:57:32: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:57:32: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:57:32: # Command line: callpeak -t ERX012711.bam -f BAM -g dm -n ERX012711.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX012711.10 # format = BAM # ChIP-seq file = ['ERX012711.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 @ Wed, 30 Jan 2019 15:57:32: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:57:32: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:57:32: # Command line: callpeak -t ERX012711.bam -f BAM -g dm -n ERX012711.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX012711.05 # format = BAM # ChIP-seq file = ['ERX012711.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 @ Wed, 30 Jan 2019 15:57:32: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:57:32: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:57:38: 1000000 INFO @ Wed, 30 Jan 2019 15:57:39: 1000000 INFO @ Wed, 30 Jan 2019 15:57:39: 1000000 INFO @ Wed, 30 Jan 2019 15:57:44: 2000000 INFO @ Wed, 30 Jan 2019 15:57:45: 2000000 INFO @ Wed, 30 Jan 2019 15:57:46: 2000000 INFO @ Wed, 30 Jan 2019 15:57:50: 3000000 INFO @ Wed, 30 Jan 2019 15:57:52: 3000000 INFO @ Wed, 30 Jan 2019 15:57:52: 3000000 INFO @ Wed, 30 Jan 2019 15:57:56: 4000000 INFO @ Wed, 30 Jan 2019 15:57:58: 4000000 INFO @ Wed, 30 Jan 2019 15:57:58: 4000000 INFO @ Wed, 30 Jan 2019 15:58:02: 5000000 INFO @ Wed, 30 Jan 2019 15:58:04: 5000000 INFO @ Wed, 30 Jan 2019 15:58:04: 5000000 INFO @ Wed, 30 Jan 2019 15:58:07: 6000000 INFO @ Wed, 30 Jan 2019 15:58:11: 6000000 INFO @ Wed, 30 Jan 2019 15:58:11: 6000000 INFO @ Wed, 30 Jan 2019 15:58:13: 7000000 INFO @ Wed, 30 Jan 2019 15:58:17: 7000000 INFO @ Wed, 30 Jan 2019 15:58:17: 7000000 INFO @ Wed, 30 Jan 2019 15:58:19: 8000000 INFO @ Wed, 30 Jan 2019 15:58:23: 8000000 INFO @ Wed, 30 Jan 2019 15:58:24: 8000000 INFO @ Wed, 30 Jan 2019 15:58:25: 9000000 INFO @ Wed, 30 Jan 2019 15:58:30: 9000000 INFO @ Wed, 30 Jan 2019 15:58:30: 10000000 INFO @ Wed, 30 Jan 2019 15:58:31: 9000000 INFO @ Wed, 30 Jan 2019 15:58:36: 11000000 INFO @ Wed, 30 Jan 2019 15:58:37: 10000000 INFO @ Wed, 30 Jan 2019 15:58:37: 10000000 INFO @ Wed, 30 Jan 2019 15:58:42: 12000000 INFO @ Wed, 30 Jan 2019 15:58:43: 11000000 INFO @ Wed, 30 Jan 2019 15:58:44: 11000000 INFO @ Wed, 30 Jan 2019 15:58:48: 13000000 INFO @ Wed, 30 Jan 2019 15:58:49: 12000000 INFO @ Wed, 30 Jan 2019 15:58:50: 12000000 INFO @ Wed, 30 Jan 2019 15:58:54: 14000000 INFO @ Wed, 30 Jan 2019 15:58:55: 13000000 INFO @ Wed, 30 Jan 2019 15:58:56: 13000000 INFO @ Wed, 30 Jan 2019 15:59:00: 15000000 INFO @ Wed, 30 Jan 2019 15:59:01: 14000000 INFO @ Wed, 30 Jan 2019 15:59:03: 14000000 INFO @ Wed, 30 Jan 2019 15:59:06: 16000000 INFO @ Wed, 30 Jan 2019 15:59:08: 15000000 INFO @ Wed, 30 Jan 2019 15:59:09: 15000000 INFO @ Wed, 30 Jan 2019 15:59:12: 17000000 INFO @ Wed, 30 Jan 2019 15:59:15: 16000000 INFO @ Wed, 30 Jan 2019 15:59:16: 16000000 INFO @ Wed, 30 Jan 2019 15:59:18: 18000000 INFO @ Wed, 30 Jan 2019 15:59:21: 17000000 INFO @ Wed, 30 Jan 2019 15:59:22: 17000000 INFO @ Wed, 30 Jan 2019 15:59:24: 19000000 INFO @ Wed, 30 Jan 2019 15:59:28: 18000000 INFO @ Wed, 30 Jan 2019 15:59:28: 18000000 INFO @ Wed, 30 Jan 2019 15:59:30: 20000000 INFO @ Wed, 30 Jan 2019 15:59:35: 19000000 INFO @ Wed, 30 Jan 2019 15:59:35: 19000000 INFO @ Wed, 30 Jan 2019 15:59:36: 21000000 INFO @ Wed, 30 Jan 2019 15:59:41: 20000000 INFO @ Wed, 30 Jan 2019 15:59:41: 20000000 INFO @ Wed, 30 Jan 2019 15:59:42: 22000000 INFO @ Wed, 30 Jan 2019 15:59:47: 21000000 INFO @ Wed, 30 Jan 2019 15:59:47: 21000000 INFO @ Wed, 30 Jan 2019 15:59:47: 23000000 INFO @ Wed, 30 Jan 2019 15:59:53: 24000000 INFO @ Wed, 30 Jan 2019 15:59:53: 22000000 INFO @ Wed, 30 Jan 2019 15:59:54: 22000000 INFO @ Wed, 30 Jan 2019 15:59:59: 25000000 INFO @ Wed, 30 Jan 2019 16:00:00: 23000000 INFO @ Wed, 30 Jan 2019 16:00:00: 23000000 INFO @ Wed, 30 Jan 2019 16:00:05: 26000000 INFO @ Wed, 30 Jan 2019 16:00:06: 24000000 INFO @ Wed, 30 Jan 2019 16:00:06: 24000000 INFO @ Wed, 30 Jan 2019 16:00:11: 27000000 INFO @ Wed, 30 Jan 2019 16:00:12: 25000000 INFO @ Wed, 30 Jan 2019 16:00:13: 25000000 INFO @ Wed, 30 Jan 2019 16:00:17: 28000000 INFO @ Wed, 30 Jan 2019 16:00:18: 26000000 INFO @ Wed, 30 Jan 2019 16:00:19: 26000000 INFO @ Wed, 30 Jan 2019 16:00:23: 29000000 INFO @ Wed, 30 Jan 2019 16:00:24: 27000000 INFO @ Wed, 30 Jan 2019 16:00:25: 27000000 INFO @ Wed, 30 Jan 2019 16:00:29: 30000000 INFO @ Wed, 30 Jan 2019 16:00:30: 28000000 INFO @ Wed, 30 Jan 2019 16:00:31: 28000000 INFO @ Wed, 30 Jan 2019 16:00:35: 31000000 INFO @ Wed, 30 Jan 2019 16:00:36: 29000000 INFO @ Wed, 30 Jan 2019 16:00:38: 29000000 INFO @ Wed, 30 Jan 2019 16:00:40: 32000000 INFO @ Wed, 30 Jan 2019 16:00:42: 30000000 INFO @ Wed, 30 Jan 2019 16:00:44: 30000000 INFO @ Wed, 30 Jan 2019 16:00:46: 33000000 INFO @ Wed, 30 Jan 2019 16:00:48: 31000000 INFO @ Wed, 30 Jan 2019 16:00:50: 31000000 INFO @ Wed, 30 Jan 2019 16:00:52: 34000000 INFO @ Wed, 30 Jan 2019 16:00:55: 32000000 INFO @ Wed, 30 Jan 2019 16:00:56: 32000000 INFO @ Wed, 30 Jan 2019 16:00:58: 35000000 INFO @ Wed, 30 Jan 2019 16:01:01: 33000000 INFO @ Wed, 30 Jan 2019 16:01:03: 33000000 INFO @ Wed, 30 Jan 2019 16:01:04: 36000000 INFO @ Wed, 30 Jan 2019 16:01:08: 34000000 INFO @ Wed, 30 Jan 2019 16:01:09: 34000000 INFO @ Wed, 30 Jan 2019 16:01:10: 37000000 INFO @ Wed, 30 Jan 2019 16:01:14: #1 tag size is determined as 36 bps INFO @ Wed, 30 Jan 2019 16:01:14: #1 tag size = 36 INFO @ Wed, 30 Jan 2019 16:01:14: #1 total tags in treatment: 17443077 INFO @ Wed, 30 Jan 2019 16:01:14: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:01:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:01:14: #1 tags after filtering in treatment: 15473020 INFO @ Wed, 30 Jan 2019 16:01:14: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 30 Jan 2019 16:01:14: #1 finished! INFO @ Wed, 30 Jan 2019 16:01:14: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:01:15: 35000000 INFO @ Wed, 30 Jan 2019 16:01:15: 35000000 INFO @ Wed, 30 Jan 2019 16:01:15: #2 number of paired peaks: 1433 INFO @ Wed, 30 Jan 2019 16:01:15: start model_add_line... INFO @ Wed, 30 Jan 2019 16:01:16: start X-correlation... INFO @ Wed, 30 Jan 2019 16:01:16: end of X-cor INFO @ Wed, 30 Jan 2019 16:01:16: #2 finished! INFO @ Wed, 30 Jan 2019 16:01:16: #2 predicted fragment length is 325 bps INFO @ Wed, 30 Jan 2019 16:01:16: #2 alternative fragment length(s) may be 325 bps INFO @ Wed, 30 Jan 2019 16:01:16: #2.2 Generate R script for model : ERX012711.20_model.r INFO @ Wed, 30 Jan 2019 16:01:16: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:01:21: 36000000 INFO @ Wed, 30 Jan 2019 16:01:22: 36000000 INFO @ Wed, 30 Jan 2019 16:01:27: 37000000 INFO @ Wed, 30 Jan 2019 16:01:28: 37000000 INFO @ Wed, 30 Jan 2019 16:01:31: #1 tag size is determined as 36 bps INFO @ Wed, 30 Jan 2019 16:01:31: #1 tag size = 36 INFO @ Wed, 30 Jan 2019 16:01:31: #1 total tags in treatment: 17443077 INFO @ Wed, 30 Jan 2019 16:01:31: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:01:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:01:31: #1 tags after filtering in treatment: 15473020 INFO @ Wed, 30 Jan 2019 16:01:31: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 30 Jan 2019 16:01:31: #1 finished! INFO @ Wed, 30 Jan 2019 16:01:31: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:01:32: #1 tag size is determined as 36 bps INFO @ Wed, 30 Jan 2019 16:01:32: #1 tag size = 36 INFO @ Wed, 30 Jan 2019 16:01:32: #1 total tags in treatment: 17443077 INFO @ Wed, 30 Jan 2019 16:01:32: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:01:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:01:32: #1 tags after filtering in treatment: 15473020 INFO @ Wed, 30 Jan 2019 16:01:32: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 30 Jan 2019 16:01:32: #1 finished! INFO @ Wed, 30 Jan 2019 16:01:32: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:01:32: #2 number of paired peaks: 1433 INFO @ Wed, 30 Jan 2019 16:01:32: start model_add_line... INFO @ Wed, 30 Jan 2019 16:01:33: start X-correlation... INFO @ Wed, 30 Jan 2019 16:01:33: end of X-cor INFO @ Wed, 30 Jan 2019 16:01:33: #2 finished! INFO @ Wed, 30 Jan 2019 16:01:33: #2 predicted fragment length is 325 bps INFO @ Wed, 30 Jan 2019 16:01:33: #2 alternative fragment length(s) may be 325 bps INFO @ Wed, 30 Jan 2019 16:01:33: #2.2 Generate R script for model : ERX012711.05_model.r INFO @ Wed, 30 Jan 2019 16:01:33: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:01:34: #2 number of paired peaks: 1433 INFO @ Wed, 30 Jan 2019 16:01:34: start model_add_line... INFO @ Wed, 30 Jan 2019 16:01:34: start X-correlation... INFO @ Wed, 30 Jan 2019 16:01:34: end of X-cor INFO @ Wed, 30 Jan 2019 16:01:34: #2 finished! INFO @ Wed, 30 Jan 2019 16:01:34: #2 predicted fragment length is 325 bps INFO @ Wed, 30 Jan 2019 16:01:34: #2 alternative fragment length(s) may be 325 bps INFO @ Wed, 30 Jan 2019 16:01:34: #2.2 Generate R script for model : ERX012711.10_model.r INFO @ Wed, 30 Jan 2019 16:01:34: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:02:04: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:02:19: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:02:21: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:02:27: #4 Write output xls file... ERX012711.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:02:27: #4 Write peak in narrowPeak format file... ERX012711.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:02:27: #4 Write summits bed file... ERX012711.20_summits.bed INFO @ Wed, 30 Jan 2019 16:02:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1478 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:02:41: #4 Write output xls file... ERX012711.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:02:41: #4 Write peak in narrowPeak format file... ERX012711.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:02:41: #4 Write summits bed file... ERX012711.05_summits.bed INFO @ Wed, 30 Jan 2019 16:02:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3707 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:02:42: #4 Write output xls file... ERX012711.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:02:42: #4 Write peak in narrowPeak format file... ERX012711.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:02:42: #4 Write summits bed file... ERX012711.10_summits.bed INFO @ Wed, 30 Jan 2019 16:02:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2485 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。