Job ID = 9159800 sra ファイルのダウンロード中... Completed: 2343335K bytes transferred in 22 seconds (869782K bits/sec), in 1 file, 2 directories. 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... Written 37001686 spots for /home/okishinya/chipatlas/results/dm3/SRX683497/SRR1554223.sra Written 37001686 spots total 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: 01:51:41 37001686 reads; of these: 37001686 (100.00%) were paired; of these: 4450056 (12.03%) aligned concordantly 0 times 21872280 (59.11%) aligned concordantly exactly 1 time 10679350 (28.86%) aligned concordantly >1 times ---- 4450056 pairs aligned concordantly 0 times; of these: 507492 (11.40%) aligned discordantly 1 time ---- 3942564 pairs aligned 0 times concordantly or discordantly; of these: 7885128 mates make up the pairs; of these: 6544499 (83.00%) aligned 0 times 784493 (9.95%) aligned exactly 1 time 556136 (7.05%) aligned >1 times 91.16% overall alignment rate Time searching: 01:51:41 Overall time: 01:51:41 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 28 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] 20563181 / 32980842 = 0.6235 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, 28 Jun 2017 01:54:30: # Command line: callpeak -t SRX683497.bam -f BAM -g dm -n SRX683497.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX683497.10 # format = BAM # ChIP-seq file = ['SRX683497.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, 28 Jun 2017 01:54:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:54:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:54:30: # Command line: callpeak -t SRX683497.bam -f BAM -g dm -n SRX683497.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX683497.20 # format = BAM # ChIP-seq file = ['SRX683497.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, 28 Jun 2017 01:54:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:54:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:54:30: # Command line: callpeak -t SRX683497.bam -f BAM -g dm -n SRX683497.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX683497.05 # format = BAM # ChIP-seq file = ['SRX683497.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, 28 Jun 2017 01:54:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:54:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:54:36: 1000000 INFO @ Wed, 28 Jun 2017 01:54:36: 1000000 INFO @ Wed, 28 Jun 2017 01:54:36: 1000000 INFO @ Wed, 28 Jun 2017 01:54:42: 2000000 INFO @ Wed, 28 Jun 2017 01:54:42: 2000000 INFO @ Wed, 28 Jun 2017 01:54:43: 2000000 INFO @ Wed, 28 Jun 2017 01:54:47: 3000000 INFO @ Wed, 28 Jun 2017 01:54:49: 3000000 INFO @ Wed, 28 Jun 2017 01:54:49: 3000000 INFO @ Wed, 28 Jun 2017 01:54:53: 4000000 INFO @ Wed, 28 Jun 2017 01:54:55: 4000000 INFO @ Wed, 28 Jun 2017 01:54:55: 4000000 INFO @ Wed, 28 Jun 2017 01:54:59: 5000000 INFO @ Wed, 28 Jun 2017 01:55:02: 5000000 INFO @ Wed, 28 Jun 2017 01:55:02: 5000000 INFO @ Wed, 28 Jun 2017 01:55:05: 6000000 INFO @ Wed, 28 Jun 2017 01:55:08: 6000000 INFO @ Wed, 28 Jun 2017 01:55:09: 6000000 INFO @ Wed, 28 Jun 2017 01:55:10: 7000000 INFO @ Wed, 28 Jun 2017 01:55:15: 7000000 INFO @ Wed, 28 Jun 2017 01:55:16: 7000000 INFO @ Wed, 28 Jun 2017 01:55:16: 8000000 INFO @ Wed, 28 Jun 2017 01:55:22: 8000000 INFO @ Wed, 28 Jun 2017 01:55:22: 9000000 INFO @ Wed, 28 Jun 2017 01:55:23: 8000000 INFO @ Wed, 28 Jun 2017 01:55:28: 10000000 INFO @ Wed, 28 Jun 2017 01:55:29: 9000000 INFO @ Wed, 28 Jun 2017 01:55:30: 9000000 INFO @ Wed, 28 Jun 2017 01:55:33: 11000000 INFO @ Wed, 28 Jun 2017 01:55:35: 10000000 INFO @ Wed, 28 Jun 2017 01:55:37: 10000000 INFO @ Wed, 28 Jun 2017 01:55:39: 12000000 INFO @ Wed, 28 Jun 2017 01:55:42: 11000000 INFO @ Wed, 28 Jun 2017 01:55:44: 11000000 INFO @ Wed, 28 Jun 2017 01:55:45: 13000000 INFO @ Wed, 28 Jun 2017 01:55:49: 12000000 INFO @ Wed, 28 Jun 2017 01:55:50: 12000000 INFO @ Wed, 28 Jun 2017 01:55:51: 14000000 INFO @ Wed, 28 Jun 2017 01:55:55: 13000000 INFO @ Wed, 28 Jun 2017 01:55:56: 15000000 INFO @ Wed, 28 Jun 2017 01:55:57: 13000000 INFO @ Wed, 28 Jun 2017 01:56:02: 14000000 INFO @ Wed, 28 Jun 2017 01:56:02: 16000000 INFO @ Wed, 28 Jun 2017 01:56:04: 14000000 INFO @ Wed, 28 Jun 2017 01:56:08: 17000000 INFO @ Wed, 28 Jun 2017 01:56:08: 15000000 INFO @ Wed, 28 Jun 2017 01:56:11: 15000000 INFO @ Wed, 28 Jun 2017 01:56:14: 18000000 INFO @ Wed, 28 Jun 2017 01:56:15: 16000000 INFO @ Wed, 28 Jun 2017 01:56:17: 16000000 INFO @ Wed, 28 Jun 2017 01:56:19: 19000000 INFO @ Wed, 28 Jun 2017 01:56:21: 17000000 INFO @ Wed, 28 Jun 2017 01:56:24: 17000000 INFO @ Wed, 28 Jun 2017 01:56:25: 20000000 INFO @ Wed, 28 Jun 2017 01:56:28: 18000000 INFO @ Wed, 28 Jun 2017 01:56:31: 18000000 INFO @ Wed, 28 Jun 2017 01:56:32: 21000000 INFO @ Wed, 28 Jun 2017 01:56:35: 19000000 INFO @ Wed, 28 Jun 2017 01:56:37: 22000000 INFO @ Wed, 28 Jun 2017 01:56:38: 19000000 INFO @ Wed, 28 Jun 2017 01:56:42: 20000000 INFO @ Wed, 28 Jun 2017 01:56:43: 23000000 INFO @ Wed, 28 Jun 2017 01:56:45: 20000000 INFO @ Wed, 28 Jun 2017 01:56:49: 21000000 INFO @ Wed, 28 Jun 2017 01:56:49: 24000000 INFO @ Wed, 28 Jun 2017 01:56:52: 21000000 INFO @ Wed, 28 Jun 2017 01:56:55: 25000000 INFO @ Wed, 28 Jun 2017 01:56:55: 22000000 INFO @ Wed, 28 Jun 2017 01:56:59: 22000000 INFO @ Wed, 28 Jun 2017 01:57:00: 26000000 INFO @ Wed, 28 Jun 2017 01:57:02: 23000000 INFO @ Wed, 28 Jun 2017 01:57:02: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 01:57:02: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 01:57:02: #1 total tags in treatment: 12243900 INFO @ Wed, 28 Jun 2017 01:57:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:57:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:57:03: #1 tags after filtering in treatment: 11336637 INFO @ Wed, 28 Jun 2017 01:57:03: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:57:03: #1 finished! INFO @ Wed, 28 Jun 2017 01:57:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:57:03: #2 number of paired peaks: 703 WARNING @ Wed, 28 Jun 2017 01:57:03: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Wed, 28 Jun 2017 01:57:03: start model_add_line... INFO @ Wed, 28 Jun 2017 01:57:04: start X-correlation... INFO @ Wed, 28 Jun 2017 01:57:04: end of X-cor INFO @ Wed, 28 Jun 2017 01:57:04: #2 finished! INFO @ Wed, 28 Jun 2017 01:57:04: #2 predicted fragment length is 105 bps INFO @ Wed, 28 Jun 2017 01:57:04: #2 alternative fragment length(s) may be 105 bps INFO @ Wed, 28 Jun 2017 01:57:04: #2.2 Generate R script for model : SRX683497.05_model.r INFO @ Wed, 28 Jun 2017 01:57:04: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:57:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:57:05: 23000000 INFO @ Wed, 28 Jun 2017 01:57:09: 24000000 INFO @ Wed, 28 Jun 2017 01:57:13: 24000000 INFO @ Wed, 28 Jun 2017 01:57:16: 25000000 INFO @ Wed, 28 Jun 2017 01:57:21: 25000000 INFO @ Wed, 28 Jun 2017 01:57:24: 26000000 INFO @ Wed, 28 Jun 2017 01:57:27: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 01:57:27: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 01:57:27: #1 total tags in treatment: 12243900 INFO @ Wed, 28 Jun 2017 01:57:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:57:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:57:27: #1 tags after filtering in treatment: 11336637 INFO @ Wed, 28 Jun 2017 01:57:27: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:57:27: #1 finished! INFO @ Wed, 28 Jun 2017 01:57:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:57:28: #2 number of paired peaks: 703 WARNING @ Wed, 28 Jun 2017 01:57:28: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Wed, 28 Jun 2017 01:57:28: start model_add_line... INFO @ Wed, 28 Jun 2017 01:57:28: start X-correlation... INFO @ Wed, 28 Jun 2017 01:57:28: end of X-cor INFO @ Wed, 28 Jun 2017 01:57:28: #2 finished! INFO @ Wed, 28 Jun 2017 01:57:28: #2 predicted fragment length is 105 bps INFO @ Wed, 28 Jun 2017 01:57:28: #2 alternative fragment length(s) may be 105 bps INFO @ Wed, 28 Jun 2017 01:57:28: #2.2 Generate R script for model : SRX683497.10_model.r INFO @ Wed, 28 Jun 2017 01:57:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:57:29: 26000000 INFO @ Wed, 28 Jun 2017 01:57:29: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:57:32: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 01:57:32: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 01:57:32: #1 total tags in treatment: 12243900 INFO @ Wed, 28 Jun 2017 01:57:32: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:57:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:57:32: #1 tags after filtering in treatment: 11336637 INFO @ Wed, 28 Jun 2017 01:57:32: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:57:32: #1 finished! INFO @ Wed, 28 Jun 2017 01:57:32: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:57:33: #2 number of paired peaks: 703 WARNING @ Wed, 28 Jun 2017 01:57:33: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Wed, 28 Jun 2017 01:57:33: start model_add_line... INFO @ Wed, 28 Jun 2017 01:57:33: start X-correlation... INFO @ Wed, 28 Jun 2017 01:57:33: end of X-cor INFO @ Wed, 28 Jun 2017 01:57:33: #2 finished! INFO @ Wed, 28 Jun 2017 01:57:33: #2 predicted fragment length is 105 bps INFO @ Wed, 28 Jun 2017 01:57:33: #2 alternative fragment length(s) may be 105 bps INFO @ Wed, 28 Jun 2017 01:57:33: #2.2 Generate R script for model : SRX683497.20_model.r INFO @ Wed, 28 Jun 2017 01:57:33: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:57:43: #4 Write output xls file... SRX683497.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:57:43: #4 Write peak in narrowPeak format file... SRX683497.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:57:43: #4 Write summits bed file... SRX683497.05_summits.bed INFO @ Wed, 28 Jun 2017 01:57:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2529 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:57:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:57:58: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:58:07: #4 Write output xls file... SRX683497.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:58:07: #4 Write peak in narrowPeak format file... SRX683497.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:58:07: #4 Write summits bed file... SRX683497.10_summits.bed INFO @ Wed, 28 Jun 2017 01:58:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1520 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:58:13: #4 Write output xls file... SRX683497.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:58:13: #4 Write peak in narrowPeak format file... SRX683497.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:58:13: #4 Write summits bed file... SRX683497.20_summits.bed INFO @ Wed, 28 Jun 2017 01:58:13: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (890 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。