Job ID = 10320353 sra ファイルのダウンロード中... Completed: 369273K bytes transferred in 55 seconds (54132K 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... Written 17349130 spots for /home/okishinya/chipatlas/results/dm3/SRX3293405/SRR6183232.sra Written 17349130 spots total 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: 00:41:36 17349130 reads; of these: 17349130 (100.00%) were paired; of these: 5704087 (32.88%) aligned concordantly 0 times 5940390 (34.24%) aligned concordantly exactly 1 time 5704653 (32.88%) aligned concordantly >1 times ---- 5704087 pairs aligned concordantly 0 times; of these: 466944 (8.19%) aligned discordantly 1 time ---- 5237143 pairs aligned 0 times concordantly or discordantly; of these: 10474286 mates make up the pairs; of these: 7905666 (75.48%) aligned 0 times 875855 (8.36%) aligned exactly 1 time 1692765 (16.16%) aligned >1 times 77.22% overall alignment rate Time searching: 00:41:36 Overall time: 00:41:36 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 8 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] 1949047 / 11921398 = 0.1635 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 @ Thu, 11 Jan 2018 02:55:05: # Command line: callpeak -t SRX3293405.bam -f BAM -g dm -n SRX3293405.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3293405.05 # format = BAM # ChIP-seq file = ['SRX3293405.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 @ Thu, 11 Jan 2018 02:55:05: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:55:05: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:55:05: # Command line: callpeak -t SRX3293405.bam -f BAM -g dm -n SRX3293405.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3293405.20 # format = BAM # ChIP-seq file = ['SRX3293405.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 @ Thu, 11 Jan 2018 02:55:05: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:55:05: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:55:05: # Command line: callpeak -t SRX3293405.bam -f BAM -g dm -n SRX3293405.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3293405.10 # format = BAM # ChIP-seq file = ['SRX3293405.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 @ Thu, 11 Jan 2018 02:55:05: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:55:05: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:55:11: 1000000 INFO @ Thu, 11 Jan 2018 02:55:11: 1000000 INFO @ Thu, 11 Jan 2018 02:55:11: 1000000 INFO @ Thu, 11 Jan 2018 02:55:16: 2000000 INFO @ Thu, 11 Jan 2018 02:55:16: 2000000 INFO @ Thu, 11 Jan 2018 02:55:16: 2000000 INFO @ Thu, 11 Jan 2018 02:55:21: 3000000 INFO @ Thu, 11 Jan 2018 02:55:22: 3000000 INFO @ Thu, 11 Jan 2018 02:55:22: 3000000 INFO @ Thu, 11 Jan 2018 02:55:27: 4000000 INFO @ Thu, 11 Jan 2018 02:55:28: 4000000 INFO @ Thu, 11 Jan 2018 02:55:28: 4000000 INFO @ Thu, 11 Jan 2018 02:55:32: 5000000 INFO @ Thu, 11 Jan 2018 02:55:33: 5000000 INFO @ Thu, 11 Jan 2018 02:55:33: 5000000 INFO @ Thu, 11 Jan 2018 02:55:37: 6000000 INFO @ Thu, 11 Jan 2018 02:55:39: 6000000 INFO @ Thu, 11 Jan 2018 02:55:39: 6000000 INFO @ Thu, 11 Jan 2018 02:55:43: 7000000 INFO @ Thu, 11 Jan 2018 02:55:44: 7000000 INFO @ Thu, 11 Jan 2018 02:55:44: 7000000 INFO @ Thu, 11 Jan 2018 02:55:48: 8000000 INFO @ Thu, 11 Jan 2018 02:55:50: 8000000 INFO @ Thu, 11 Jan 2018 02:55:50: 8000000 INFO @ Thu, 11 Jan 2018 02:55:54: 9000000 INFO @ Thu, 11 Jan 2018 02:55:56: 9000000 INFO @ Thu, 11 Jan 2018 02:55:57: 9000000 INFO @ Thu, 11 Jan 2018 02:55:59: 10000000 INFO @ Thu, 11 Jan 2018 02:56:02: 10000000 INFO @ Thu, 11 Jan 2018 02:56:04: 10000000 INFO @ Thu, 11 Jan 2018 02:56:05: 11000000 INFO @ Thu, 11 Jan 2018 02:56:09: 11000000 INFO @ Thu, 11 Jan 2018 02:56:10: 12000000 INFO @ Thu, 11 Jan 2018 02:56:10: 11000000 INFO @ Thu, 11 Jan 2018 02:56:15: 12000000 INFO @ Thu, 11 Jan 2018 02:56:16: 13000000 INFO @ Thu, 11 Jan 2018 02:56:17: 12000000 INFO @ Thu, 11 Jan 2018 02:56:21: 13000000 INFO @ Thu, 11 Jan 2018 02:56:21: 14000000 INFO @ Thu, 11 Jan 2018 02:56:24: 13000000 INFO @ Thu, 11 Jan 2018 02:56:27: 15000000 INFO @ Thu, 11 Jan 2018 02:56:27: 14000000 INFO @ Thu, 11 Jan 2018 02:56:30: 14000000 INFO @ Thu, 11 Jan 2018 02:56:32: 16000000 INFO @ Thu, 11 Jan 2018 02:56:33: 15000000 INFO @ Thu, 11 Jan 2018 02:56:37: 15000000 INFO @ Thu, 11 Jan 2018 02:56:37: 17000000 INFO @ Thu, 11 Jan 2018 02:56:39: 16000000 INFO @ Thu, 11 Jan 2018 02:56:43: 18000000 INFO @ Thu, 11 Jan 2018 02:56:43: 16000000 INFO @ Thu, 11 Jan 2018 02:56:45: 17000000 INFO @ Thu, 11 Jan 2018 02:56:48: 19000000 INFO @ Thu, 11 Jan 2018 02:56:50: 17000000 INFO @ Thu, 11 Jan 2018 02:56:51: 18000000 INFO @ Thu, 11 Jan 2018 02:56:54: 20000000 INFO @ Thu, 11 Jan 2018 02:56:57: 18000000 INFO @ Thu, 11 Jan 2018 02:56:57: 19000000 INFO @ Thu, 11 Jan 2018 02:56:59: 21000000 INFO @ Thu, 11 Jan 2018 02:57:03: 19000000 INFO @ Thu, 11 Jan 2018 02:57:03: 20000000 INFO @ Thu, 11 Jan 2018 02:57:05: 22000000 INFO @ Thu, 11 Jan 2018 02:57:10: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:57:10: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:57:10: #1 total tags in treatment: 9698742 INFO @ Thu, 11 Jan 2018 02:57:10: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:57:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:57:10: 21000000 INFO @ Thu, 11 Jan 2018 02:57:10: #1 tags after filtering in treatment: 7632935 INFO @ Thu, 11 Jan 2018 02:57:10: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 11 Jan 2018 02:57:10: #1 finished! INFO @ Thu, 11 Jan 2018 02:57:10: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:57:10: 20000000 INFO @ Thu, 11 Jan 2018 02:57:10: #2 number of paired peaks: 588 WARNING @ Thu, 11 Jan 2018 02:57:10: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Thu, 11 Jan 2018 02:57:10: start model_add_line... INFO @ Thu, 11 Jan 2018 02:57:11: start X-correlation... INFO @ Thu, 11 Jan 2018 02:57:11: end of X-cor INFO @ Thu, 11 Jan 2018 02:57:11: #2 finished! INFO @ Thu, 11 Jan 2018 02:57:11: #2 predicted fragment length is 130 bps INFO @ Thu, 11 Jan 2018 02:57:11: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 11 Jan 2018 02:57:11: #2.2 Generate R script for model : SRX3293405.10_model.r INFO @ Thu, 11 Jan 2018 02:57:11: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:57:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:57:16: 22000000 INFO @ Thu, 11 Jan 2018 02:57:16: 21000000 INFO @ Thu, 11 Jan 2018 02:57:21: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:57:21: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:57:21: #1 total tags in treatment: 9698742 INFO @ Thu, 11 Jan 2018 02:57:21: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:57:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:57:22: #1 tags after filtering in treatment: 7632935 INFO @ Thu, 11 Jan 2018 02:57:22: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 11 Jan 2018 02:57:22: #1 finished! INFO @ Thu, 11 Jan 2018 02:57:22: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:57:22: #2 number of paired peaks: 588 WARNING @ Thu, 11 Jan 2018 02:57:22: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Thu, 11 Jan 2018 02:57:22: start model_add_line... INFO @ Thu, 11 Jan 2018 02:57:22: start X-correlation... INFO @ Thu, 11 Jan 2018 02:57:22: end of X-cor INFO @ Thu, 11 Jan 2018 02:57:22: #2 finished! INFO @ Thu, 11 Jan 2018 02:57:22: #2 predicted fragment length is 130 bps INFO @ Thu, 11 Jan 2018 02:57:22: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 11 Jan 2018 02:57:22: #2.2 Generate R script for model : SRX3293405.05_model.r INFO @ Thu, 11 Jan 2018 02:57:22: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:57:23: 22000000 INFO @ Thu, 11 Jan 2018 02:57:28: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:57:28: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:57:28: #1 total tags in treatment: 9698742 INFO @ Thu, 11 Jan 2018 02:57:28: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:57:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:57:28: #1 tags after filtering in treatment: 7632935 INFO @ Thu, 11 Jan 2018 02:57:28: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 11 Jan 2018 02:57:28: #1 finished! INFO @ Thu, 11 Jan 2018 02:57:28: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:57:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:57:28: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:57:29: #2 number of paired peaks: 588 WARNING @ Thu, 11 Jan 2018 02:57:29: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Thu, 11 Jan 2018 02:57:29: start model_add_line... INFO @ Thu, 11 Jan 2018 02:57:29: start X-correlation... INFO @ Thu, 11 Jan 2018 02:57:29: end of X-cor INFO @ Thu, 11 Jan 2018 02:57:29: #2 finished! INFO @ Thu, 11 Jan 2018 02:57:29: #2 predicted fragment length is 130 bps INFO @ Thu, 11 Jan 2018 02:57:29: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 11 Jan 2018 02:57:29: #2.2 Generate R script for model : SRX3293405.20_model.r INFO @ Thu, 11 Jan 2018 02:57:29: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:57:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:57:37: #4 Write output xls file... SRX3293405.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:57:37: #4 Write peak in narrowPeak format file... SRX3293405.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:57:37: #4 Write summits bed file... SRX3293405.10_summits.bed INFO @ Thu, 11 Jan 2018 02:57:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:57:41: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:57:46: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:57:51: #4 Write output xls file... SRX3293405.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:57:51: #4 Write peak in narrowPeak format file... SRX3293405.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:57:51: #4 Write summits bed file... SRX3293405.05_summits.bed INFO @ Thu, 11 Jan 2018 02:57:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1488 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:57:57: #4 Write output xls file... SRX3293405.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:57:57: #4 Write peak in narrowPeak format file... SRX3293405.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:57:57: #4 Write summits bed file... SRX3293405.20_summits.bed INFO @ Thu, 11 Jan 2018 02:57:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。