Job ID = 1293363 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 19,023,509 reads read : 38,047,018 reads written : 38,047,018 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: 00:52:44 19023509 reads; of these: 19023509 (100.00%) were paired; of these: 2328011 (12.24%) aligned concordantly 0 times 12504322 (65.73%) aligned concordantly exactly 1 time 4191176 (22.03%) aligned concordantly >1 times ---- 2328011 pairs aligned concordantly 0 times; of these: 154378 (6.63%) aligned discordantly 1 time ---- 2173633 pairs aligned 0 times concordantly or discordantly; of these: 4347266 mates make up the pairs; of these: 3460631 (79.60%) aligned 0 times 486750 (11.20%) aligned exactly 1 time 399885 (9.20%) aligned >1 times 90.90% overall alignment rate Time searching: 00:52:44 Overall time: 00:52:44 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] 4988149 / 16828735 = 0.2964 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 00:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.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 00:28:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:28:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.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 00:28:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:28:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.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 00:28:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:28:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:28:36: 1000000 INFO @ Mon, 03 Jun 2019 00:28:37: 1000000 INFO @ Mon, 03 Jun 2019 00:28:38: 1000000 INFO @ Mon, 03 Jun 2019 00:28:44: 2000000 INFO @ Mon, 03 Jun 2019 00:28:46: 2000000 INFO @ Mon, 03 Jun 2019 00:28:49: 2000000 INFO @ Mon, 03 Jun 2019 00:28:53: 3000000 INFO @ Mon, 03 Jun 2019 00:28:55: 3000000 INFO @ Mon, 03 Jun 2019 00:28:59: 3000000 INFO @ Mon, 03 Jun 2019 00:29:02: 4000000 INFO @ Mon, 03 Jun 2019 00:29:03: 4000000 INFO @ Mon, 03 Jun 2019 00:29:10: 4000000 INFO @ Mon, 03 Jun 2019 00:29:10: 5000000 INFO @ Mon, 03 Jun 2019 00:29:11: 5000000 INFO @ Mon, 03 Jun 2019 00:29:17: 6000000 INFO @ Mon, 03 Jun 2019 00:29:20: 6000000 INFO @ Mon, 03 Jun 2019 00:29:20: 5000000 INFO @ Mon, 03 Jun 2019 00:29:25: 7000000 INFO @ Mon, 03 Jun 2019 00:29:28: 7000000 INFO @ Mon, 03 Jun 2019 00:29:30: 6000000 INFO @ Mon, 03 Jun 2019 00:29:33: 8000000 INFO @ Mon, 03 Jun 2019 00:29:36: 8000000 INFO @ Mon, 03 Jun 2019 00:29:40: 7000000 INFO @ Mon, 03 Jun 2019 00:29:41: 9000000 INFO @ Mon, 03 Jun 2019 00:29:44: 9000000 INFO @ Mon, 03 Jun 2019 00:29:49: 10000000 INFO @ Mon, 03 Jun 2019 00:29:50: 8000000 INFO @ Mon, 03 Jun 2019 00:29:53: 10000000 INFO @ Mon, 03 Jun 2019 00:29:56: 11000000 INFO @ Mon, 03 Jun 2019 00:30:00: 9000000 INFO @ Mon, 03 Jun 2019 00:30:01: 11000000 INFO @ Mon, 03 Jun 2019 00:30:04: 12000000 INFO @ Mon, 03 Jun 2019 00:30:09: 12000000 INFO @ Mon, 03 Jun 2019 00:30:10: 10000000 INFO @ Mon, 03 Jun 2019 00:30:12: 13000000 INFO @ Mon, 03 Jun 2019 00:30:18: 13000000 INFO @ Mon, 03 Jun 2019 00:30:20: 11000000 INFO @ Mon, 03 Jun 2019 00:30:21: 14000000 INFO @ Mon, 03 Jun 2019 00:30:26: 14000000 INFO @ Mon, 03 Jun 2019 00:30:29: 15000000 INFO @ Mon, 03 Jun 2019 00:30:29: 12000000 INFO @ Mon, 03 Jun 2019 00:30:33: 15000000 INFO @ Mon, 03 Jun 2019 00:30:37: 16000000 INFO @ Mon, 03 Jun 2019 00:30:39: 13000000 INFO @ Mon, 03 Jun 2019 00:30:40: 16000000 INFO @ Mon, 03 Jun 2019 00:30:44: 17000000 INFO @ Mon, 03 Jun 2019 00:30:48: 17000000 INFO @ Mon, 03 Jun 2019 00:30:49: 14000000 INFO @ Mon, 03 Jun 2019 00:30:52: 18000000 INFO @ Mon, 03 Jun 2019 00:30:56: 18000000 INFO @ Mon, 03 Jun 2019 00:30:58: 15000000 INFO @ Mon, 03 Jun 2019 00:30:59: 19000000 INFO @ Mon, 03 Jun 2019 00:31:04: 19000000 INFO @ Mon, 03 Jun 2019 00:31:07: 20000000 INFO @ Mon, 03 Jun 2019 00:31:07: 16000000 INFO @ Mon, 03 Jun 2019 00:31:12: 20000000 INFO @ Mon, 03 Jun 2019 00:31:14: 21000000 INFO @ Mon, 03 Jun 2019 00:31:16: 17000000 INFO @ Mon, 03 Jun 2019 00:31:20: 21000000 INFO @ Mon, 03 Jun 2019 00:31:22: 22000000 INFO @ Mon, 03 Jun 2019 00:31:26: 18000000 INFO @ Mon, 03 Jun 2019 00:31:28: 22000000 INFO @ Mon, 03 Jun 2019 00:31:31: 23000000 INFO @ Mon, 03 Jun 2019 00:31:35: 19000000 INFO @ Mon, 03 Jun 2019 00:31:36: 23000000 INFO @ Mon, 03 Jun 2019 00:31:39: 24000000 INFO @ Mon, 03 Jun 2019 00:31:44: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:31:44: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:31:44: #1 total tags in treatment: 11728476 INFO @ Mon, 03 Jun 2019 00:31:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:31:44: #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 00:31:44: #1 tags after filtering in treatment: 11060013 INFO @ Mon, 03 Jun 2019 00:31:44: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 00:31:44: #1 finished! INFO @ Mon, 03 Jun 2019 00:31:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:31:45: 20000000 INFO @ Mon, 03 Jun 2019 00:31:45: 24000000 INFO @ Mon, 03 Jun 2019 00:31:45: #2 number of paired peaks: 374 WARNING @ Mon, 03 Jun 2019 00:31:45: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 03 Jun 2019 00:31:45: start model_add_line... INFO @ Mon, 03 Jun 2019 00:31:45: start X-correlation... INFO @ Mon, 03 Jun 2019 00:31:45: end of X-cor INFO @ Mon, 03 Jun 2019 00:31:45: #2 finished! INFO @ Mon, 03 Jun 2019 00:31:45: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 00:31:45: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 00:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.05_model.r INFO @ Mon, 03 Jun 2019 00:31:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:31:50: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:31:50: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:31:50: #1 total tags in treatment: 11728476 INFO @ Mon, 03 Jun 2019 00:31:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:31:50: #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 00:31:50: #1 tags after filtering in treatment: 11060013 INFO @ Mon, 03 Jun 2019 00:31:50: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 00:31:50: #1 finished! INFO @ Mon, 03 Jun 2019 00:31:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:31:51: #2 number of paired peaks: 374 WARNING @ Mon, 03 Jun 2019 00:31:51: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 03 Jun 2019 00:31:51: start model_add_line... INFO @ Mon, 03 Jun 2019 00:31:51: start X-correlation... INFO @ Mon, 03 Jun 2019 00:31:51: end of X-cor INFO @ Mon, 03 Jun 2019 00:31:51: #2 finished! INFO @ Mon, 03 Jun 2019 00:31:51: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 00:31:51: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 00:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.10_model.r INFO @ Mon, 03 Jun 2019 00:31:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:31:54: 21000000 INFO @ Mon, 03 Jun 2019 00:32:03: 22000000 INFO @ Mon, 03 Jun 2019 00:32:12: 23000000 INFO @ Mon, 03 Jun 2019 00:32:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:32:21: 24000000 INFO @ Mon, 03 Jun 2019 00:32:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:32:26: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:32:26: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:32:26: #1 total tags in treatment: 11728476 INFO @ Mon, 03 Jun 2019 00:32:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:32:26: #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 00:32:26: #1 tags after filtering in treatment: 11060013 INFO @ Mon, 03 Jun 2019 00:32:26: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 00:32:26: #1 finished! INFO @ Mon, 03 Jun 2019 00:32:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:32:27: #2 number of paired peaks: 374 WARNING @ Mon, 03 Jun 2019 00:32:27: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 03 Jun 2019 00:32:27: start model_add_line... INFO @ Mon, 03 Jun 2019 00:32:28: start X-correlation... INFO @ Mon, 03 Jun 2019 00:32:28: end of X-cor INFO @ Mon, 03 Jun 2019 00:32:28: #2 finished! INFO @ Mon, 03 Jun 2019 00:32:28: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 00:32:28: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 00:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.20_model.r INFO @ Mon, 03 Jun 2019 00:32:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.05_summits.bed INFO @ Mon, 03 Jun 2019 00:32:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3784 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.10_summits.bed INFO @ Mon, 03 Jun 2019 00:32:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1849 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:33:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818283/ERX1818283.20_summits.bed INFO @ Mon, 03 Jun 2019 00:33:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。