Job ID = 1294618 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,336,520 reads read : 18,336,520 reads written : 18,336,520 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: 00:08:14 18336520 reads; of these: 18336520 (100.00%) were unpaired; of these: 936526 (5.11%) aligned 0 times 12129004 (66.15%) aligned exactly 1 time 5270990 (28.75%) aligned >1 times 94.89% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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_rmdupse_core] 2135574 / 17399994 = 0.1227 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 09:37:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.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 09:37:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.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 09:37:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:37:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:37:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:37:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.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 09:37:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:37:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:37:26: 1000000 INFO @ Mon, 03 Jun 2019 09:37:26: 1000000 INFO @ Mon, 03 Jun 2019 09:37:30: 1000000 INFO @ Mon, 03 Jun 2019 09:37:34: 2000000 INFO @ Mon, 03 Jun 2019 09:37:34: 2000000 INFO @ Mon, 03 Jun 2019 09:37:40: 2000000 INFO @ Mon, 03 Jun 2019 09:37:41: 3000000 INFO @ Mon, 03 Jun 2019 09:37:42: 3000000 INFO @ Mon, 03 Jun 2019 09:37:49: 4000000 INFO @ Mon, 03 Jun 2019 09:37:49: 4000000 INFO @ Mon, 03 Jun 2019 09:37:50: 3000000 INFO @ Mon, 03 Jun 2019 09:37:57: 5000000 INFO @ Mon, 03 Jun 2019 09:37:58: 5000000 INFO @ Mon, 03 Jun 2019 09:38:01: 4000000 INFO @ Mon, 03 Jun 2019 09:38:04: 6000000 INFO @ Mon, 03 Jun 2019 09:38:05: 6000000 INFO @ Mon, 03 Jun 2019 09:38:11: 5000000 INFO @ Mon, 03 Jun 2019 09:38:12: 7000000 INFO @ Mon, 03 Jun 2019 09:38:13: 7000000 INFO @ Mon, 03 Jun 2019 09:38:19: 8000000 INFO @ Mon, 03 Jun 2019 09:38:21: 6000000 INFO @ Mon, 03 Jun 2019 09:38:21: 8000000 INFO @ Mon, 03 Jun 2019 09:38:27: 9000000 INFO @ Mon, 03 Jun 2019 09:38:30: 9000000 INFO @ Mon, 03 Jun 2019 09:38:32: 7000000 INFO @ Mon, 03 Jun 2019 09:38:35: 10000000 INFO @ Mon, 03 Jun 2019 09:38:38: 10000000 INFO @ Mon, 03 Jun 2019 09:38:43: 11000000 INFO @ Mon, 03 Jun 2019 09:38:43: 8000000 INFO @ Mon, 03 Jun 2019 09:38:46: 11000000 INFO @ Mon, 03 Jun 2019 09:38:51: 12000000 INFO @ Mon, 03 Jun 2019 09:38:53: 9000000 INFO @ Mon, 03 Jun 2019 09:38:54: 12000000 INFO @ Mon, 03 Jun 2019 09:38:59: 13000000 INFO @ Mon, 03 Jun 2019 09:39:02: 13000000 INFO @ Mon, 03 Jun 2019 09:39:03: 10000000 INFO @ Mon, 03 Jun 2019 09:39:06: 14000000 INFO @ Mon, 03 Jun 2019 09:39:10: 14000000 INFO @ Mon, 03 Jun 2019 09:39:14: 11000000 INFO @ Mon, 03 Jun 2019 09:39:14: 15000000 INFO @ Mon, 03 Jun 2019 09:39:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:39:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:39:16: #1 total tags in treatment: 15264420 INFO @ Mon, 03 Jun 2019 09:39:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:39:16: #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 09:39:16: #1 tags after filtering in treatment: 15264420 INFO @ Mon, 03 Jun 2019 09:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:39:16: #1 finished! INFO @ Mon, 03 Jun 2019 09:39:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:39:17: #2 number of paired peaks: 297 WARNING @ Mon, 03 Jun 2019 09:39:17: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Mon, 03 Jun 2019 09:39:17: start model_add_line... INFO @ Mon, 03 Jun 2019 09:39:17: start X-correlation... INFO @ Mon, 03 Jun 2019 09:39:17: end of X-cor INFO @ Mon, 03 Jun 2019 09:39:17: #2 finished! INFO @ Mon, 03 Jun 2019 09:39:17: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 09:39:17: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 09:39:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.05_model.r WARNING @ Mon, 03 Jun 2019 09:39:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:39:17: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 09:39:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:39:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:39:18: 15000000 INFO @ Mon, 03 Jun 2019 09:39:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:39:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:39:20: #1 total tags in treatment: 15264420 INFO @ Mon, 03 Jun 2019 09:39:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:39:20: #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 09:39:20: #1 tags after filtering in treatment: 15264420 INFO @ Mon, 03 Jun 2019 09:39:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:39:20: #1 finished! INFO @ Mon, 03 Jun 2019 09:39:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:39:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:39:21: #2 number of paired peaks: 297 WARNING @ Mon, 03 Jun 2019 09:39:21: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Mon, 03 Jun 2019 09:39:21: start model_add_line... INFO @ Mon, 03 Jun 2019 09:39:21: start X-correlation... INFO @ Mon, 03 Jun 2019 09:39:21: end of X-cor INFO @ Mon, 03 Jun 2019 09:39:21: #2 finished! INFO @ Mon, 03 Jun 2019 09:39:21: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 09:39:21: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 09:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.20_model.r WARNING @ Mon, 03 Jun 2019 09:39:21: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:39:21: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 09:39:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:39:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:39:24: 12000000 INFO @ Mon, 03 Jun 2019 09:39:33: 13000000 INFO @ Mon, 03 Jun 2019 09:39:44: 14000000 INFO @ Mon, 03 Jun 2019 09:39:55: 15000000 INFO @ Mon, 03 Jun 2019 09:39:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:39:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:39:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:39:57: #1 total tags in treatment: 15264420 INFO @ Mon, 03 Jun 2019 09:39:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:39:57: #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 09:39:57: #1 tags after filtering in treatment: 15264420 INFO @ Mon, 03 Jun 2019 09:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:39:57: #1 finished! INFO @ Mon, 03 Jun 2019 09:39:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:39:59: #2 number of paired peaks: 297 WARNING @ Mon, 03 Jun 2019 09:39:59: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Mon, 03 Jun 2019 09:39:59: start model_add_line... INFO @ Mon, 03 Jun 2019 09:39:59: start X-correlation... INFO @ Mon, 03 Jun 2019 09:39:59: end of X-cor INFO @ Mon, 03 Jun 2019 09:39:59: #2 finished! INFO @ Mon, 03 Jun 2019 09:39:59: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 09:39:59: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 09:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.10_model.r WARNING @ Mon, 03 Jun 2019 09:39:59: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:39:59: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 09:39:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:39:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:40:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.05_summits.bed INFO @ Mon, 03 Jun 2019 09:40:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1777 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:40:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.20_summits.bed INFO @ Mon, 03 Jun 2019 09:40:20: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1148 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:40:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287783/SRX287783.10_summits.bed INFO @ Mon, 03 Jun 2019 09:40:58: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1502 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。