Job ID = 1305947 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,804,609 reads read : 13,804,609 reads written : 13,804,609 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: 00:04:32 13804609 reads; of these: 13804609 (100.00%) were unpaired; of these: 738447 (5.35%) aligned 0 times 11523689 (83.48%) aligned exactly 1 time 1542473 (11.17%) aligned >1 times 94.65% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 3810170 / 13066162 = 0.2916 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 21:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.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 21:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.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 21:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.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 21:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:41:06: 1000000 INFO @ Mon, 03 Jun 2019 21:41:06: 1000000 INFO @ Mon, 03 Jun 2019 21:41:08: 1000000 INFO @ Mon, 03 Jun 2019 21:41:16: 2000000 INFO @ Mon, 03 Jun 2019 21:41:17: 2000000 INFO @ Mon, 03 Jun 2019 21:41:21: 2000000 INFO @ Mon, 03 Jun 2019 21:41:26: 3000000 INFO @ Mon, 03 Jun 2019 21:41:27: 3000000 INFO @ Mon, 03 Jun 2019 21:41:33: 3000000 INFO @ Mon, 03 Jun 2019 21:41:35: 4000000 INFO @ Mon, 03 Jun 2019 21:41:37: 4000000 INFO @ Mon, 03 Jun 2019 21:41:45: 5000000 INFO @ Mon, 03 Jun 2019 21:41:45: 4000000 INFO @ Mon, 03 Jun 2019 21:41:46: 5000000 INFO @ Mon, 03 Jun 2019 21:41:54: 6000000 INFO @ Mon, 03 Jun 2019 21:41:55: 6000000 INFO @ Mon, 03 Jun 2019 21:41:56: 5000000 INFO @ Mon, 03 Jun 2019 21:42:04: 7000000 INFO @ Mon, 03 Jun 2019 21:42:05: 7000000 INFO @ Mon, 03 Jun 2019 21:42:08: 6000000 INFO @ Mon, 03 Jun 2019 21:42:14: 8000000 INFO @ Mon, 03 Jun 2019 21:42:15: 8000000 INFO @ Mon, 03 Jun 2019 21:42:20: 7000000 INFO @ Mon, 03 Jun 2019 21:42:24: 9000000 INFO @ Mon, 03 Jun 2019 21:42:25: 9000000 INFO @ Mon, 03 Jun 2019 21:42:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:42:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:42:27: #1 total tags in treatment: 9255992 INFO @ Mon, 03 Jun 2019 21:42:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:42:27: #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 21:42:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:42:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:42:27: #1 total tags in treatment: 9255992 INFO @ Mon, 03 Jun 2019 21:42:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:42:27: #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 21:42:27: #1 tags after filtering in treatment: 9255992 INFO @ Mon, 03 Jun 2019 21:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:42:27: #1 finished! INFO @ Mon, 03 Jun 2019 21:42:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:42:27: #1 tags after filtering in treatment: 9255992 INFO @ Mon, 03 Jun 2019 21:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:42:27: #1 finished! INFO @ Mon, 03 Jun 2019 21:42:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:42:28: #2 number of paired peaks: 1941 INFO @ Mon, 03 Jun 2019 21:42:28: start model_add_line... INFO @ Mon, 03 Jun 2019 21:42:28: #2 number of paired peaks: 1941 INFO @ Mon, 03 Jun 2019 21:42:28: start model_add_line... INFO @ Mon, 03 Jun 2019 21:42:28: start X-correlation... INFO @ Mon, 03 Jun 2019 21:42:28: end of X-cor INFO @ Mon, 03 Jun 2019 21:42:28: #2 finished! INFO @ Mon, 03 Jun 2019 21:42:28: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 21:42:28: #2 alternative fragment length(s) may be 4,34 bps INFO @ Mon, 03 Jun 2019 21:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.10_model.r WARNING @ Mon, 03 Jun 2019 21:42:28: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:42:28: #2 You may need to consider one of the other alternative d(s): 4,34 WARNING @ Mon, 03 Jun 2019 21:42:28: #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 21:42:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:42:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:42:28: start X-correlation... INFO @ Mon, 03 Jun 2019 21:42:28: end of X-cor INFO @ Mon, 03 Jun 2019 21:42:28: #2 finished! INFO @ Mon, 03 Jun 2019 21:42:28: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 21:42:28: #2 alternative fragment length(s) may be 4,34 bps INFO @ Mon, 03 Jun 2019 21:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.20_model.r WARNING @ Mon, 03 Jun 2019 21:42:28: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:42:28: #2 You may need to consider one of the other alternative d(s): 4,34 WARNING @ Mon, 03 Jun 2019 21:42:28: #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 21:42:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:42:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:42:32: 8000000 INFO @ Mon, 03 Jun 2019 21:42:44: 9000000 INFO @ Mon, 03 Jun 2019 21:42:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:42:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:42:47: #1 total tags in treatment: 9255992 INFO @ Mon, 03 Jun 2019 21:42:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:42:47: #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 21:42:47: #1 tags after filtering in treatment: 9255992 INFO @ Mon, 03 Jun 2019 21:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:42:47: #1 finished! INFO @ Mon, 03 Jun 2019 21:42:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:42:48: #2 number of paired peaks: 1941 INFO @ Mon, 03 Jun 2019 21:42:48: start model_add_line... INFO @ Mon, 03 Jun 2019 21:42:48: start X-correlation... INFO @ Mon, 03 Jun 2019 21:42:48: end of X-cor INFO @ Mon, 03 Jun 2019 21:42:48: #2 finished! INFO @ Mon, 03 Jun 2019 21:42:48: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 21:42:48: #2 alternative fragment length(s) may be 4,34 bps INFO @ Mon, 03 Jun 2019 21:42:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.05_model.r WARNING @ Mon, 03 Jun 2019 21:42:48: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:42:48: #2 You may need to consider one of the other alternative d(s): 4,34 WARNING @ Mon, 03 Jun 2019 21:42:48: #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 21:42:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:42:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:42:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:42:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.20_summits.bed INFO @ Mon, 03 Jun 2019 21:43:07: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.10_summits.bed INFO @ Mon, 03 Jun 2019 21:43:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1083 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:43:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:43:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:43:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:43:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495312/SRX495312.05_summits.bed INFO @ Mon, 03 Jun 2019 21:43:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3882 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。