Job ID = 4178412 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,362,554 reads read : 4,725,108 reads written : 4,725,108 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:48 2362554 reads; of these: 2362554 (100.00%) were paired; of these: 254436 (10.77%) aligned concordantly 0 times 1584103 (67.05%) aligned concordantly exactly 1 time 524015 (22.18%) aligned concordantly >1 times ---- 254436 pairs aligned concordantly 0 times; of these: 117113 (46.03%) aligned discordantly 1 time ---- 137323 pairs aligned 0 times concordantly or discordantly; of these: 274646 mates make up the pairs; of these: 138922 (50.58%) aligned 0 times 62640 (22.81%) aligned exactly 1 time 73084 (26.61%) aligned >1 times 97.06% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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_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] 408618 / 2222038 = 0.1839 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.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, 05 Dec 2019 12:29:03: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:03: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:12: 1000000 INFO @ Thu, 05 Dec 2019 12:29:20: 2000000 INFO @ Thu, 05 Dec 2019 12:29:28: 3000000 INFO @ Thu, 05 Dec 2019 12:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.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, 05 Dec 2019 12:29:33: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:33: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:35: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:35: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:35: #1 total tags in treatment: 1716103 INFO @ Thu, 05 Dec 2019 12:29:35: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:29:35: #1 tags after filtering in treatment: 1678373 INFO @ Thu, 05 Dec 2019 12:29:35: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:29:35: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:35: #2 number of paired peaks: 326 WARNING @ Thu, 05 Dec 2019 12:29:35: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:35: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:35: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:35: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:35: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:35: #2 predicted fragment length is 151 bps INFO @ Thu, 05 Dec 2019 12:29:35: #2 alternative fragment length(s) may be 151,596 bps INFO @ Thu, 05 Dec 2019 12:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.05_model.r WARNING @ Thu, 05 Dec 2019 12:29:35: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:29:35: #2 You may need to consider one of the other alternative d(s): 151,596 WARNING @ Thu, 05 Dec 2019 12:29:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:29:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:41: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:29:41: 1000000 INFO @ Thu, 05 Dec 2019 12:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.05_summits.bed INFO @ Thu, 05 Dec 2019 12:29:43: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (564 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:29:50: 2000000 INFO @ Thu, 05 Dec 2019 12:29:59: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.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, 05 Dec 2019 12:30:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:05: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:05: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:05: #1 total tags in treatment: 1716103 INFO @ Thu, 05 Dec 2019 12:30:05: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:05: #1 tags after filtering in treatment: 1678373 INFO @ Thu, 05 Dec 2019 12:30:05: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:30:05: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:05: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:06: #2 number of paired peaks: 326 WARNING @ Thu, 05 Dec 2019 12:30:06: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:06: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:06: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:06: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:06: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:06: #2 predicted fragment length is 151 bps INFO @ Thu, 05 Dec 2019 12:30:06: #2 alternative fragment length(s) may be 151,596 bps INFO @ Thu, 05 Dec 2019 12:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.10_model.r WARNING @ Thu, 05 Dec 2019 12:30:06: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:30:06: #2 You may need to consider one of the other alternative d(s): 151,596 WARNING @ Thu, 05 Dec 2019 12:30:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:30:06: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:11: 1000000 INFO @ Thu, 05 Dec 2019 12:30:11: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.10_summits.bed INFO @ Thu, 05 Dec 2019 12:30:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:19: 2000000 INFO @ Thu, 05 Dec 2019 12:30:28: 3000000 INFO @ Thu, 05 Dec 2019 12:30:34: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:34: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:34: #1 total tags in treatment: 1716103 INFO @ Thu, 05 Dec 2019 12:30:34: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:34: #1 tags after filtering in treatment: 1678373 INFO @ Thu, 05 Dec 2019 12:30:34: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:30:34: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:34: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:34: #2 number of paired peaks: 326 WARNING @ Thu, 05 Dec 2019 12:30:34: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:34: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:34: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:34: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:34: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:34: #2 predicted fragment length is 151 bps INFO @ Thu, 05 Dec 2019 12:30:34: #2 alternative fragment length(s) may be 151,596 bps INFO @ Thu, 05 Dec 2019 12:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.20_model.r WARNING @ Thu, 05 Dec 2019 12:30:34: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:30:34: #2 You may need to consider one of the other alternative d(s): 151,596 WARNING @ Thu, 05 Dec 2019 12:30:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:30:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:40: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095153/SRX2095153.20_summits.bed INFO @ Thu, 05 Dec 2019 12:30:42: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。