Job ID = 10609078 sra ファイルのダウンロード中... Completed: 161229K bytes transferred in 5 seconds (243606K 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... Read 3010819 spots for /home/okishinya/chipatlas/results/dm3/SRX2200903/SRR4309626.sra Written 3010819 spots for /home/okishinya/chipatlas/results/dm3/SRX2200903/SRR4309626.sra 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: 00:07:32 3010819 reads; of these: 3010819 (100.00%) were paired; of these: 1315207 (43.68%) aligned concordantly 0 times 1158346 (38.47%) aligned concordantly exactly 1 time 537266 (17.84%) aligned concordantly >1 times ---- 1315207 pairs aligned concordantly 0 times; of these: 21953 (1.67%) aligned discordantly 1 time ---- 1293254 pairs aligned 0 times concordantly or discordantly; of these: 2586508 mates make up the pairs; of these: 2496863 (96.53%) aligned 0 times 45853 (1.77%) aligned exactly 1 time 43792 (1.69%) aligned >1 times 58.54% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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_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] 24547 / 1670510 = 0.0147 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 @ Fri, 04 May 2018 07:12:40: # Command line: callpeak -t SRX2200903.bam -f BAM -g dm -n SRX2200903.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2200903.10 # format = BAM # ChIP-seq file = ['SRX2200903.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 @ Fri, 04 May 2018 07:12:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:40: # Command line: callpeak -t SRX2200903.bam -f BAM -g dm -n SRX2200903.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2200903.05 # format = BAM # ChIP-seq file = ['SRX2200903.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 @ Fri, 04 May 2018 07:12:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:40: # Command line: callpeak -t SRX2200903.bam -f BAM -g dm -n SRX2200903.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2200903.20 # format = BAM # ChIP-seq file = ['SRX2200903.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 @ Fri, 04 May 2018 07:12:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:47: 1000000 INFO @ Fri, 04 May 2018 07:12:47: 1000000 INFO @ Fri, 04 May 2018 07:12:47: 1000000 INFO @ Fri, 04 May 2018 07:12:53: 2000000 INFO @ Fri, 04 May 2018 07:12:53: 2000000 INFO @ Fri, 04 May 2018 07:12:53: 2000000 INFO @ Fri, 04 May 2018 07:12:59: 3000000 INFO @ Fri, 04 May 2018 07:12:59: 3000000 INFO @ Fri, 04 May 2018 07:12:59: 3000000 INFO @ Fri, 04 May 2018 07:13:01: #1 tag size is determined as 81 bps INFO @ Fri, 04 May 2018 07:13:01: #1 tag size = 81 INFO @ Fri, 04 May 2018 07:13:01: #1 total tags in treatment: 1671089 INFO @ Fri, 04 May 2018 07:13:01: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:02: #1 tags after filtering in treatment: 1623846 INFO @ Fri, 04 May 2018 07:13:02: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:13:02: #1 finished! INFO @ Fri, 04 May 2018 07:13:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:02: #2 number of paired peaks: 1348 INFO @ Fri, 04 May 2018 07:13:02: start model_add_line... INFO @ Fri, 04 May 2018 07:13:02: start X-correlation... INFO @ Fri, 04 May 2018 07:13:02: end of X-cor INFO @ Fri, 04 May 2018 07:13:02: #2 finished! INFO @ Fri, 04 May 2018 07:13:02: #2 predicted fragment length is 146 bps INFO @ Fri, 04 May 2018 07:13:02: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 04 May 2018 07:13:02: #2.2 Generate R script for model : SRX2200903.10_model.r WARNING @ Fri, 04 May 2018 07:13:02: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:13:02: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 04 May 2018 07:13:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:13:02: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:02: #1 tag size is determined as 81 bps INFO @ Fri, 04 May 2018 07:13:02: #1 tag size = 81 INFO @ Fri, 04 May 2018 07:13:02: #1 total tags in treatment: 1671089 INFO @ Fri, 04 May 2018 07:13:02: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:02: #1 tags after filtering in treatment: 1623846 INFO @ Fri, 04 May 2018 07:13:02: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:13:02: #1 finished! INFO @ Fri, 04 May 2018 07:13:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:02: #2 number of paired peaks: 1348 INFO @ Fri, 04 May 2018 07:13:02: start model_add_line... INFO @ Fri, 04 May 2018 07:13:02: start X-correlation... INFO @ Fri, 04 May 2018 07:13:02: end of X-cor INFO @ Fri, 04 May 2018 07:13:02: #2 finished! INFO @ Fri, 04 May 2018 07:13:02: #2 predicted fragment length is 146 bps INFO @ Fri, 04 May 2018 07:13:02: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 04 May 2018 07:13:02: #2.2 Generate R script for model : SRX2200903.20_model.r WARNING @ Fri, 04 May 2018 07:13:02: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:13:02: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 04 May 2018 07:13:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:13:02: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:02: #1 tag size is determined as 81 bps INFO @ Fri, 04 May 2018 07:13:02: #1 tag size = 81 INFO @ Fri, 04 May 2018 07:13:02: #1 total tags in treatment: 1671089 INFO @ Fri, 04 May 2018 07:13:02: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:02: #1 tags after filtering in treatment: 1623846 INFO @ Fri, 04 May 2018 07:13:02: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:13:02: #1 finished! INFO @ Fri, 04 May 2018 07:13:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:03: #2 number of paired peaks: 1348 INFO @ Fri, 04 May 2018 07:13:03: start model_add_line... INFO @ Fri, 04 May 2018 07:13:03: start X-correlation... INFO @ Fri, 04 May 2018 07:13:03: end of X-cor INFO @ Fri, 04 May 2018 07:13:03: #2 finished! INFO @ Fri, 04 May 2018 07:13:03: #2 predicted fragment length is 146 bps INFO @ Fri, 04 May 2018 07:13:03: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 04 May 2018 07:13:03: #2.2 Generate R script for model : SRX2200903.05_model.r WARNING @ Fri, 04 May 2018 07:13:03: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:13:03: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 04 May 2018 07:13:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:13:03: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:06: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:06: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:13:08: #4 Write output xls file... SRX2200903.10_peaks.xls INFO @ Fri, 04 May 2018 07:13:08: #4 Write peak in narrowPeak format file... SRX2200903.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:08: #4 Write summits bed file... SRX2200903.10_summits.bed INFO @ Fri, 04 May 2018 07:13:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:13:08: #4 Write output xls file... SRX2200903.20_peaks.xls INFO @ Fri, 04 May 2018 07:13:08: #4 Write peak in narrowPeak format file... SRX2200903.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:08: #4 Write summits bed file... SRX2200903.20_summits.bed INFO @ Fri, 04 May 2018 07:13:09: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:13:09: #4 Write output xls file... SRX2200903.05_peaks.xls INFO @ Fri, 04 May 2018 07:13:09: #4 Write peak in narrowPeak format file... SRX2200903.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:13:09: #4 Write summits bed file... SRX2200903.05_summits.bed INFO @ Fri, 04 May 2018 07:13:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (841 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。