Job ID = 9159957 sra ファイルのダウンロード中... Completed: 1300440K bytes transferred in 14 seconds (738190K bits/sec), in 1 file, 2 directories. 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... Written 8486332 spots for /home/okishinya/chipatlas/results/dm3/SRX970862/SRR1943298.sra Written 8486332 spots total 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: 00:22:17 8486332 reads; of these: 8486332 (100.00%) were paired; of these: 1413950 (16.66%) aligned concordantly 0 times 5956878 (70.19%) aligned concordantly exactly 1 time 1115504 (13.14%) aligned concordantly >1 times ---- 1413950 pairs aligned concordantly 0 times; of these: 514141 (36.36%) aligned discordantly 1 time ---- 899809 pairs aligned 0 times concordantly or discordantly; of these: 1799618 mates make up the pairs; of these: 1360492 (75.60%) aligned 0 times 223153 (12.40%) aligned exactly 1 time 215973 (12.00%) aligned >1 times 91.98% overall alignment rate Time searching: 00:22:17 Overall time: 00:22:17 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_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] 4354971 / 7516772 = 0.5794 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 @ Wed, 28 Jun 2017 01:50:25: # Command line: callpeak -t SRX970862.bam -f BAM -g dm -n SRX970862.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX970862.10 # format = BAM # ChIP-seq file = ['SRX970862.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 @ Wed, 28 Jun 2017 01:50:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:50:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:50:25: # Command line: callpeak -t SRX970862.bam -f BAM -g dm -n SRX970862.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX970862.05 # format = BAM # ChIP-seq file = ['SRX970862.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 @ Wed, 28 Jun 2017 01:50:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:50:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:50:25: # Command line: callpeak -t SRX970862.bam -f BAM -g dm -n SRX970862.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX970862.20 # format = BAM # ChIP-seq file = ['SRX970862.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 @ Wed, 28 Jun 2017 01:50:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:50:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:50:32: 1000000 INFO @ Wed, 28 Jun 2017 01:50:32: 1000000 INFO @ Wed, 28 Jun 2017 01:50:32: 1000000 INFO @ Wed, 28 Jun 2017 01:50:39: 2000000 INFO @ Wed, 28 Jun 2017 01:50:40: 2000000 INFO @ Wed, 28 Jun 2017 01:50:41: 2000000 INFO @ Wed, 28 Jun 2017 01:50:47: 3000000 INFO @ Wed, 28 Jun 2017 01:50:48: 3000000 INFO @ Wed, 28 Jun 2017 01:50:49: 3000000 INFO @ Wed, 28 Jun 2017 01:50:54: 4000000 INFO @ Wed, 28 Jun 2017 01:50:57: 4000000 INFO @ Wed, 28 Jun 2017 01:50:57: 4000000 INFO @ Wed, 28 Jun 2017 01:51:01: 5000000 INFO @ Wed, 28 Jun 2017 01:51:05: 5000000 INFO @ Wed, 28 Jun 2017 01:51:06: 5000000 INFO @ Wed, 28 Jun 2017 01:51:08: 6000000 INFO @ Wed, 28 Jun 2017 01:51:13: 6000000 INFO @ Wed, 28 Jun 2017 01:51:14: 6000000 INFO @ Wed, 28 Jun 2017 01:51:15: #1 tag size is determined as 111 bps INFO @ Wed, 28 Jun 2017 01:51:15: #1 tag size = 111 INFO @ Wed, 28 Jun 2017 01:51:15: #1 total tags in treatment: 2932541 INFO @ Wed, 28 Jun 2017 01:51:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:51:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:51:15: #1 tags after filtering in treatment: 2799221 INFO @ Wed, 28 Jun 2017 01:51:15: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 01:51:15: #1 finished! INFO @ Wed, 28 Jun 2017 01:51:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:51:15: #2 number of paired peaks: 135 WARNING @ Wed, 28 Jun 2017 01:51:15: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Wed, 28 Jun 2017 01:51:15: start model_add_line... INFO @ Wed, 28 Jun 2017 01:51:15: start X-correlation... INFO @ Wed, 28 Jun 2017 01:51:15: end of X-cor INFO @ Wed, 28 Jun 2017 01:51:15: #2 finished! INFO @ Wed, 28 Jun 2017 01:51:15: #2 predicted fragment length is 141 bps INFO @ Wed, 28 Jun 2017 01:51:15: #2 alternative fragment length(s) may be 141,531,568 bps INFO @ Wed, 28 Jun 2017 01:51:15: #2.2 Generate R script for model : SRX970862.05_model.r WARNING @ Wed, 28 Jun 2017 01:51:15: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:51:15: #2 You may need to consider one of the other alternative d(s): 141,531,568 WARNING @ Wed, 28 Jun 2017 01:51:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:51:15: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:51:20: #1 tag size is determined as 111 bps INFO @ Wed, 28 Jun 2017 01:51:20: #1 tag size = 111 INFO @ Wed, 28 Jun 2017 01:51:20: #1 total tags in treatment: 2932541 INFO @ Wed, 28 Jun 2017 01:51:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:51:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:51:20: #1 tags after filtering in treatment: 2799221 INFO @ Wed, 28 Jun 2017 01:51:20: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 01:51:20: #1 finished! INFO @ Wed, 28 Jun 2017 01:51:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:51:21: #2 number of paired peaks: 135 WARNING @ Wed, 28 Jun 2017 01:51:21: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Wed, 28 Jun 2017 01:51:21: start model_add_line... INFO @ Wed, 28 Jun 2017 01:51:21: start X-correlation... INFO @ Wed, 28 Jun 2017 01:51:21: end of X-cor INFO @ Wed, 28 Jun 2017 01:51:21: #2 finished! INFO @ Wed, 28 Jun 2017 01:51:21: #2 predicted fragment length is 141 bps INFO @ Wed, 28 Jun 2017 01:51:21: #2 alternative fragment length(s) may be 141,531,568 bps INFO @ Wed, 28 Jun 2017 01:51:21: #2.2 Generate R script for model : SRX970862.20_model.r WARNING @ Wed, 28 Jun 2017 01:51:21: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:51:21: #2 You may need to consider one of the other alternative d(s): 141,531,568 WARNING @ Wed, 28 Jun 2017 01:51:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:51:21: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:51:21: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:51:22: #1 tag size is determined as 111 bps INFO @ Wed, 28 Jun 2017 01:51:22: #1 tag size = 111 INFO @ Wed, 28 Jun 2017 01:51:22: #1 total tags in treatment: 2932541 INFO @ Wed, 28 Jun 2017 01:51:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:51:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:51:22: #1 tags after filtering in treatment: 2799221 INFO @ Wed, 28 Jun 2017 01:51:22: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 01:51:22: #1 finished! INFO @ Wed, 28 Jun 2017 01:51:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:51:22: #2 number of paired peaks: 135 WARNING @ Wed, 28 Jun 2017 01:51:22: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Wed, 28 Jun 2017 01:51:22: start model_add_line... INFO @ Wed, 28 Jun 2017 01:51:22: start X-correlation... INFO @ Wed, 28 Jun 2017 01:51:22: end of X-cor INFO @ Wed, 28 Jun 2017 01:51:22: #2 finished! INFO @ Wed, 28 Jun 2017 01:51:22: #2 predicted fragment length is 141 bps INFO @ Wed, 28 Jun 2017 01:51:22: #2 alternative fragment length(s) may be 141,531,568 bps INFO @ Wed, 28 Jun 2017 01:51:22: #2.2 Generate R script for model : SRX970862.10_model.r WARNING @ Wed, 28 Jun 2017 01:51:22: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:51:22: #2 You may need to consider one of the other alternative d(s): 141,531,568 WARNING @ Wed, 28 Jun 2017 01:51:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:51:22: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:51:25: #4 Write output xls file... SRX970862.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:51:25: #4 Write peak in narrowPeak format file... SRX970862.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:51:25: #4 Write summits bed file... SRX970862.05_summits.bed INFO @ Wed, 28 Jun 2017 01:51:25: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:51:27: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:51:28: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:51:31: #4 Write output xls file... SRX970862.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:51:31: #4 Write peak in narrowPeak format file... SRX970862.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:51:31: #4 Write summits bed file... SRX970862.20_summits.bed INFO @ Wed, 28 Jun 2017 01:51:31: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:51:32: #4 Write output xls file... SRX970862.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:51:32: #4 Write peak in narrowPeak format file... SRX970862.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:51:32: #4 Write summits bed file... SRX970862.10_summits.bed INFO @ Wed, 28 Jun 2017 01:51:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。