Job ID = 10937349 sra ファイルのダウンロード中... Completed: 415220K bytes transferred in 6 seconds (492957K 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 5759899 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198709/SRR4304439.sra Written 5759899 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198709/SRR4304439.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: 00:06:51 5759899 reads; of these: 5759899 (100.00%) were paired; of these: 1174832 (20.40%) aligned concordantly 0 times 3150667 (54.70%) aligned concordantly exactly 1 time 1434400 (24.90%) aligned concordantly >1 times ---- 1174832 pairs aligned concordantly 0 times; of these: 76063 (6.47%) aligned discordantly 1 time ---- 1098769 pairs aligned 0 times concordantly or discordantly; of these: 2197538 mates make up the pairs; of these: 1974745 (89.86%) aligned 0 times 96473 (4.39%) aligned exactly 1 time 126320 (5.75%) aligned >1 times 82.86% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 194446 / 4645249 = 0.0419 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, 10 Aug 2018 01:57:35: # Command line: callpeak -t SRX2198709.bam -f BAM -g 12100000 -n SRX2198709.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198709.05 # format = BAM # ChIP-seq file = ['SRX2198709.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Aug 2018 01:57:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:57:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:57:35: # Command line: callpeak -t SRX2198709.bam -f BAM -g 12100000 -n SRX2198709.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198709.10 # format = BAM # ChIP-seq file = ['SRX2198709.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Aug 2018 01:57:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:57:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:57:35: # Command line: callpeak -t SRX2198709.bam -f BAM -g 12100000 -n SRX2198709.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198709.20 # format = BAM # ChIP-seq file = ['SRX2198709.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Aug 2018 01:57:35: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:57:35: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:57:42: 1000000 INFO @ Fri, 10 Aug 2018 01:57:43: 1000000 INFO @ Fri, 10 Aug 2018 01:57:43: 1000000 INFO @ Fri, 10 Aug 2018 01:57:49: 2000000 INFO @ Fri, 10 Aug 2018 01:57:50: 2000000 INFO @ Fri, 10 Aug 2018 01:57:50: 2000000 INFO @ Fri, 10 Aug 2018 01:57:55: 3000000 INFO @ Fri, 10 Aug 2018 01:57:58: 3000000 INFO @ Fri, 10 Aug 2018 01:57:58: 3000000 INFO @ Fri, 10 Aug 2018 01:58:02: 4000000 INFO @ Fri, 10 Aug 2018 01:58:05: 4000000 INFO @ Fri, 10 Aug 2018 01:58:05: 4000000 INFO @ Fri, 10 Aug 2018 01:58:09: 5000000 INFO @ Fri, 10 Aug 2018 01:58:13: 5000000 INFO @ Fri, 10 Aug 2018 01:58:13: 5000000 INFO @ Fri, 10 Aug 2018 01:58:16: 6000000 INFO @ Fri, 10 Aug 2018 01:58:20: 6000000 INFO @ Fri, 10 Aug 2018 01:58:20: 6000000 INFO @ Fri, 10 Aug 2018 01:58:22: 7000000 INFO @ Fri, 10 Aug 2018 01:58:28: 7000000 INFO @ Fri, 10 Aug 2018 01:58:28: 7000000 INFO @ Fri, 10 Aug 2018 01:58:29: 8000000 INFO @ Fri, 10 Aug 2018 01:58:35: 8000000 INFO @ Fri, 10 Aug 2018 01:58:35: 8000000 INFO @ Fri, 10 Aug 2018 01:58:36: 9000000 INFO @ Fri, 10 Aug 2018 01:58:37: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:58:37: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:58:37: #1 total tags in treatment: 4391449 INFO @ Fri, 10 Aug 2018 01:58:37: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:58:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:58:37: #1 tags after filtering in treatment: 2991527 INFO @ Fri, 10 Aug 2018 01:58:37: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 10 Aug 2018 01:58:37: #1 finished! INFO @ Fri, 10 Aug 2018 01:58:37: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:58:38: #2 number of paired peaks: 134 WARNING @ Fri, 10 Aug 2018 01:58:38: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 10 Aug 2018 01:58:38: start model_add_line... INFO @ Fri, 10 Aug 2018 01:58:38: start X-correlation... INFO @ Fri, 10 Aug 2018 01:58:38: end of X-cor INFO @ Fri, 10 Aug 2018 01:58:38: #2 finished! INFO @ Fri, 10 Aug 2018 01:58:38: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 01:58:38: #2 alternative fragment length(s) may be 1,40,65,86,102,589 bps INFO @ Fri, 10 Aug 2018 01:58:38: #2.2 Generate R script for model : SRX2198709.05_model.r WARNING @ Fri, 10 Aug 2018 01:58:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 01:58:38: #2 You may need to consider one of the other alternative d(s): 1,40,65,86,102,589 WARNING @ Fri, 10 Aug 2018 01:58:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 01:58:38: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:58:42: 9000000 INFO @ Fri, 10 Aug 2018 01:58:42: 9000000 INFO @ Fri, 10 Aug 2018 01:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:58:43: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:58:43: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:58:43: #1 total tags in treatment: 4391449 INFO @ Fri, 10 Aug 2018 01:58:43: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:58:43: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:58:43: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:58:43: #1 total tags in treatment: 4391449 INFO @ Fri, 10 Aug 2018 01:58:43: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:58:43: #1 tags after filtering in treatment: 2991527 INFO @ Fri, 10 Aug 2018 01:58:43: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 10 Aug 2018 01:58:43: #1 finished! INFO @ Fri, 10 Aug 2018 01:58:43: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:58:43: #1 tags after filtering in treatment: 2991527 INFO @ Fri, 10 Aug 2018 01:58:43: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 10 Aug 2018 01:58:43: #1 finished! INFO @ Fri, 10 Aug 2018 01:58:43: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:58:44: #2 number of paired peaks: 134 WARNING @ Fri, 10 Aug 2018 01:58:44: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 10 Aug 2018 01:58:44: start model_add_line... INFO @ Fri, 10 Aug 2018 01:58:44: start X-correlation... INFO @ Fri, 10 Aug 2018 01:58:44: end of X-cor INFO @ Fri, 10 Aug 2018 01:58:44: #2 finished! INFO @ Fri, 10 Aug 2018 01:58:44: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 01:58:44: #2 alternative fragment length(s) may be 1,40,65,86,102,589 bps INFO @ Fri, 10 Aug 2018 01:58:44: #2.2 Generate R script for model : SRX2198709.10_model.r WARNING @ Fri, 10 Aug 2018 01:58:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 01:58:44: #2 You may need to consider one of the other alternative d(s): 1,40,65,86,102,589 WARNING @ Fri, 10 Aug 2018 01:58:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 01:58:44: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:58:44: #2 number of paired peaks: 134 WARNING @ Fri, 10 Aug 2018 01:58:44: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 10 Aug 2018 01:58:44: start model_add_line... INFO @ Fri, 10 Aug 2018 01:58:44: start X-correlation... INFO @ Fri, 10 Aug 2018 01:58:44: end of X-cor INFO @ Fri, 10 Aug 2018 01:58:44: #2 finished! INFO @ Fri, 10 Aug 2018 01:58:44: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 01:58:44: #2 alternative fragment length(s) may be 1,40,65,86,102,589 bps INFO @ Fri, 10 Aug 2018 01:58:44: #2.2 Generate R script for model : SRX2198709.20_model.r WARNING @ Fri, 10 Aug 2018 01:58:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 01:58:44: #2 You may need to consider one of the other alternative d(s): 1,40,65,86,102,589 WARNING @ Fri, 10 Aug 2018 01:58:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 01:58:44: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:58:45: #4 Write output xls file... SRX2198709.05_peaks.xls INFO @ Fri, 10 Aug 2018 01:58:45: #4 Write peak in narrowPeak format file... SRX2198709.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:58:45: #4 Write summits bed file... SRX2198709.05_summits.bed INFO @ Fri, 10 Aug 2018 01:58:45: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:58:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:58:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:58:50: #4 Write output xls file... SRX2198709.20_peaks.xls INFO @ Fri, 10 Aug 2018 01:58:50: #4 Write peak in narrowPeak format file... SRX2198709.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:58:50: #4 Write summits bed file... SRX2198709.20_summits.bed INFO @ Fri, 10 Aug 2018 01:58:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:58:51: #4 Write output xls file... SRX2198709.10_peaks.xls INFO @ Fri, 10 Aug 2018 01:58:51: #4 Write peak in narrowPeak format file... SRX2198709.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:58:51: #4 Write summits bed file... SRX2198709.10_summits.bed INFO @ Fri, 10 Aug 2018 01:58:51: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。