Job ID = 11193218 sra ファイルのダウンロード中... Completed: 357707K bytes transferred in 6 seconds (484315K 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 8329007 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977504/SRR1951350.sra Written 8329007 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977504/SRR1951350.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: 00:04:19 8329007 reads; of these: 8329007 (100.00%) were paired; of these: 3537784 (42.48%) aligned concordantly 0 times 4281210 (51.40%) aligned concordantly exactly 1 time 510013 (6.12%) aligned concordantly >1 times ---- 3537784 pairs aligned concordantly 0 times; of these: 231023 (6.53%) aligned discordantly 1 time ---- 3306761 pairs aligned 0 times concordantly or discordantly; of these: 6613522 mates make up the pairs; of these: 6360861 (96.18%) aligned 0 times 182667 (2.76%) aligned exactly 1 time 69994 (1.06%) aligned >1 times 61.82% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 1375196 / 4961202 = 0.2772 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 @ Sat, 15 Sep 2018 11:19:09: # Command line: callpeak -t SRX977504.bam -f BAM -g 12100000 -n SRX977504.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977504.20 # format = BAM # ChIP-seq file = ['SRX977504.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 @ Sat, 15 Sep 2018 11:19:09: # Command line: callpeak -t SRX977504.bam -f BAM -g 12100000 -n SRX977504.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977504.10 # format = BAM # ChIP-seq file = ['SRX977504.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 @ Sat, 15 Sep 2018 11:19:09: # Command line: callpeak -t SRX977504.bam -f BAM -g 12100000 -n SRX977504.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977504.05 # format = BAM # ChIP-seq file = ['SRX977504.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 @ Sat, 15 Sep 2018 11:19:09: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:19:09: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:19:09: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:19:09: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:19:09: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:19:09: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:19:15: 1000000 INFO @ Sat, 15 Sep 2018 11:19:16: 1000000 INFO @ Sat, 15 Sep 2018 11:19:16: 1000000 INFO @ Sat, 15 Sep 2018 11:19:22: 2000000 INFO @ Sat, 15 Sep 2018 11:19:22: 2000000 INFO @ Sat, 15 Sep 2018 11:19:24: 2000000 INFO @ Sat, 15 Sep 2018 11:19:28: 3000000 INFO @ Sat, 15 Sep 2018 11:19:28: 3000000 INFO @ Sat, 15 Sep 2018 11:19:31: 3000000 INFO @ Sat, 15 Sep 2018 11:19:34: 4000000 INFO @ Sat, 15 Sep 2018 11:19:35: 4000000 INFO @ Sat, 15 Sep 2018 11:19:38: 4000000 INFO @ Sat, 15 Sep 2018 11:19:40: 5000000 INFO @ Sat, 15 Sep 2018 11:19:41: 5000000 INFO @ Sat, 15 Sep 2018 11:19:44: 5000000 INFO @ Sat, 15 Sep 2018 11:19:46: 6000000 INFO @ Sat, 15 Sep 2018 11:19:47: 6000000 INFO @ Sat, 15 Sep 2018 11:19:49: 6000000 INFO @ Sat, 15 Sep 2018 11:19:52: 7000000 INFO @ Sat, 15 Sep 2018 11:19:53: 7000000 INFO @ Sat, 15 Sep 2018 11:19:54: 7000000 INFO @ Sat, 15 Sep 2018 11:19:55: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:19:55: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:19:55: #1 total tags in treatment: 3478196 INFO @ Sat, 15 Sep 2018 11:19:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:19:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:19:55: #1 tags after filtering in treatment: 2520708 INFO @ Sat, 15 Sep 2018 11:19:55: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Sep 2018 11:19:55: #1 finished! INFO @ Sat, 15 Sep 2018 11:19:55: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:19:55: #2 number of paired peaks: 133 WARNING @ Sat, 15 Sep 2018 11:19:55: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 15 Sep 2018 11:19:55: start model_add_line... INFO @ Sat, 15 Sep 2018 11:19:55: start X-correlation... INFO @ Sat, 15 Sep 2018 11:19:55: end of X-cor INFO @ Sat, 15 Sep 2018 11:19:55: #2 finished! INFO @ Sat, 15 Sep 2018 11:19:55: #2 predicted fragment length is 1 bps INFO @ Sat, 15 Sep 2018 11:19:55: #2 alternative fragment length(s) may be 1 bps INFO @ Sat, 15 Sep 2018 11:19:55: #2.2 Generate R script for model : SRX977504.10_model.r WARNING @ Sat, 15 Sep 2018 11:19:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:19:55: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sat, 15 Sep 2018 11:19:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:19:55: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:19:56: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:19:56: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:19:56: #1 total tags in treatment: 3478196 INFO @ Sat, 15 Sep 2018 11:19:56: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:19:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:19:56: #1 tags after filtering in treatment: 2520708 INFO @ Sat, 15 Sep 2018 11:19:56: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Sep 2018 11:19:56: #1 finished! INFO @ Sat, 15 Sep 2018 11:19:56: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:19:56: #2 number of paired peaks: 133 WARNING @ Sat, 15 Sep 2018 11:19:56: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 15 Sep 2018 11:19:56: start model_add_line... INFO @ Sat, 15 Sep 2018 11:19:56: start X-correlation... INFO @ Sat, 15 Sep 2018 11:19:56: end of X-cor INFO @ Sat, 15 Sep 2018 11:19:56: #2 finished! INFO @ Sat, 15 Sep 2018 11:19:56: #2 predicted fragment length is 1 bps INFO @ Sat, 15 Sep 2018 11:19:56: #2 alternative fragment length(s) may be 1 bps INFO @ Sat, 15 Sep 2018 11:19:56: #2.2 Generate R script for model : SRX977504.20_model.r WARNING @ Sat, 15 Sep 2018 11:19:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:19:56: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sat, 15 Sep 2018 11:19:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:19:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:19:57: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:19:57: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:19:57: #1 total tags in treatment: 3478196 INFO @ Sat, 15 Sep 2018 11:19:57: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:19:58: #1 tags after filtering in treatment: 2520708 INFO @ Sat, 15 Sep 2018 11:19:58: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Sep 2018 11:19:58: #1 finished! INFO @ Sat, 15 Sep 2018 11:19:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:19:58: #2 number of paired peaks: 133 WARNING @ Sat, 15 Sep 2018 11:19:58: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 15 Sep 2018 11:19:58: start model_add_line... INFO @ Sat, 15 Sep 2018 11:19:58: start X-correlation... INFO @ Sat, 15 Sep 2018 11:19:58: end of X-cor INFO @ Sat, 15 Sep 2018 11:19:58: #2 finished! INFO @ Sat, 15 Sep 2018 11:19:58: #2 predicted fragment length is 1 bps INFO @ Sat, 15 Sep 2018 11:19:58: #2 alternative fragment length(s) may be 1 bps INFO @ Sat, 15 Sep 2018 11:19:58: #2.2 Generate R script for model : SRX977504.05_model.r WARNING @ Sat, 15 Sep 2018 11:19:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:19:58: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sat, 15 Sep 2018 11:19:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:19:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:19:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:20:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:20:01: #4 Write output xls file... SRX977504.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:20:01: #4 Write peak in narrowPeak format file... SRX977504.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:20:01: #4 Write summits bed file... SRX977504.10_summits.bed INFO @ Sat, 15 Sep 2018 11:20:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:20:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:20:02: #4 Write output xls file... SRX977504.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:20:02: #4 Write peak in narrowPeak format file... SRX977504.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:20:02: #4 Write summits bed file... SRX977504.20_summits.bed INFO @ Sat, 15 Sep 2018 11:20:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:20:03: #4 Write output xls file... SRX977504.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:20:03: #4 Write peak in narrowPeak format file... SRX977504.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:20:03: #4 Write summits bed file... SRX977504.05_summits.bed INFO @ Sat, 15 Sep 2018 11:20:03: Done! pass1 - making usageList (0 chroms): 1 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。