Job ID = 10937529 sra ファイルのダウンロード中... Completed: 471135K bytes transferred in 22 seconds (169544K 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 4823901 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010326/SRR5833325.sra Written 4823901 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010326/SRR5833325.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: 00:06:17 4823901 reads; of these: 4823901 (100.00%) were paired; of these: 420900 (8.73%) aligned concordantly 0 times 3945152 (81.78%) aligned concordantly exactly 1 time 457849 (9.49%) aligned concordantly >1 times ---- 420900 pairs aligned concordantly 0 times; of these: 42184 (10.02%) aligned discordantly 1 time ---- 378716 pairs aligned 0 times concordantly or discordantly; of these: 757432 mates make up the pairs; of these: 695385 (91.81%) aligned 0 times 42002 (5.55%) aligned exactly 1 time 20045 (2.65%) aligned >1 times 92.79% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 65210 / 4439670 = 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, 10 Aug 2018 02:42:08: # Command line: callpeak -t SRX3010326.bam -f BAM -g 12100000 -n SRX3010326.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010326.10 # format = BAM # ChIP-seq file = ['SRX3010326.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 02:42:08: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:42:08: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:42:08: # Command line: callpeak -t SRX3010326.bam -f BAM -g 12100000 -n SRX3010326.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010326.20 # format = BAM # ChIP-seq file = ['SRX3010326.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 02:42:08: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:42:08: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:42:08: # Command line: callpeak -t SRX3010326.bam -f BAM -g 12100000 -n SRX3010326.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010326.05 # format = BAM # ChIP-seq file = ['SRX3010326.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 02:42:08: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:42:08: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:42:16: 1000000 INFO @ Fri, 10 Aug 2018 02:42:16: 1000000 INFO @ Fri, 10 Aug 2018 02:42:16: 1000000 INFO @ Fri, 10 Aug 2018 02:42:24: 2000000 INFO @ Fri, 10 Aug 2018 02:42:24: 2000000 INFO @ Fri, 10 Aug 2018 02:42:24: 2000000 INFO @ Fri, 10 Aug 2018 02:42:32: 3000000 INFO @ Fri, 10 Aug 2018 02:42:33: 3000000 INFO @ Fri, 10 Aug 2018 02:42:33: 3000000 INFO @ Fri, 10 Aug 2018 02:42:40: 4000000 INFO @ Fri, 10 Aug 2018 02:42:41: 4000000 INFO @ Fri, 10 Aug 2018 02:42:41: 4000000 INFO @ Fri, 10 Aug 2018 02:42:49: 5000000 INFO @ Fri, 10 Aug 2018 02:42:50: 5000000 INFO @ Fri, 10 Aug 2018 02:42:50: 5000000 INFO @ Fri, 10 Aug 2018 02:42:57: 6000000 INFO @ Fri, 10 Aug 2018 02:42:58: 6000000 INFO @ Fri, 10 Aug 2018 02:42:58: 6000000 INFO @ Fri, 10 Aug 2018 02:43:06: 7000000 INFO @ Fri, 10 Aug 2018 02:43:07: 7000000 INFO @ Fri, 10 Aug 2018 02:43:07: 7000000 INFO @ Fri, 10 Aug 2018 02:43:14: 8000000 INFO @ Fri, 10 Aug 2018 02:43:15: 8000000 INFO @ Fri, 10 Aug 2018 02:43:16: 8000000 INFO @ Fri, 10 Aug 2018 02:43:21: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:43:21: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:43:21: #1 total tags in treatment: 4337979 INFO @ Fri, 10 Aug 2018 02:43:21: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:43:21: #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 02:43:22: #1 tags after filtering in treatment: 3510215 INFO @ Fri, 10 Aug 2018 02:43:22: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:43:22: #1 finished! INFO @ Fri, 10 Aug 2018 02:43:22: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:43:22: #2 number of paired peaks: 103 WARNING @ Fri, 10 Aug 2018 02:43:22: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Fri, 10 Aug 2018 02:43:22: start model_add_line... INFO @ Fri, 10 Aug 2018 02:43:22: start X-correlation... INFO @ Fri, 10 Aug 2018 02:43:22: end of X-cor INFO @ Fri, 10 Aug 2018 02:43:22: #2 finished! INFO @ Fri, 10 Aug 2018 02:43:22: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 02:43:22: #2 alternative fragment length(s) may be 1,18,52,82,128,160,170,192,195,282,351,416,468,535,571 bps INFO @ Fri, 10 Aug 2018 02:43:22: #2.2 Generate R script for model : SRX3010326.20_model.r WARNING @ Fri, 10 Aug 2018 02:43:22: #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 02:43:22: #2 You may need to consider one of the other alternative d(s): 1,18,52,82,128,160,170,192,195,282,351,416,468,535,571 WARNING @ Fri, 10 Aug 2018 02:43:22: #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 02:43:22: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:43:22: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:43:22: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:43:22: #1 total tags in treatment: 4337979 INFO @ Fri, 10 Aug 2018 02:43:22: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:43:22: #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 02:43:23: #1 tags after filtering in treatment: 3510215 INFO @ Fri, 10 Aug 2018 02:43:23: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:43:23: #1 finished! INFO @ Fri, 10 Aug 2018 02:43:23: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:43:23: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:43:23: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:43:23: #1 total tags in treatment: 4337979 INFO @ Fri, 10 Aug 2018 02:43:23: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:43:23: #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 02:43:23: #2 number of paired peaks: 103 WARNING @ Fri, 10 Aug 2018 02:43:23: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Fri, 10 Aug 2018 02:43:23: start model_add_line... INFO @ Fri, 10 Aug 2018 02:43:23: start X-correlation... INFO @ Fri, 10 Aug 2018 02:43:23: end of X-cor INFO @ Fri, 10 Aug 2018 02:43:23: #2 finished! INFO @ Fri, 10 Aug 2018 02:43:23: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 02:43:23: #2 alternative fragment length(s) may be 1,18,52,82,128,160,170,192,195,282,351,416,468,535,571 bps INFO @ Fri, 10 Aug 2018 02:43:23: #2.2 Generate R script for model : SRX3010326.05_model.r WARNING @ Fri, 10 Aug 2018 02:43:23: #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 02:43:23: #2 You may need to consider one of the other alternative d(s): 1,18,52,82,128,160,170,192,195,282,351,416,468,535,571 WARNING @ Fri, 10 Aug 2018 02:43:23: #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 02:43:23: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:43:23: #1 tags after filtering in treatment: 3510215 INFO @ Fri, 10 Aug 2018 02:43:23: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:43:23: #1 finished! INFO @ Fri, 10 Aug 2018 02:43:23: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:43:23: #2 number of paired peaks: 103 WARNING @ Fri, 10 Aug 2018 02:43:23: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Fri, 10 Aug 2018 02:43:23: start model_add_line... INFO @ Fri, 10 Aug 2018 02:43:23: start X-correlation... INFO @ Fri, 10 Aug 2018 02:43:23: end of X-cor INFO @ Fri, 10 Aug 2018 02:43:23: #2 finished! INFO @ Fri, 10 Aug 2018 02:43:23: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 02:43:23: #2 alternative fragment length(s) may be 1,18,52,82,128,160,170,192,195,282,351,416,468,535,571 bps INFO @ Fri, 10 Aug 2018 02:43:23: #2.2 Generate R script for model : SRX3010326.10_model.r WARNING @ Fri, 10 Aug 2018 02:43:23: #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 02:43:23: #2 You may need to consider one of the other alternative d(s): 1,18,52,82,128,160,170,192,195,282,351,416,468,535,571 WARNING @ Fri, 10 Aug 2018 02:43:23: #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 02:43:23: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:43:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:43:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:43:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:43:29: #4 Write output xls file... SRX3010326.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:43:29: #4 Write peak in narrowPeak format file... SRX3010326.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:43:29: #4 Write summits bed file... SRX3010326.20_summits.bed INFO @ Fri, 10 Aug 2018 02:43:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:43:30: #4 Write output xls file... SRX3010326.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:43:30: #4 Write peak in narrowPeak format file... SRX3010326.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:43:30: #4 Write summits bed file... SRX3010326.05_summits.bed INFO @ Fri, 10 Aug 2018 02:43:30: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:43:31: #4 Write output xls file... SRX3010326.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:43:31: #4 Write peak in narrowPeak format file... SRX3010326.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:43:31: #4 Write summits bed file... SRX3010326.10_summits.bed INFO @ Fri, 10 Aug 2018 02:43:31: 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。