Job ID = 10536361 sra ファイルのダウンロード中... Completed: 884681K bytes transferred in 16 seconds (450013K 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... Written 22165444 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433223/SRR6333864.sra Written 22165444 spots total 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: 00:11:19 22165444 reads; of these: 22165444 (100.00%) were paired; of these: 8401064 (37.90%) aligned concordantly 0 times 12613871 (56.91%) aligned concordantly exactly 1 time 1150509 (5.19%) aligned concordantly >1 times ---- 8401064 pairs aligned concordantly 0 times; of these: 157373 (1.87%) aligned discordantly 1 time ---- 8243691 pairs aligned 0 times concordantly or discordantly; of these: 16487382 mates make up the pairs; of these: 16160014 (98.01%) aligned 0 times 262976 (1.60%) aligned exactly 1 time 64392 (0.39%) aligned >1 times 63.55% overall alignment rate Time searching: 00:11:19 Overall time: 00:11:19 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_sort_core] merging from 12 files... [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] 9639748 / 13781960 = 0.6994 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 @ Thu, 05 Apr 2018 09:09:36: # Command line: callpeak -t SRX3433223.bam -f BAM -g 12100000 -n SRX3433223.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433223.10 # format = BAM # ChIP-seq file = ['SRX3433223.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 @ Thu, 05 Apr 2018 09:09:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:09:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:09:36: # Command line: callpeak -t SRX3433223.bam -f BAM -g 12100000 -n SRX3433223.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433223.20 # format = BAM # ChIP-seq file = ['SRX3433223.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 @ Thu, 05 Apr 2018 09:09:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:09:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:09:36: # Command line: callpeak -t SRX3433223.bam -f BAM -g 12100000 -n SRX3433223.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433223.05 # format = BAM # ChIP-seq file = ['SRX3433223.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 @ Thu, 05 Apr 2018 09:09:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:09:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:09:42: 1000000 INFO @ Thu, 05 Apr 2018 09:09:42: 1000000 INFO @ Thu, 05 Apr 2018 09:09:42: 1000000 INFO @ Thu, 05 Apr 2018 09:09:47: 2000000 INFO @ Thu, 05 Apr 2018 09:09:47: 2000000 INFO @ Thu, 05 Apr 2018 09:09:47: 2000000 INFO @ Thu, 05 Apr 2018 09:09:52: 3000000 INFO @ Thu, 05 Apr 2018 09:09:52: 3000000 INFO @ Thu, 05 Apr 2018 09:09:52: 3000000 INFO @ Thu, 05 Apr 2018 09:09:57: 4000000 INFO @ Thu, 05 Apr 2018 09:09:57: 4000000 INFO @ Thu, 05 Apr 2018 09:09:58: 4000000 INFO @ Thu, 05 Apr 2018 09:10:02: 5000000 INFO @ Thu, 05 Apr 2018 09:10:02: 5000000 INFO @ Thu, 05 Apr 2018 09:10:03: 5000000 INFO @ Thu, 05 Apr 2018 09:10:07: 6000000 INFO @ Thu, 05 Apr 2018 09:10:08: 6000000 INFO @ Thu, 05 Apr 2018 09:10:08: 6000000 INFO @ Thu, 05 Apr 2018 09:10:13: 7000000 INFO @ Thu, 05 Apr 2018 09:10:13: 7000000 INFO @ Thu, 05 Apr 2018 09:10:14: 7000000 INFO @ Thu, 05 Apr 2018 09:10:18: 8000000 INFO @ Thu, 05 Apr 2018 09:10:18: 8000000 INFO @ Thu, 05 Apr 2018 09:10:19: 8000000 INFO @ Thu, 05 Apr 2018 09:10:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:10:22: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:10:22: #1 total tags in treatment: 4137554 INFO @ Thu, 05 Apr 2018 09:10:22: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:10:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:10:22: #1 tags after filtering in treatment: 3366973 INFO @ Thu, 05 Apr 2018 09:10:22: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 05 Apr 2018 09:10:22: #1 finished! INFO @ Thu, 05 Apr 2018 09:10:22: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:10:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:10:23: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:10:23: #1 total tags in treatment: 4137554 INFO @ Thu, 05 Apr 2018 09:10:23: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:10:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:10:23: #2 number of paired peaks: 104 WARNING @ Thu, 05 Apr 2018 09:10:23: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Thu, 05 Apr 2018 09:10:23: start model_add_line... INFO @ Thu, 05 Apr 2018 09:10:23: start X-correlation... INFO @ Thu, 05 Apr 2018 09:10:23: end of X-cor INFO @ Thu, 05 Apr 2018 09:10:23: #2 finished! INFO @ Thu, 05 Apr 2018 09:10:23: #2 predicted fragment length is 81 bps INFO @ Thu, 05 Apr 2018 09:10:23: #2 alternative fragment length(s) may be 2,65,81,107,143,151,159,226 bps INFO @ Thu, 05 Apr 2018 09:10:23: #2.2 Generate R script for model : SRX3433223.05_model.r WARNING @ Thu, 05 Apr 2018 09:10:23: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:10:23: #2 You may need to consider one of the other alternative d(s): 2,65,81,107,143,151,159,226 WARNING @ Thu, 05 Apr 2018 09:10:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 09:10:23: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:10:23: #1 tags after filtering in treatment: 3366973 INFO @ Thu, 05 Apr 2018 09:10:23: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 05 Apr 2018 09:10:23: #1 finished! INFO @ Thu, 05 Apr 2018 09:10:23: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:10:23: #2 number of paired peaks: 104 WARNING @ Thu, 05 Apr 2018 09:10:23: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Thu, 05 Apr 2018 09:10:23: start model_add_line... INFO @ Thu, 05 Apr 2018 09:10:23: start X-correlation... INFO @ Thu, 05 Apr 2018 09:10:23: end of X-cor INFO @ Thu, 05 Apr 2018 09:10:23: #2 finished! INFO @ Thu, 05 Apr 2018 09:10:23: #2 predicted fragment length is 81 bps INFO @ Thu, 05 Apr 2018 09:10:23: #2 alternative fragment length(s) may be 2,65,81,107,143,151,159,226 bps INFO @ Thu, 05 Apr 2018 09:10:23: #2.2 Generate R script for model : SRX3433223.20_model.r WARNING @ Thu, 05 Apr 2018 09:10:23: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:10:23: #2 You may need to consider one of the other alternative d(s): 2,65,81,107,143,151,159,226 WARNING @ Thu, 05 Apr 2018 09:10:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 09:10:23: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:10:24: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:10:24: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:10:24: #1 total tags in treatment: 4137554 INFO @ Thu, 05 Apr 2018 09:10:24: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:10:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:10:24: #1 tags after filtering in treatment: 3366973 INFO @ Thu, 05 Apr 2018 09:10:24: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 05 Apr 2018 09:10:24: #1 finished! INFO @ Thu, 05 Apr 2018 09:10:24: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:10:24: #2 number of paired peaks: 104 WARNING @ Thu, 05 Apr 2018 09:10:24: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Thu, 05 Apr 2018 09:10:24: start model_add_line... INFO @ Thu, 05 Apr 2018 09:10:24: start X-correlation... INFO @ Thu, 05 Apr 2018 09:10:24: end of X-cor INFO @ Thu, 05 Apr 2018 09:10:24: #2 finished! INFO @ Thu, 05 Apr 2018 09:10:24: #2 predicted fragment length is 81 bps INFO @ Thu, 05 Apr 2018 09:10:24: #2 alternative fragment length(s) may be 2,65,81,107,143,151,159,226 bps INFO @ Thu, 05 Apr 2018 09:10:24: #2.2 Generate R script for model : SRX3433223.10_model.r WARNING @ Thu, 05 Apr 2018 09:10:24: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:10:24: #2 You may need to consider one of the other alternative d(s): 2,65,81,107,143,151,159,226 WARNING @ Thu, 05 Apr 2018 09:10:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 09:10:24: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:10:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:10:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:10:32: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:10:33: #4 Write output xls file... SRX3433223.05_peaks.xls INFO @ Thu, 05 Apr 2018 09:10:33: #4 Write peak in narrowPeak format file... SRX3433223.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:10:33: #4 Write summits bed file... SRX3433223.05_summits.bed INFO @ Thu, 05 Apr 2018 09:10:33: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1091 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:10:33: #4 Write output xls file... SRX3433223.20_peaks.xls INFO @ Thu, 05 Apr 2018 09:10:33: #4 Write peak in narrowPeak format file... SRX3433223.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:10:33: #4 Write summits bed file... SRX3433223.20_summits.bed INFO @ Thu, 05 Apr 2018 09:10:33: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (234 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:10:35: #4 Write output xls file... SRX3433223.10_peaks.xls INFO @ Thu, 05 Apr 2018 09:10:35: #4 Write peak in narrowPeak format file... SRX3433223.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:10:35: #4 Write summits bed file... SRX3433223.10_summits.bed INFO @ Thu, 05 Apr 2018 09:10:35: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。