Job ID = 11193139 sra ファイルのダウンロード中... Completed: 474882K bytes transferred in 12 seconds (306592K 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 13887825 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337731/SRR7467872.sra Written 13887825 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337731/SRR7467872.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: 00:07:35 13887825 reads; of these: 13887825 (100.00%) were paired; of these: 12659517 (91.16%) aligned concordantly 0 times 415633 (2.99%) aligned concordantly exactly 1 time 812675 (5.85%) aligned concordantly >1 times ---- 12659517 pairs aligned concordantly 0 times; of these: 294350 (2.33%) aligned discordantly 1 time ---- 12365167 pairs aligned 0 times concordantly or discordantly; of these: 24730334 mates make up the pairs; of these: 19913323 (80.52%) aligned 0 times 2209712 (8.94%) aligned exactly 1 time 2607299 (10.54%) aligned >1 times 28.31% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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] 769687 / 1461963 = 0.5265 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 11:10:38: # Command line: callpeak -t SRX4337731.bam -f BAM -g 12100000 -n SRX4337731.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337731.10 # format = BAM # ChIP-seq file = ['SRX4337731.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 11:10:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:38: # Command line: callpeak -t SRX4337731.bam -f BAM -g 12100000 -n SRX4337731.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337731.05 # format = BAM # ChIP-seq file = ['SRX4337731.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 11:10:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:38: # Command line: callpeak -t SRX4337731.bam -f BAM -g 12100000 -n SRX4337731.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337731.20 # format = BAM # ChIP-seq file = ['SRX4337731.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 11:10:39: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:39: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:43: 1000000 INFO @ Sat, 15 Sep 2018 11:10:43: 1000000 INFO @ Sat, 15 Sep 2018 11:10:43: 1000000 INFO @ Sat, 15 Sep 2018 11:10:47: 2000000 INFO @ Sat, 15 Sep 2018 11:10:48: 2000000 INFO @ Sat, 15 Sep 2018 11:10:48: 2000000 INFO @ Sat, 15 Sep 2018 11:10:51: 3000000 INFO @ Sat, 15 Sep 2018 11:10:52: 3000000 INFO @ Sat, 15 Sep 2018 11:10:53: 3000000 INFO @ Sat, 15 Sep 2018 11:10:56: 4000000 INFO @ Sat, 15 Sep 2018 11:10:57: 4000000 INFO @ Sat, 15 Sep 2018 11:10:58: 4000000 INFO @ Sat, 15 Sep 2018 11:11:00: 5000000 INFO @ Sat, 15 Sep 2018 11:11:02: 5000000 INFO @ Sat, 15 Sep 2018 11:11:03: 5000000 INFO @ Sat, 15 Sep 2018 11:11:04: 6000000 INFO @ Sat, 15 Sep 2018 11:11:06: #1 tag size is determined as 33 bps INFO @ Sat, 15 Sep 2018 11:11:06: #1 tag size = 33 INFO @ Sat, 15 Sep 2018 11:11:06: #1 total tags in treatment: 585617 INFO @ Sat, 15 Sep 2018 11:11:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:11:06: #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 11:11:06: #1 tags after filtering in treatment: 162680 INFO @ Sat, 15 Sep 2018 11:11:06: #1 Redundant rate of treatment: 0.72 INFO @ Sat, 15 Sep 2018 11:11:06: #1 finished! INFO @ Sat, 15 Sep 2018 11:11:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:11:06: #2 number of paired peaks: 388 WARNING @ Sat, 15 Sep 2018 11:11:06: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sat, 15 Sep 2018 11:11:06: start model_add_line... INFO @ Sat, 15 Sep 2018 11:11:06: start X-correlation... INFO @ Sat, 15 Sep 2018 11:11:06: end of X-cor INFO @ Sat, 15 Sep 2018 11:11:06: #2 finished! INFO @ Sat, 15 Sep 2018 11:11:06: #2 predicted fragment length is 226 bps INFO @ Sat, 15 Sep 2018 11:11:06: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 15 Sep 2018 11:11:06: #2.2 Generate R script for model : SRX4337731.20_model.r INFO @ Sat, 15 Sep 2018 11:11:06: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:11:06: 6000000 INFO @ Sat, 15 Sep 2018 11:11:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:11:07: #4 Write output xls file... SRX4337731.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:11:07: #4 Write peak in narrowPeak format file... SRX4337731.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:11:07: #4 Write summits bed file... SRX4337731.20_summits.bed INFO @ Sat, 15 Sep 2018 11:11:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:11:08: #1 tag size is determined as 33 bps INFO @ Sat, 15 Sep 2018 11:11:08: #1 tag size = 33 INFO @ Sat, 15 Sep 2018 11:11:08: #1 total tags in treatment: 585617 INFO @ Sat, 15 Sep 2018 11:11:08: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:11:08: #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 11:11:08: #1 tags after filtering in treatment: 162680 INFO @ Sat, 15 Sep 2018 11:11:08: #1 Redundant rate of treatment: 0.72 INFO @ Sat, 15 Sep 2018 11:11:08: #1 finished! INFO @ Sat, 15 Sep 2018 11:11:08: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:11:08: #2 number of paired peaks: 388 WARNING @ Sat, 15 Sep 2018 11:11:08: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sat, 15 Sep 2018 11:11:08: start model_add_line... INFO @ Sat, 15 Sep 2018 11:11:08: start X-correlation... INFO @ Sat, 15 Sep 2018 11:11:08: end of X-cor INFO @ Sat, 15 Sep 2018 11:11:08: #2 finished! INFO @ Sat, 15 Sep 2018 11:11:08: #2 predicted fragment length is 226 bps INFO @ Sat, 15 Sep 2018 11:11:08: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 15 Sep 2018 11:11:08: #2.2 Generate R script for model : SRX4337731.10_model.r INFO @ Sat, 15 Sep 2018 11:11:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:11:08: 6000000 INFO @ Sat, 15 Sep 2018 11:11:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:11:09: #4 Write output xls file... SRX4337731.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:11:09: #4 Write peak in narrowPeak format file... SRX4337731.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:11:09: #4 Write summits bed file... SRX4337731.10_summits.bed INFO @ Sat, 15 Sep 2018 11:11:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:11:09: #1 tag size is determined as 33 bps INFO @ Sat, 15 Sep 2018 11:11:09: #1 tag size = 33 INFO @ Sat, 15 Sep 2018 11:11:09: #1 total tags in treatment: 585617 INFO @ Sat, 15 Sep 2018 11:11:09: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:11:09: #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 11:11:09: #1 tags after filtering in treatment: 162680 INFO @ Sat, 15 Sep 2018 11:11:09: #1 Redundant rate of treatment: 0.72 INFO @ Sat, 15 Sep 2018 11:11:09: #1 finished! INFO @ Sat, 15 Sep 2018 11:11:09: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:11:09: #2 number of paired peaks: 388 WARNING @ Sat, 15 Sep 2018 11:11:09: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sat, 15 Sep 2018 11:11:09: start model_add_line... INFO @ Sat, 15 Sep 2018 11:11:09: start X-correlation... INFO @ Sat, 15 Sep 2018 11:11:09: end of X-cor INFO @ Sat, 15 Sep 2018 11:11:09: #2 finished! INFO @ Sat, 15 Sep 2018 11:11:09: #2 predicted fragment length is 226 bps INFO @ Sat, 15 Sep 2018 11:11:09: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 15 Sep 2018 11:11:09: #2.2 Generate R script for model : SRX4337731.05_model.r INFO @ Sat, 15 Sep 2018 11:11:09: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:11:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:11:11: #4 Write output xls file... SRX4337731.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:11:11: #4 Write peak in narrowPeak format file... SRX4337731.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:11:11: #4 Write summits bed file... SRX4337731.05_summits.bed INFO @ Sat, 15 Sep 2018 11:11:11: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。