Job ID = 11170876 sra ファイルのダウンロード中... Completed: 487424K bytes transferred in 25 seconds (158296K 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: SINGLE fastq に変換中... Read 17233149 spots for /home/okishinya/chipatlas/results/ce10/SRX3942554/SRR7010075.sra Written 17233149 spots for /home/okishinya/chipatlas/results/ce10/SRX3942554/SRR7010075.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: 00:07:12 17233149 reads; of these: 17233149 (100.00%) were unpaired; of these: 2849363 (16.53%) aligned 0 times 10659697 (61.86%) aligned exactly 1 time 3724089 (21.61%) aligned >1 times 83.47% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9442950 / 14383786 = 0.6565 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, 08 Sep 2018 11:36:51: # Command line: callpeak -t SRX3942554.bam -f BAM -g ce -n SRX3942554.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3942554.05 # format = BAM # ChIP-seq file = ['SRX3942554.bam'] # control file = None # effective genome size = 9.00e+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, 08 Sep 2018 11:36:51: # Command line: callpeak -t SRX3942554.bam -f BAM -g ce -n SRX3942554.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3942554.10 # format = BAM # ChIP-seq file = ['SRX3942554.bam'] # control file = None # effective genome size = 9.00e+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, 08 Sep 2018 11:36:51: # Command line: callpeak -t SRX3942554.bam -f BAM -g ce -n SRX3942554.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3942554.20 # format = BAM # ChIP-seq file = ['SRX3942554.bam'] # control file = None # effective genome size = 9.00e+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, 08 Sep 2018 11:36:51: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:51: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:51: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:51: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:51: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:51: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:58: 1000000 INFO @ Sat, 08 Sep 2018 11:36:58: 1000000 INFO @ Sat, 08 Sep 2018 11:36:58: 1000000 INFO @ Sat, 08 Sep 2018 11:37:06: 2000000 INFO @ Sat, 08 Sep 2018 11:37:06: 2000000 INFO @ Sat, 08 Sep 2018 11:37:06: 2000000 INFO @ Sat, 08 Sep 2018 11:37:13: 3000000 INFO @ Sat, 08 Sep 2018 11:37:13: 3000000 INFO @ Sat, 08 Sep 2018 11:37:13: 3000000 INFO @ Sat, 08 Sep 2018 11:37:20: 4000000 INFO @ Sat, 08 Sep 2018 11:37:21: 4000000 INFO @ Sat, 08 Sep 2018 11:37:21: 4000000 INFO @ Sat, 08 Sep 2018 11:37:27: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:27: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:27: #1 total tags in treatment: 4940836 INFO @ Sat, 08 Sep 2018 11:37:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:37:27: #1 tags after filtering in treatment: 4940836 INFO @ Sat, 08 Sep 2018 11:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:27: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:27: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:27: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:27: #1 total tags in treatment: 4940836 INFO @ Sat, 08 Sep 2018 11:37:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:37:28: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:28: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:28: #1 total tags in treatment: 4940836 INFO @ Sat, 08 Sep 2018 11:37:28: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:37:28: #1 tags after filtering in treatment: 4940836 INFO @ Sat, 08 Sep 2018 11:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:28: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:28: #1 tags after filtering in treatment: 4940836 INFO @ Sat, 08 Sep 2018 11:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:28: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:28: #2 number of paired peaks: 2744 INFO @ Sat, 08 Sep 2018 11:37:28: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:28: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:28: #2 number of paired peaks: 2744 INFO @ Sat, 08 Sep 2018 11:37:28: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:28: #2 number of paired peaks: 2744 INFO @ Sat, 08 Sep 2018 11:37:28: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:28: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:28: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:28: #2 predicted fragment length is 111 bps INFO @ Sat, 08 Sep 2018 11:37:28: #2 alternative fragment length(s) may be 3,98,111 bps INFO @ Sat, 08 Sep 2018 11:37:28: #2.2 Generate R script for model : SRX3942554.05_model.r WARNING @ Sat, 08 Sep 2018 11:37:28: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:28: #2 You may need to consider one of the other alternative d(s): 3,98,111 WARNING @ Sat, 08 Sep 2018 11:37:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:37:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:28: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:28: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:28: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:28: #2 predicted fragment length is 111 bps INFO @ Sat, 08 Sep 2018 11:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:28: #2 alternative fragment length(s) may be 3,98,111 bps INFO @ Sat, 08 Sep 2018 11:37:28: #2.2 Generate R script for model : SRX3942554.10_model.r WARNING @ Sat, 08 Sep 2018 11:37:28: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:28: #2 You may need to consider one of the other alternative d(s): 3,98,111 WARNING @ Sat, 08 Sep 2018 11:37:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:37:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:28: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:28: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:28: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:28: #2 predicted fragment length is 111 bps INFO @ Sat, 08 Sep 2018 11:37:28: #2 alternative fragment length(s) may be 3,98,111 bps INFO @ Sat, 08 Sep 2018 11:37:28: #2.2 Generate R script for model : SRX3942554.20_model.r WARNING @ Sat, 08 Sep 2018 11:37:28: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:28: #2 You may need to consider one of the other alternative d(s): 3,98,111 WARNING @ Sat, 08 Sep 2018 11:37:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:37:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:43: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:49: #4 Write output xls file... SRX3942554.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:49: #4 Write peak in narrowPeak format file... SRX3942554.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:49: #4 Write summits bed file... SRX3942554.10_summits.bed INFO @ Sat, 08 Sep 2018 11:37:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (727 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:37:49: #4 Write output xls file... SRX3942554.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:49: #4 Write peak in narrowPeak format file... SRX3942554.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:49: #4 Write summits bed file... SRX3942554.20_summits.bed INFO @ Sat, 08 Sep 2018 11:37:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:37:50: #4 Write output xls file... SRX3942554.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:50: #4 Write peak in narrowPeak format file... SRX3942554.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:50: #4 Write summits bed file... SRX3942554.05_summits.bed INFO @ Sat, 08 Sep 2018 11:37:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。