Job ID = 11170824 sra ファイルのダウンロード中... Completed: 1211245K bytes transferred in 93 seconds (106658K 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 41967833 spots for /home/okishinya/chipatlas/results/ce10/SRX3043417/SRR5875901.sra Written 41967833 spots for /home/okishinya/chipatlas/results/ce10/SRX3043417/SRR5875901.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: 00:06:37 41967833 reads; of these: 41967833 (100.00%) were unpaired; of these: 34651812 (82.57%) aligned 0 times 6270122 (14.94%) aligned exactly 1 time 1045899 (2.49%) aligned >1 times 17.43% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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_rmdupse_core] 685397 / 7316021 = 0.0937 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 11:36:56: # Command line: callpeak -t SRX3043417.bam -f BAM -g ce -n SRX3043417.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043417.05 # format = BAM # ChIP-seq file = ['SRX3043417.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 11:36:56: # Command line: callpeak -t SRX3043417.bam -f BAM -g ce -n SRX3043417.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043417.20 # format = BAM # ChIP-seq file = ['SRX3043417.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 11:36:56: # Command line: callpeak -t SRX3043417.bam -f BAM -g ce -n SRX3043417.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043417.10 # format = BAM # ChIP-seq file = ['SRX3043417.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 11:36:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:37:03: 1000000 INFO @ Sat, 08 Sep 2018 11:37:04: 1000000 INFO @ Sat, 08 Sep 2018 11:37:04: 1000000 INFO @ Sat, 08 Sep 2018 11:37:10: 2000000 INFO @ Sat, 08 Sep 2018 11:37:11: 2000000 INFO @ Sat, 08 Sep 2018 11:37:11: 2000000 INFO @ Sat, 08 Sep 2018 11:37:18: 3000000 INFO @ Sat, 08 Sep 2018 11:37:18: 3000000 INFO @ Sat, 08 Sep 2018 11:37:18: 3000000 INFO @ Sat, 08 Sep 2018 11:37:25: 4000000 INFO @ Sat, 08 Sep 2018 11:37:25: 4000000 INFO @ Sat, 08 Sep 2018 11:37:25: 4000000 INFO @ Sat, 08 Sep 2018 11:37:32: 5000000 INFO @ Sat, 08 Sep 2018 11:37:32: 5000000 INFO @ Sat, 08 Sep 2018 11:37:32: 5000000 INFO @ Sat, 08 Sep 2018 11:37:39: 6000000 INFO @ Sat, 08 Sep 2018 11:37:39: 6000000 INFO @ Sat, 08 Sep 2018 11:37:39: 6000000 INFO @ Sat, 08 Sep 2018 11:37:43: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:37:43: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:37:43: #1 total tags in treatment: 6630624 INFO @ Sat, 08 Sep 2018 11:37:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:43: #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 11:37:43: #1 tags after filtering in treatment: 6630624 INFO @ Sat, 08 Sep 2018 11:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:43: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:44: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:37:44: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:37:44: #1 total tags in treatment: 6630624 INFO @ Sat, 08 Sep 2018 11:37:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:44: #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 11:37:44: #1 tags after filtering in treatment: 6630624 INFO @ Sat, 08 Sep 2018 11:37:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:44: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:44: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:37:44: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:37:44: #1 total tags in treatment: 6630624 INFO @ Sat, 08 Sep 2018 11:37:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:44: #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 11:37:44: #1 tags after filtering in treatment: 6630624 INFO @ Sat, 08 Sep 2018 11:37:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:44: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:44: #2 number of paired peaks: 823 WARNING @ Sat, 08 Sep 2018 11:37:44: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sat, 08 Sep 2018 11:37:44: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:44: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:44: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:44: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:44: #2 predicted fragment length is 109 bps INFO @ Sat, 08 Sep 2018 11:37:44: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 08 Sep 2018 11:37:44: #2.2 Generate R script for model : SRX3043417.10_model.r WARNING @ Sat, 08 Sep 2018 11:37:44: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:44: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 08 Sep 2018 11:37:44: #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 11:37:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:44: #2 number of paired peaks: 823 WARNING @ Sat, 08 Sep 2018 11:37:44: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sat, 08 Sep 2018 11:37:44: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:44: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:44: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:44: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:44: #2 predicted fragment length is 109 bps INFO @ Sat, 08 Sep 2018 11:37:44: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 08 Sep 2018 11:37:44: #2.2 Generate R script for model : SRX3043417.05_model.r WARNING @ Sat, 08 Sep 2018 11:37:44: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:44: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 08 Sep 2018 11:37:44: #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 11:37:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:44: #2 number of paired peaks: 823 WARNING @ Sat, 08 Sep 2018 11:37:44: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sat, 08 Sep 2018 11:37:44: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:44: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:44: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:44: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:44: #2 predicted fragment length is 109 bps INFO @ Sat, 08 Sep 2018 11:37:44: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 08 Sep 2018 11:37:44: #2.2 Generate R script for model : SRX3043417.20_model.r WARNING @ Sat, 08 Sep 2018 11:37:44: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:44: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 08 Sep 2018 11:37:44: #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 11:37:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:38:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:38:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:38:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write output xls file... SRX3043417.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write peak in narrowPeak format file... SRX3043417.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write summits bed file... SRX3043417.10_summits.bed INFO @ Sat, 08 Sep 2018 11:38:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1909 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write output xls file... SRX3043417.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write peak in narrowPeak format file... SRX3043417.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write summits bed file... SRX3043417.05_summits.bed INFO @ Sat, 08 Sep 2018 11:38:09: Done! INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write output xls file... SRX3043417.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write peak in narrowPeak format file... SRX3043417.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:38:09: #4 Write summits bed file... SRX3043417.20_summits.bed INFO @ Sat, 08 Sep 2018 11:38:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3087 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (709 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。