Job ID = 9157203 sra ファイルのダウンロード中... Completed: 515248K bytes transferred in 6 seconds (611968K bits/sec), in 1 file, 2 directories. 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... Written 11412023 spots for /home/okishinya/chipatlas/results/ce10/SRX2228916/SRR4380372.sra Written 11412023 spots total 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: 00:04:10 11412023 reads; of these: 11412023 (100.00%) were unpaired; of these: 306784 (2.69%) aligned 0 times 9368023 (82.09%) aligned exactly 1 time 1737216 (15.22%) aligned >1 times 97.31% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 2913124 / 11105239 = 0.2623 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 @ Tue, 27 Jun 2017 11:08:54: # Command line: callpeak -t SRX2228916.bam -f BAM -g ce -n SRX2228916.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228916.20 # format = BAM # ChIP-seq file = ['SRX2228916.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 @ Tue, 27 Jun 2017 11:08:54: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:08:54: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:08:54: # Command line: callpeak -t SRX2228916.bam -f BAM -g ce -n SRX2228916.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228916.05 # format = BAM # ChIP-seq file = ['SRX2228916.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 @ Tue, 27 Jun 2017 11:08:54: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:08:54: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:08:54: # Command line: callpeak -t SRX2228916.bam -f BAM -g ce -n SRX2228916.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228916.10 # format = BAM # ChIP-seq file = ['SRX2228916.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 @ Tue, 27 Jun 2017 11:08:54: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:08:54: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:09:02: 1000000 INFO @ Tue, 27 Jun 2017 11:09:02: 1000000 INFO @ Tue, 27 Jun 2017 11:09:02: 1000000 INFO @ Tue, 27 Jun 2017 11:09:10: 2000000 INFO @ Tue, 27 Jun 2017 11:09:11: 2000000 INFO @ Tue, 27 Jun 2017 11:09:11: 2000000 INFO @ Tue, 27 Jun 2017 11:09:18: 3000000 INFO @ Tue, 27 Jun 2017 11:09:19: 3000000 INFO @ Tue, 27 Jun 2017 11:09:19: 3000000 INFO @ Tue, 27 Jun 2017 11:09:26: 4000000 INFO @ Tue, 27 Jun 2017 11:09:28: 4000000 INFO @ Tue, 27 Jun 2017 11:09:28: 4000000 INFO @ Tue, 27 Jun 2017 11:09:34: 5000000 INFO @ Tue, 27 Jun 2017 11:09:36: 5000000 INFO @ Tue, 27 Jun 2017 11:09:37: 5000000 INFO @ Tue, 27 Jun 2017 11:09:42: 6000000 INFO @ Tue, 27 Jun 2017 11:09:45: 6000000 INFO @ Tue, 27 Jun 2017 11:09:45: 6000000 INFO @ Tue, 27 Jun 2017 11:09:50: 7000000 INFO @ Tue, 27 Jun 2017 11:09:53: 7000000 INFO @ Tue, 27 Jun 2017 11:09:54: 7000000 INFO @ Tue, 27 Jun 2017 11:09:58: 8000000 INFO @ Tue, 27 Jun 2017 11:10:00: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 11:10:00: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 11:10:00: #1 total tags in treatment: 8192115 INFO @ Tue, 27 Jun 2017 11:10:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:10:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:10:00: #1 tags after filtering in treatment: 8192115 INFO @ Tue, 27 Jun 2017 11:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:10:00: #1 finished! INFO @ Tue, 27 Jun 2017 11:10:00: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:10:01: #2 number of paired peaks: 350 WARNING @ Tue, 27 Jun 2017 11:10:01: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 27 Jun 2017 11:10:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:10:01: start X-correlation... INFO @ Tue, 27 Jun 2017 11:10:01: end of X-cor INFO @ Tue, 27 Jun 2017 11:10:01: #2 finished! INFO @ Tue, 27 Jun 2017 11:10:01: #2 predicted fragment length is 75 bps INFO @ Tue, 27 Jun 2017 11:10:01: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 27 Jun 2017 11:10:01: #2.2 Generate R script for model : SRX2228916.10_model.r WARNING @ Tue, 27 Jun 2017 11:10:01: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:10:01: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 27 Jun 2017 11:10:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:10:01: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:10:02: 8000000 INFO @ Tue, 27 Jun 2017 11:10:03: 8000000 INFO @ Tue, 27 Jun 2017 11:10:03: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 11:10:03: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 11:10:03: #1 total tags in treatment: 8192115 INFO @ Tue, 27 Jun 2017 11:10:03: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:10:03: #1 tags after filtering in treatment: 8192115 INFO @ Tue, 27 Jun 2017 11:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:10:03: #1 finished! INFO @ Tue, 27 Jun 2017 11:10:03: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:10:04: #2 number of paired peaks: 350 WARNING @ Tue, 27 Jun 2017 11:10:04: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 27 Jun 2017 11:10:04: start model_add_line... INFO @ Tue, 27 Jun 2017 11:10:04: start X-correlation... INFO @ Tue, 27 Jun 2017 11:10:04: end of X-cor INFO @ Tue, 27 Jun 2017 11:10:04: #2 finished! INFO @ Tue, 27 Jun 2017 11:10:04: #2 predicted fragment length is 75 bps INFO @ Tue, 27 Jun 2017 11:10:04: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 27 Jun 2017 11:10:04: #2.2 Generate R script for model : SRX2228916.20_model.r WARNING @ Tue, 27 Jun 2017 11:10:04: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:10:04: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 27 Jun 2017 11:10:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:10:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:10:04: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 11:10:04: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 11:10:04: #1 total tags in treatment: 8192115 INFO @ Tue, 27 Jun 2017 11:10:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:10:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:10:05: #1 tags after filtering in treatment: 8192115 INFO @ Tue, 27 Jun 2017 11:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:10:05: #1 finished! INFO @ Tue, 27 Jun 2017 11:10:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:10:05: #2 number of paired peaks: 350 WARNING @ Tue, 27 Jun 2017 11:10:05: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 27 Jun 2017 11:10:05: start model_add_line... INFO @ Tue, 27 Jun 2017 11:10:05: start X-correlation... INFO @ Tue, 27 Jun 2017 11:10:05: end of X-cor INFO @ Tue, 27 Jun 2017 11:10:05: #2 finished! INFO @ Tue, 27 Jun 2017 11:10:05: #2 predicted fragment length is 75 bps INFO @ Tue, 27 Jun 2017 11:10:05: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 27 Jun 2017 11:10:05: #2.2 Generate R script for model : SRX2228916.05_model.r WARNING @ Tue, 27 Jun 2017 11:10:05: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:10:05: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 27 Jun 2017 11:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:10:05: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:10:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:10:29: #4 Write output xls file... SRX2228916.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:10:29: #4 Write peak in narrowPeak format file... SRX2228916.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:10:29: #4 Write summits bed file... SRX2228916.10_summits.bed INFO @ Tue, 27 Jun 2017 11:10:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:10:33: #4 Write output xls file... SRX2228916.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:10:33: #4 Write peak in narrowPeak format file... SRX2228916.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:10:33: #4 Write summits bed file... SRX2228916.05_summits.bed INFO @ Tue, 27 Jun 2017 11:10:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (523 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:10:34: #4 Write output xls file... SRX2228916.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:10:34: #4 Write peak in narrowPeak format file... SRX2228916.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:10:34: #4 Write summits bed file... SRX2228916.20_summits.bed INFO @ Tue, 27 Jun 2017 11:10:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (218 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。