Job ID = 9157141 sra ファイルのダウンロード中... Completed: 641107K bytes transferred in 7 seconds (687051K 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 18247478 spots for /home/okishinya/chipatlas/results/ce10/SRX2228871/SRR4380327.sra Written 18247478 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: 00:05:09 18247478 reads; of these: 18247478 (100.00%) were unpaired; of these: 278948 (1.53%) aligned 0 times 14786775 (81.03%) aligned exactly 1 time 3181755 (17.44%) aligned >1 times 98.47% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1734154 / 17968530 = 0.0965 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 10:49:38: # Command line: callpeak -t SRX2228871.bam -f BAM -g ce -n SRX2228871.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228871.10 # format = BAM # ChIP-seq file = ['SRX2228871.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 10:49:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:38: # Command line: callpeak -t SRX2228871.bam -f BAM -g ce -n SRX2228871.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228871.05 # format = BAM # ChIP-seq file = ['SRX2228871.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 10:49:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:38: # Command line: callpeak -t SRX2228871.bam -f BAM -g ce -n SRX2228871.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228871.20 # format = BAM # ChIP-seq file = ['SRX2228871.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 10:49:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:49:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:49:47: 1000000 INFO @ Tue, 27 Jun 2017 10:49:47: 1000000 INFO @ Tue, 27 Jun 2017 10:49:47: 1000000 INFO @ Tue, 27 Jun 2017 10:49:56: 2000000 INFO @ Tue, 27 Jun 2017 10:49:56: 2000000 INFO @ Tue, 27 Jun 2017 10:49:56: 2000000 INFO @ Tue, 27 Jun 2017 10:50:06: 3000000 INFO @ Tue, 27 Jun 2017 10:50:06: 3000000 INFO @ Tue, 27 Jun 2017 10:50:06: 3000000 INFO @ Tue, 27 Jun 2017 10:50:15: 4000000 INFO @ Tue, 27 Jun 2017 10:50:15: 4000000 INFO @ Tue, 27 Jun 2017 10:50:15: 4000000 INFO @ Tue, 27 Jun 2017 10:50:25: 5000000 INFO @ Tue, 27 Jun 2017 10:50:25: 5000000 INFO @ Tue, 27 Jun 2017 10:50:25: 5000000 INFO @ Tue, 27 Jun 2017 10:50:34: 6000000 INFO @ Tue, 27 Jun 2017 10:50:34: 6000000 INFO @ Tue, 27 Jun 2017 10:50:34: 6000000 INFO @ Tue, 27 Jun 2017 10:50:44: 7000000 INFO @ Tue, 27 Jun 2017 10:50:44: 7000000 INFO @ Tue, 27 Jun 2017 10:50:44: 7000000 INFO @ Tue, 27 Jun 2017 10:50:53: 8000000 INFO @ Tue, 27 Jun 2017 10:50:53: 8000000 INFO @ Tue, 27 Jun 2017 10:50:53: 8000000 INFO @ Tue, 27 Jun 2017 10:51:03: 9000000 INFO @ Tue, 27 Jun 2017 10:51:03: 9000000 INFO @ Tue, 27 Jun 2017 10:51:03: 9000000 INFO @ Tue, 27 Jun 2017 10:51:12: 10000000 INFO @ Tue, 27 Jun 2017 10:51:12: 10000000 INFO @ Tue, 27 Jun 2017 10:51:12: 10000000 INFO @ Tue, 27 Jun 2017 10:51:22: 11000000 INFO @ Tue, 27 Jun 2017 10:51:22: 11000000 INFO @ Tue, 27 Jun 2017 10:51:22: 11000000 INFO @ Tue, 27 Jun 2017 10:51:31: 12000000 INFO @ Tue, 27 Jun 2017 10:51:31: 12000000 INFO @ Tue, 27 Jun 2017 10:51:31: 12000000 INFO @ Tue, 27 Jun 2017 10:51:40: 13000000 INFO @ Tue, 27 Jun 2017 10:51:40: 13000000 INFO @ Tue, 27 Jun 2017 10:51:40: 13000000 INFO @ Tue, 27 Jun 2017 10:51:49: 14000000 INFO @ Tue, 27 Jun 2017 10:51:49: 14000000 INFO @ Tue, 27 Jun 2017 10:51:49: 14000000 INFO @ Tue, 27 Jun 2017 10:51:58: 15000000 INFO @ Tue, 27 Jun 2017 10:51:58: 15000000 INFO @ Tue, 27 Jun 2017 10:51:58: 15000000 INFO @ Tue, 27 Jun 2017 10:52:06: 16000000 INFO @ Tue, 27 Jun 2017 10:52:06: 16000000 INFO @ Tue, 27 Jun 2017 10:52:06: 16000000 INFO @ Tue, 27 Jun 2017 10:52:08: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:52:08: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:52:08: #1 total tags in treatment: 16234376 INFO @ Tue, 27 Jun 2017 10:52:08: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:52:08: #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 10:52:08: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:52:08: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:52:08: #1 total tags in treatment: 16234376 INFO @ Tue, 27 Jun 2017 10:52:08: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:52:08: #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 10:52:08: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:52:08: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:52:08: #1 total tags in treatment: 16234376 INFO @ Tue, 27 Jun 2017 10:52:08: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:52:08: #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 10:52:08: #1 tags after filtering in treatment: 16234376 INFO @ Tue, 27 Jun 2017 10:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:52:08: #1 finished! INFO @ Tue, 27 Jun 2017 10:52:08: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:52:08: #1 tags after filtering in treatment: 16234376 INFO @ Tue, 27 Jun 2017 10:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:52:08: #1 finished! INFO @ Tue, 27 Jun 2017 10:52:08: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:52:08: #1 tags after filtering in treatment: 16234376 INFO @ Tue, 27 Jun 2017 10:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:52:08: #1 finished! INFO @ Tue, 27 Jun 2017 10:52:08: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:52:09: #2 number of paired peaks: 222 WARNING @ Tue, 27 Jun 2017 10:52:09: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 27 Jun 2017 10:52:09: start model_add_line... INFO @ Tue, 27 Jun 2017 10:52:10: #2 number of paired peaks: 222 WARNING @ Tue, 27 Jun 2017 10:52:10: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 27 Jun 2017 10:52:10: start model_add_line... INFO @ Tue, 27 Jun 2017 10:52:10: #2 number of paired peaks: 222 WARNING @ Tue, 27 Jun 2017 10:52:10: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 27 Jun 2017 10:52:10: start model_add_line... INFO @ Tue, 27 Jun 2017 10:52:10: start X-correlation... INFO @ Tue, 27 Jun 2017 10:52:10: end of X-cor INFO @ Tue, 27 Jun 2017 10:52:10: #2 finished! INFO @ Tue, 27 Jun 2017 10:52:10: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 10:52:10: #2 alternative fragment length(s) may be 2,46,511 bps INFO @ Tue, 27 Jun 2017 10:52:10: #2.2 Generate R script for model : SRX2228871.05_model.r WARNING @ Tue, 27 Jun 2017 10:52:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:52:10: #2 You may need to consider one of the other alternative d(s): 2,46,511 WARNING @ Tue, 27 Jun 2017 10:52:10: #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 10:52:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:52:10: start X-correlation... INFO @ Tue, 27 Jun 2017 10:52:10: end of X-cor INFO @ Tue, 27 Jun 2017 10:52:10: #2 finished! INFO @ Tue, 27 Jun 2017 10:52:10: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 10:52:10: #2 alternative fragment length(s) may be 2,46,511 bps INFO @ Tue, 27 Jun 2017 10:52:10: #2.2 Generate R script for model : SRX2228871.10_model.r WARNING @ Tue, 27 Jun 2017 10:52:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:52:10: #2 You may need to consider one of the other alternative d(s): 2,46,511 WARNING @ Tue, 27 Jun 2017 10:52:10: #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 10:52:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:52:10: start X-correlation... INFO @ Tue, 27 Jun 2017 10:52:10: end of X-cor INFO @ Tue, 27 Jun 2017 10:52:10: #2 finished! INFO @ Tue, 27 Jun 2017 10:52:10: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 10:52:10: #2 alternative fragment length(s) may be 2,46,511 bps INFO @ Tue, 27 Jun 2017 10:52:10: #2.2 Generate R script for model : SRX2228871.20_model.r WARNING @ Tue, 27 Jun 2017 10:52:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:52:10: #2 You may need to consider one of the other alternative d(s): 2,46,511 WARNING @ Tue, 27 Jun 2017 10:52:10: #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 10:52:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:52:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:52:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:52:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:52:58: #4 Write output xls file... SRX2228871.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:52:58: #4 Write peak in narrowPeak format file... SRX2228871.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:52:58: #4 Write summits bed file... SRX2228871.05_summits.bed INFO @ Tue, 27 Jun 2017 10:52:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (711 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:52:58: #4 Write output xls file... SRX2228871.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:52:58: #4 Write peak in narrowPeak format file... SRX2228871.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:52:58: #4 Write summits bed file... SRX2228871.10_summits.bed INFO @ Tue, 27 Jun 2017 10:52:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (408 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:53:00: #4 Write output xls file... SRX2228871.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:53:00: #4 Write peak in narrowPeak format file... SRX2228871.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:53:00: #4 Write summits bed file... SRX2228871.20_summits.bed INFO @ Tue, 27 Jun 2017 10:53:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。