Job ID = 9158137 sra ファイルのダウンロード中... Completed: 709197K bytes transferred in 7 seconds (735376K 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 28586485 spots for /home/okishinya/chipatlas/results/dm3/SRX1037259/SRR2038537.sra Written 28586485 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: 00:08:40 28586485 reads; of these: 28586485 (100.00%) were unpaired; of these: 3486645 (12.20%) aligned 0 times 20258450 (70.87%) aligned exactly 1 time 4841390 (16.94%) aligned >1 times 87.80% overall alignment rate Time searching: 00:08:40 Overall time: 00:08:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 17099961 / 25099840 = 0.6813 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 15:34:45: # Command line: callpeak -t SRX1037259.bam -f BAM -g dm -n SRX1037259.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037259.05 # format = BAM # ChIP-seq file = ['SRX1037259.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:34:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:34:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:34:45: # Command line: callpeak -t SRX1037259.bam -f BAM -g dm -n SRX1037259.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037259.20 # format = BAM # ChIP-seq file = ['SRX1037259.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:34:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:34:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:34:45: # Command line: callpeak -t SRX1037259.bam -f BAM -g dm -n SRX1037259.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037259.10 # format = BAM # ChIP-seq file = ['SRX1037259.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:34:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:34:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:34:53: 1000000 INFO @ Tue, 27 Jun 2017 15:34:53: 1000000 INFO @ Tue, 27 Jun 2017 15:34:53: 1000000 INFO @ Tue, 27 Jun 2017 15:35:00: 2000000 INFO @ Tue, 27 Jun 2017 15:35:00: 2000000 INFO @ Tue, 27 Jun 2017 15:35:00: 2000000 INFO @ Tue, 27 Jun 2017 15:35:07: 3000000 INFO @ Tue, 27 Jun 2017 15:35:07: 3000000 INFO @ Tue, 27 Jun 2017 15:35:07: 3000000 INFO @ Tue, 27 Jun 2017 15:35:14: 4000000 INFO @ Tue, 27 Jun 2017 15:35:14: 4000000 INFO @ Tue, 27 Jun 2017 15:35:14: 4000000 INFO @ Tue, 27 Jun 2017 15:35:21: 5000000 INFO @ Tue, 27 Jun 2017 15:35:21: 5000000 INFO @ Tue, 27 Jun 2017 15:35:21: 5000000 INFO @ Tue, 27 Jun 2017 15:35:28: 6000000 INFO @ Tue, 27 Jun 2017 15:35:28: 6000000 INFO @ Tue, 27 Jun 2017 15:35:28: 6000000 INFO @ Tue, 27 Jun 2017 15:35:35: 7000000 INFO @ Tue, 27 Jun 2017 15:35:35: 7000000 INFO @ Tue, 27 Jun 2017 15:35:35: 7000000 INFO @ Tue, 27 Jun 2017 15:35:42: #1 tag size is determined as 40 bps INFO @ Tue, 27 Jun 2017 15:35:42: #1 tag size = 40 INFO @ Tue, 27 Jun 2017 15:35:42: #1 total tags in treatment: 7999879 INFO @ Tue, 27 Jun 2017 15:35:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:35:42: #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 15:35:42: #1 tags after filtering in treatment: 7999879 INFO @ Tue, 27 Jun 2017 15:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:35:42: #1 finished! INFO @ Tue, 27 Jun 2017 15:35:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:35:42: #1 tag size is determined as 40 bps INFO @ Tue, 27 Jun 2017 15:35:42: #1 tag size = 40 INFO @ Tue, 27 Jun 2017 15:35:42: #1 total tags in treatment: 7999879 INFO @ Tue, 27 Jun 2017 15:35:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:35:42: #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 15:35:42: #1 tag size is determined as 40 bps INFO @ Tue, 27 Jun 2017 15:35:42: #1 tag size = 40 INFO @ Tue, 27 Jun 2017 15:35:42: #1 total tags in treatment: 7999879 INFO @ Tue, 27 Jun 2017 15:35:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:35:42: #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 15:35:42: #1 tags after filtering in treatment: 7999879 INFO @ Tue, 27 Jun 2017 15:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:35:42: #1 finished! INFO @ Tue, 27 Jun 2017 15:35:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:35:42: #1 tags after filtering in treatment: 7999879 INFO @ Tue, 27 Jun 2017 15:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:35:42: #1 finished! INFO @ Tue, 27 Jun 2017 15:35:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:35:43: #2 number of paired peaks: 5740 INFO @ Tue, 27 Jun 2017 15:35:43: start model_add_line... INFO @ Tue, 27 Jun 2017 15:35:43: start X-correlation... INFO @ Tue, 27 Jun 2017 15:35:43: end of X-cor INFO @ Tue, 27 Jun 2017 15:35:43: #2 finished! INFO @ Tue, 27 Jun 2017 15:35:43: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 15:35:43: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 27 Jun 2017 15:35:43: #2.2 Generate R script for model : SRX1037259.10_model.r WARNING @ Tue, 27 Jun 2017 15:35:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:35:43: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 27 Jun 2017 15:35:43: #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 15:35:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:35:44: #2 number of paired peaks: 5740 INFO @ Tue, 27 Jun 2017 15:35:44: start model_add_line... INFO @ Tue, 27 Jun 2017 15:35:44: #2 number of paired peaks: 5740 INFO @ Tue, 27 Jun 2017 15:35:44: start model_add_line... INFO @ Tue, 27 Jun 2017 15:35:44: start X-correlation... INFO @ Tue, 27 Jun 2017 15:35:44: end of X-cor INFO @ Tue, 27 Jun 2017 15:35:44: #2 finished! INFO @ Tue, 27 Jun 2017 15:35:44: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 15:35:44: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 27 Jun 2017 15:35:44: #2.2 Generate R script for model : SRX1037259.20_model.r WARNING @ Tue, 27 Jun 2017 15:35:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:35:44: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 27 Jun 2017 15:35:44: #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 15:35:44: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:35:44: start X-correlation... INFO @ Tue, 27 Jun 2017 15:35:44: end of X-cor INFO @ Tue, 27 Jun 2017 15:35:44: #2 finished! INFO @ Tue, 27 Jun 2017 15:35:44: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 15:35:44: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 27 Jun 2017 15:35:44: #2.2 Generate R script for model : SRX1037259.05_model.r WARNING @ Tue, 27 Jun 2017 15:35:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:35:44: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 27 Jun 2017 15:35:44: #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 15:35:44: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:35:57: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:35:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:35:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:36:05: #4 Write output xls file... SRX1037259.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:36:05: #4 Write peak in narrowPeak format file... SRX1037259.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:36:05: #4 Write summits bed file... SRX1037259.20_summits.bed INFO @ Tue, 27 Jun 2017 15:36:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:36:06: #4 Write output xls file... SRX1037259.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:36:06: #4 Write peak in narrowPeak format file... SRX1037259.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:36:06: #4 Write summits bed file... SRX1037259.10_summits.bed INFO @ Tue, 27 Jun 2017 15:36:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:36:06: #4 Write output xls file... SRX1037259.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:36:06: #4 Write peak in narrowPeak format file... SRX1037259.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:36:06: #4 Write summits bed file... SRX1037259.05_summits.bed INFO @ Tue, 27 Jun 2017 15:36:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。