Job ID = 9157163 sra ファイルのダウンロード中... Completed: 423397K bytes transferred in 6 seconds (544389K 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 20205412 spots for /home/okishinya/chipatlas/results/ce10/SRX2228885/SRR4380341.sra Written 20205412 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: 00:05:47 20205412 reads; of these: 20205412 (100.00%) were unpaired; of these: 2661241 (13.17%) aligned 0 times 14705339 (72.78%) aligned exactly 1 time 2838832 (14.05%) aligned >1 times 86.83% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 3163496 / 17544171 = 0.1803 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 10:59:15: # Command line: callpeak -t SRX2228885.bam -f BAM -g ce -n SRX2228885.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228885.05 # format = BAM # ChIP-seq file = ['SRX2228885.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 10:59:15: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:59:15: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:59:15: # Command line: callpeak -t SRX2228885.bam -f BAM -g ce -n SRX2228885.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228885.10 # format = BAM # ChIP-seq file = ['SRX2228885.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 10:59:15: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:59:15: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:59:15: # Command line: callpeak -t SRX2228885.bam -f BAM -g ce -n SRX2228885.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228885.20 # format = BAM # ChIP-seq file = ['SRX2228885.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 10:59:15: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:59:15: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:59:22: 1000000 INFO @ Tue, 27 Jun 2017 10:59:22: 1000000 INFO @ Tue, 27 Jun 2017 10:59:23: 1000000 INFO @ Tue, 27 Jun 2017 10:59:29: 2000000 INFO @ Tue, 27 Jun 2017 10:59:29: 2000000 INFO @ Tue, 27 Jun 2017 10:59:30: 2000000 INFO @ Tue, 27 Jun 2017 10:59:35: 3000000 INFO @ Tue, 27 Jun 2017 10:59:36: 3000000 INFO @ Tue, 27 Jun 2017 10:59:37: 3000000 INFO @ Tue, 27 Jun 2017 10:59:42: 4000000 INFO @ Tue, 27 Jun 2017 10:59:43: 4000000 INFO @ Tue, 27 Jun 2017 10:59:44: 4000000 INFO @ Tue, 27 Jun 2017 10:59:49: 5000000 INFO @ Tue, 27 Jun 2017 10:59:51: 5000000 INFO @ Tue, 27 Jun 2017 10:59:51: 5000000 INFO @ Tue, 27 Jun 2017 10:59:56: 6000000 INFO @ Tue, 27 Jun 2017 10:59:58: 6000000 INFO @ Tue, 27 Jun 2017 10:59:58: 6000000 INFO @ Tue, 27 Jun 2017 11:00:03: 7000000 INFO @ Tue, 27 Jun 2017 11:00:05: 7000000 INFO @ Tue, 27 Jun 2017 11:00:05: 7000000 INFO @ Tue, 27 Jun 2017 11:00:10: 8000000 INFO @ Tue, 27 Jun 2017 11:00:12: 8000000 INFO @ Tue, 27 Jun 2017 11:00:12: 8000000 INFO @ Tue, 27 Jun 2017 11:00:17: 9000000 INFO @ Tue, 27 Jun 2017 11:00:19: 9000000 INFO @ Tue, 27 Jun 2017 11:00:19: 9000000 INFO @ Tue, 27 Jun 2017 11:00:24: 10000000 INFO @ Tue, 27 Jun 2017 11:00:26: 10000000 INFO @ Tue, 27 Jun 2017 11:00:27: 10000000 INFO @ Tue, 27 Jun 2017 11:00:30: 11000000 INFO @ Tue, 27 Jun 2017 11:00:33: 11000000 INFO @ Tue, 27 Jun 2017 11:00:34: 11000000 INFO @ Tue, 27 Jun 2017 11:00:37: 12000000 INFO @ Tue, 27 Jun 2017 11:00:39: 12000000 INFO @ Tue, 27 Jun 2017 11:00:41: 12000000 INFO @ Tue, 27 Jun 2017 11:00:44: 13000000 INFO @ Tue, 27 Jun 2017 11:00:46: 13000000 INFO @ Tue, 27 Jun 2017 11:00:49: 13000000 INFO @ Tue, 27 Jun 2017 11:00:51: 14000000 INFO @ Tue, 27 Jun 2017 11:00:53: 14000000 INFO @ Tue, 27 Jun 2017 11:00:54: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:00:54: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:00:54: #1 total tags in treatment: 14380675 INFO @ Tue, 27 Jun 2017 11:00:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:00:54: #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 11:00:54: #1 tags after filtering in treatment: 14380675 INFO @ Tue, 27 Jun 2017 11:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:00:54: #1 finished! INFO @ Tue, 27 Jun 2017 11:00:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:00:55: #2 number of paired peaks: 426 WARNING @ Tue, 27 Jun 2017 11:00:55: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 27 Jun 2017 11:00:55: start model_add_line... INFO @ Tue, 27 Jun 2017 11:00:55: start X-correlation... INFO @ Tue, 27 Jun 2017 11:00:55: end of X-cor INFO @ Tue, 27 Jun 2017 11:00:55: #2 finished! INFO @ Tue, 27 Jun 2017 11:00:55: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 11:00:55: #2 alternative fragment length(s) may be 4,112 bps INFO @ Tue, 27 Jun 2017 11:00:55: #2.2 Generate R script for model : SRX2228885.05_model.r INFO @ Tue, 27 Jun 2017 11:00:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:00:56: 14000000 INFO @ Tue, 27 Jun 2017 11:00:56: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:00:56: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:00:56: #1 total tags in treatment: 14380675 INFO @ Tue, 27 Jun 2017 11:00:56: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:00:56: #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 11:00:56: #1 tags after filtering in treatment: 14380675 INFO @ Tue, 27 Jun 2017 11:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:00:56: #1 finished! INFO @ Tue, 27 Jun 2017 11:00:56: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:00:57: #2 number of paired peaks: 426 WARNING @ Tue, 27 Jun 2017 11:00:57: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 27 Jun 2017 11:00:57: start model_add_line... INFO @ Tue, 27 Jun 2017 11:00:57: start X-correlation... INFO @ Tue, 27 Jun 2017 11:00:57: end of X-cor INFO @ Tue, 27 Jun 2017 11:00:57: #2 finished! INFO @ Tue, 27 Jun 2017 11:00:57: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 11:00:57: #2 alternative fragment length(s) may be 4,112 bps INFO @ Tue, 27 Jun 2017 11:00:57: #2.2 Generate R script for model : SRX2228885.20_model.r INFO @ Tue, 27 Jun 2017 11:00:57: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:00:58: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:00:58: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:00:58: #1 total tags in treatment: 14380675 INFO @ Tue, 27 Jun 2017 11:00:58: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:00:58: #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 11:00:59: #1 tags after filtering in treatment: 14380675 INFO @ Tue, 27 Jun 2017 11:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:00:59: #1 finished! INFO @ Tue, 27 Jun 2017 11:00:59: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:01:00: #2 number of paired peaks: 426 WARNING @ Tue, 27 Jun 2017 11:01:00: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 27 Jun 2017 11:01:00: start model_add_line... INFO @ Tue, 27 Jun 2017 11:01:00: start X-correlation... INFO @ Tue, 27 Jun 2017 11:01:00: end of X-cor INFO @ Tue, 27 Jun 2017 11:01:00: #2 finished! INFO @ Tue, 27 Jun 2017 11:01:00: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 11:01:00: #2 alternative fragment length(s) may be 4,112 bps INFO @ Tue, 27 Jun 2017 11:01:00: #2.2 Generate R script for model : SRX2228885.10_model.r INFO @ Tue, 27 Jun 2017 11:01:00: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:01:26: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:01:30: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:01:31: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:01:44: #4 Write output xls file... SRX2228885.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:01:44: #4 Write peak in narrowPeak format file... SRX2228885.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:01:44: #4 Write summits bed file... SRX2228885.05_summits.bed INFO @ Tue, 27 Jun 2017 11:01:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1754 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:01:47: #4 Write output xls file... SRX2228885.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:01:47: #4 Write output xls file... SRX2228885.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:01:47: #4 Write peak in narrowPeak format file... SRX2228885.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:01:47: #4 Write summits bed file... SRX2228885.20_summits.bed INFO @ Tue, 27 Jun 2017 11:01:47: Done! INFO @ Tue, 27 Jun 2017 11:01:47: #4 Write peak in narrowPeak format file... SRX2228885.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:01:47: #4 Write summits bed file... SRX2228885.10_summits.bed INFO @ Tue, 27 Jun 2017 11:01:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1098 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。