Job ID = 11597976 sra ファイルのダウンロード中... Completed: 622463K bytes transferred in 8 seconds (591356K 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 26009505 spots for /home/okishinya/chipatlas/results/dm3/SRX4664643/SRR7813070.sra Written 26009505 spots for /home/okishinya/chipatlas/results/dm3/SRX4664643/SRR7813070.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:02 26009505 reads; of these: 26009505 (100.00%) were unpaired; of these: 740211 (2.85%) aligned 0 times 17240525 (66.29%) aligned exactly 1 time 8028769 (30.87%) aligned >1 times 97.15% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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 12 files... [bam_rmdupse_core] 3933444 / 25269294 = 0.1557 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 @ Wed, 30 Jan 2019 16:54:32: # Command line: callpeak -t SRX4664643.bam -f BAM -g dm -n SRX4664643.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664643.20 # format = BAM # ChIP-seq file = ['SRX4664643.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 @ Wed, 30 Jan 2019 16:54:32: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:32: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:32: # Command line: callpeak -t SRX4664643.bam -f BAM -g dm -n SRX4664643.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664643.05 # format = BAM # ChIP-seq file = ['SRX4664643.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 @ Wed, 30 Jan 2019 16:54:32: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:32: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:32: # Command line: callpeak -t SRX4664643.bam -f BAM -g dm -n SRX4664643.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664643.10 # format = BAM # ChIP-seq file = ['SRX4664643.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 @ Wed, 30 Jan 2019 16:54:32: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:32: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:40: 1000000 INFO @ Wed, 30 Jan 2019 16:54:40: 1000000 INFO @ Wed, 30 Jan 2019 16:54:40: 1000000 INFO @ Wed, 30 Jan 2019 16:54:47: 2000000 INFO @ Wed, 30 Jan 2019 16:54:47: 2000000 INFO @ Wed, 30 Jan 2019 16:54:47: 2000000 INFO @ Wed, 30 Jan 2019 16:54:55: 3000000 INFO @ Wed, 30 Jan 2019 16:54:55: 3000000 INFO @ Wed, 30 Jan 2019 16:54:55: 3000000 INFO @ Wed, 30 Jan 2019 16:55:02: 4000000 INFO @ Wed, 30 Jan 2019 16:55:02: 4000000 INFO @ Wed, 30 Jan 2019 16:55:02: 4000000 INFO @ Wed, 30 Jan 2019 16:55:10: 5000000 INFO @ Wed, 30 Jan 2019 16:55:10: 5000000 INFO @ Wed, 30 Jan 2019 16:55:10: 5000000 INFO @ Wed, 30 Jan 2019 16:55:18: 6000000 INFO @ Wed, 30 Jan 2019 16:55:18: 6000000 INFO @ Wed, 30 Jan 2019 16:55:19: 6000000 INFO @ Wed, 30 Jan 2019 16:55:28: 7000000 INFO @ Wed, 30 Jan 2019 16:55:28: 7000000 INFO @ Wed, 30 Jan 2019 16:55:28: 7000000 INFO @ Wed, 30 Jan 2019 16:55:38: 8000000 INFO @ Wed, 30 Jan 2019 16:55:38: 8000000 INFO @ Wed, 30 Jan 2019 16:55:38: 8000000 INFO @ Wed, 30 Jan 2019 16:55:47: 9000000 INFO @ Wed, 30 Jan 2019 16:55:47: 9000000 INFO @ Wed, 30 Jan 2019 16:55:48: 9000000 INFO @ Wed, 30 Jan 2019 16:55:56: 10000000 INFO @ Wed, 30 Jan 2019 16:55:56: 10000000 INFO @ Wed, 30 Jan 2019 16:55:57: 10000000 INFO @ Wed, 30 Jan 2019 16:56:05: 11000000 INFO @ Wed, 30 Jan 2019 16:56:05: 11000000 INFO @ Wed, 30 Jan 2019 16:56:06: 11000000 INFO @ Wed, 30 Jan 2019 16:56:15: 12000000 INFO @ Wed, 30 Jan 2019 16:56:15: 12000000 INFO @ Wed, 30 Jan 2019 16:56:16: 12000000 INFO @ Wed, 30 Jan 2019 16:56:23: 13000000 INFO @ Wed, 30 Jan 2019 16:56:23: 13000000 INFO @ Wed, 30 Jan 2019 16:56:24: 13000000 INFO @ Wed, 30 Jan 2019 16:56:32: 14000000 INFO @ Wed, 30 Jan 2019 16:56:33: 14000000 INFO @ Wed, 30 Jan 2019 16:56:33: 14000000 INFO @ Wed, 30 Jan 2019 16:56:41: 15000000 INFO @ Wed, 30 Jan 2019 16:56:42: 15000000 INFO @ Wed, 30 Jan 2019 16:56:42: 15000000 INFO @ Wed, 30 Jan 2019 16:56:51: 16000000 INFO @ Wed, 30 Jan 2019 16:56:51: 16000000 INFO @ Wed, 30 Jan 2019 16:56:52: 16000000 INFO @ Wed, 30 Jan 2019 16:57:00: 17000000 INFO @ Wed, 30 Jan 2019 16:57:00: 17000000 INFO @ Wed, 30 Jan 2019 16:57:01: 17000000 INFO @ Wed, 30 Jan 2019 16:57:09: 18000000 INFO @ Wed, 30 Jan 2019 16:57:09: 18000000 INFO @ Wed, 30 Jan 2019 16:57:10: 18000000 INFO @ Wed, 30 Jan 2019 16:57:18: 19000000 INFO @ Wed, 30 Jan 2019 16:57:18: 19000000 INFO @ Wed, 30 Jan 2019 16:57:19: 19000000 INFO @ Wed, 30 Jan 2019 16:57:27: 20000000 INFO @ Wed, 30 Jan 2019 16:57:27: 20000000 INFO @ Wed, 30 Jan 2019 16:57:28: 20000000 INFO @ Wed, 30 Jan 2019 16:57:36: 21000000 INFO @ Wed, 30 Jan 2019 16:57:36: 21000000 INFO @ Wed, 30 Jan 2019 16:57:37: 21000000 INFO @ Wed, 30 Jan 2019 16:57:39: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:57:39: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:57:39: #1 total tags in treatment: 21335850 INFO @ Wed, 30 Jan 2019 16:57:39: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:57:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:57:40: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:57:40: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:57:40: #1 total tags in treatment: 21335850 INFO @ Wed, 30 Jan 2019 16:57:40: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:57:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:57:40: #1 tags after filtering in treatment: 21335850 INFO @ Wed, 30 Jan 2019 16:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:57:40: #1 finished! INFO @ Wed, 30 Jan 2019 16:57:40: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:57:40: #1 tags after filtering in treatment: 21335850 INFO @ Wed, 30 Jan 2019 16:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:57:40: #1 finished! INFO @ Wed, 30 Jan 2019 16:57:40: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:57:41: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:57:41: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:57:41: #1 total tags in treatment: 21335850 INFO @ Wed, 30 Jan 2019 16:57:41: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:57:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:57:41: #1 tags after filtering in treatment: 21335850 INFO @ Wed, 30 Jan 2019 16:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:57:41: #1 finished! INFO @ Wed, 30 Jan 2019 16:57:41: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:57:41: #2 number of paired peaks: 727 WARNING @ Wed, 30 Jan 2019 16:57:41: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Wed, 30 Jan 2019 16:57:41: start model_add_line... INFO @ Wed, 30 Jan 2019 16:57:41: #2 number of paired peaks: 727 WARNING @ Wed, 30 Jan 2019 16:57:41: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Wed, 30 Jan 2019 16:57:41: start model_add_line... INFO @ Wed, 30 Jan 2019 16:57:42: start X-correlation... INFO @ Wed, 30 Jan 2019 16:57:42: end of X-cor INFO @ Wed, 30 Jan 2019 16:57:42: #2 finished! INFO @ Wed, 30 Jan 2019 16:57:42: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 16:57:42: #2 alternative fragment length(s) may be 3,50 bps INFO @ Wed, 30 Jan 2019 16:57:42: #2.2 Generate R script for model : SRX4664643.20_model.r WARNING @ Wed, 30 Jan 2019 16:57:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:57:42: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Wed, 30 Jan 2019 16:57:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:57:42: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:57:42: start X-correlation... INFO @ Wed, 30 Jan 2019 16:57:42: end of X-cor INFO @ Wed, 30 Jan 2019 16:57:42: #2 finished! INFO @ Wed, 30 Jan 2019 16:57:42: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 16:57:42: #2 alternative fragment length(s) may be 3,50 bps INFO @ Wed, 30 Jan 2019 16:57:42: #2.2 Generate R script for model : SRX4664643.05_model.r WARNING @ Wed, 30 Jan 2019 16:57:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:57:42: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Wed, 30 Jan 2019 16:57:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:57:42: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:57:42: #2 number of paired peaks: 727 WARNING @ Wed, 30 Jan 2019 16:57:42: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Wed, 30 Jan 2019 16:57:42: start model_add_line... INFO @ Wed, 30 Jan 2019 16:57:43: start X-correlation... INFO @ Wed, 30 Jan 2019 16:57:43: end of X-cor INFO @ Wed, 30 Jan 2019 16:57:43: #2 finished! INFO @ Wed, 30 Jan 2019 16:57:43: #2 predicted fragment length is 50 bps INFO @ Wed, 30 Jan 2019 16:57:43: #2 alternative fragment length(s) may be 3,50 bps INFO @ Wed, 30 Jan 2019 16:57:43: #2.2 Generate R script for model : SRX4664643.10_model.r WARNING @ Wed, 30 Jan 2019 16:57:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:57:43: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Wed, 30 Jan 2019 16:57:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:57:43: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:58:24: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:58:26: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:58:26: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:58:47: #4 Write output xls file... SRX4664643.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:58:47: #4 Write peak in narrowPeak format file... SRX4664643.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:58:47: #4 Write summits bed file... SRX4664643.20_summits.bed INFO @ Wed, 30 Jan 2019 16:58:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1836 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:58:48: #4 Write output xls file... SRX4664643.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:58:48: #4 Write peak in narrowPeak format file... SRX4664643.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:58:48: #4 Write summits bed file... SRX4664643.05_summits.bed INFO @ Wed, 30 Jan 2019 16:58:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5477 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:58:49: #4 Write output xls file... SRX4664643.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:58:49: #4 Write peak in narrowPeak format file... SRX4664643.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:58:49: #4 Write summits bed file... SRX4664643.10_summits.bed INFO @ Wed, 30 Jan 2019 16:58:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3463 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。