Job ID = 10714497 sra ファイルのダウンロード中... Completed: 975257K bytes transferred in 10 seconds (752383K 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: PAIRED fastq に変換中... Read 15304005 spots for /home/okishinya/chipatlas/results/ce10/SRX4085414/SRR7167443.sra Written 15304005 spots for /home/okishinya/chipatlas/results/ce10/SRX4085414/SRR7167443.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: 00:10:40 15304005 reads; of these: 15304005 (100.00%) were paired; of these: 10353462 (67.65%) aligned concordantly 0 times 4169875 (27.25%) aligned concordantly exactly 1 time 780668 (5.10%) aligned concordantly >1 times ---- 10353462 pairs aligned concordantly 0 times; of these: 245773 (2.37%) aligned discordantly 1 time ---- 10107689 pairs aligned 0 times concordantly or discordantly; of these: 20215378 mates make up the pairs; of these: 14400092 (71.23%) aligned 0 times 5166646 (25.56%) aligned exactly 1 time 648640 (3.21%) aligned >1 times 52.95% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 421284 / 5078487 = 0.0830 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 @ Sun, 03 Jun 2018 13:11:30: # Command line: callpeak -t SRX4085414.bam -f BAM -g ce -n SRX4085414.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085414.10 # format = BAM # ChIP-seq file = ['SRX4085414.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 @ Sun, 03 Jun 2018 13:11:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:11:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:30: # Command line: callpeak -t SRX4085414.bam -f BAM -g ce -n SRX4085414.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085414.20 # format = BAM # ChIP-seq file = ['SRX4085414.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 @ Sun, 03 Jun 2018 13:11:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:11:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:30: # Command line: callpeak -t SRX4085414.bam -f BAM -g ce -n SRX4085414.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085414.05 # format = BAM # ChIP-seq file = ['SRX4085414.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 @ Sun, 03 Jun 2018 13:11:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:11:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:37: 1000000 INFO @ Sun, 03 Jun 2018 13:11:37: 1000000 INFO @ Sun, 03 Jun 2018 13:11:37: 1000000 INFO @ Sun, 03 Jun 2018 13:11:43: 2000000 INFO @ Sun, 03 Jun 2018 13:11:43: 2000000 INFO @ Sun, 03 Jun 2018 13:11:43: 2000000 INFO @ Sun, 03 Jun 2018 13:11:49: 3000000 INFO @ Sun, 03 Jun 2018 13:11:50: 3000000 INFO @ Sun, 03 Jun 2018 13:11:50: 3000000 INFO @ Sun, 03 Jun 2018 13:11:56: 4000000 INFO @ Sun, 03 Jun 2018 13:11:56: 4000000 INFO @ Sun, 03 Jun 2018 13:11:56: 4000000 INFO @ Sun, 03 Jun 2018 13:12:02: 5000000 INFO @ Sun, 03 Jun 2018 13:12:03: 5000000 INFO @ Sun, 03 Jun 2018 13:12:03: 5000000 INFO @ Sun, 03 Jun 2018 13:12:09: 6000000 INFO @ Sun, 03 Jun 2018 13:12:09: 6000000 INFO @ Sun, 03 Jun 2018 13:12:09: 6000000 INFO @ Sun, 03 Jun 2018 13:12:15: 7000000 INFO @ Sun, 03 Jun 2018 13:12:16: 7000000 INFO @ Sun, 03 Jun 2018 13:12:16: 7000000 INFO @ Sun, 03 Jun 2018 13:12:21: 8000000 INFO @ Sun, 03 Jun 2018 13:12:22: 8000000 INFO @ Sun, 03 Jun 2018 13:12:22: 8000000 INFO @ Sun, 03 Jun 2018 13:12:28: 9000000 INFO @ Sun, 03 Jun 2018 13:12:28: 9000000 INFO @ Sun, 03 Jun 2018 13:12:29: 9000000 INFO @ Sun, 03 Jun 2018 13:12:34: 10000000 INFO @ Sun, 03 Jun 2018 13:12:35: 10000000 INFO @ Sun, 03 Jun 2018 13:12:35: 10000000 INFO @ Sun, 03 Jun 2018 13:12:40: 11000000 INFO @ Sun, 03 Jun 2018 13:12:42: 11000000 INFO @ Sun, 03 Jun 2018 13:12:42: 11000000 INFO @ Sun, 03 Jun 2018 13:12:47: 12000000 INFO @ Sun, 03 Jun 2018 13:12:48: 12000000 INFO @ Sun, 03 Jun 2018 13:12:48: 12000000 INFO @ Sun, 03 Jun 2018 13:12:53: 13000000 INFO @ Sun, 03 Jun 2018 13:12:55: 13000000 INFO @ Sun, 03 Jun 2018 13:12:55: 13000000 INFO @ Sun, 03 Jun 2018 13:13:00: 14000000 INFO @ Sun, 03 Jun 2018 13:13:02: 14000000 INFO @ Sun, 03 Jun 2018 13:13:02: 14000000 INFO @ Sun, 03 Jun 2018 13:13:05: 15000000 INFO @ Sun, 03 Jun 2018 13:13:07: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:13:07: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:13:07: #1 total tags in treatment: 4539052 INFO @ Sun, 03 Jun 2018 13:13:07: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:13:07: #1 tags after filtering in treatment: 3980453 INFO @ Sun, 03 Jun 2018 13:13:07: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:13:07: #1 finished! INFO @ Sun, 03 Jun 2018 13:13:07: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:13:08: 15000000 INFO @ Sun, 03 Jun 2018 13:13:08: 15000000 INFO @ Sun, 03 Jun 2018 13:13:08: #2 number of paired peaks: 826 WARNING @ Sun, 03 Jun 2018 13:13:08: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Sun, 03 Jun 2018 13:13:08: start model_add_line... INFO @ Sun, 03 Jun 2018 13:13:08: start X-correlation... INFO @ Sun, 03 Jun 2018 13:13:08: end of X-cor INFO @ Sun, 03 Jun 2018 13:13:08: #2 finished! INFO @ Sun, 03 Jun 2018 13:13:08: #2 predicted fragment length is 80 bps INFO @ Sun, 03 Jun 2018 13:13:08: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 03 Jun 2018 13:13:08: #2.2 Generate R script for model : SRX4085414.10_model.r WARNING @ Sun, 03 Jun 2018 13:13:08: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:13:08: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 03 Jun 2018 13:13:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:13:08: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:13:10: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:13:10: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:13:10: #1 total tags in treatment: 4539052 INFO @ Sun, 03 Jun 2018 13:13:10: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:13:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:13:10: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:13:10: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:13:10: #1 total tags in treatment: 4539052 INFO @ Sun, 03 Jun 2018 13:13:10: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:13:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:13:10: #1 tags after filtering in treatment: 3980453 INFO @ Sun, 03 Jun 2018 13:13:10: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:13:10: #1 finished! INFO @ Sun, 03 Jun 2018 13:13:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:13:10: #1 tags after filtering in treatment: 3980453 INFO @ Sun, 03 Jun 2018 13:13:10: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:13:10: #1 finished! INFO @ Sun, 03 Jun 2018 13:13:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:13:10: #2 number of paired peaks: 826 WARNING @ Sun, 03 Jun 2018 13:13:10: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Sun, 03 Jun 2018 13:13:10: start model_add_line... INFO @ Sun, 03 Jun 2018 13:13:10: start X-correlation... INFO @ Sun, 03 Jun 2018 13:13:10: end of X-cor INFO @ Sun, 03 Jun 2018 13:13:10: #2 finished! INFO @ Sun, 03 Jun 2018 13:13:10: #2 predicted fragment length is 80 bps INFO @ Sun, 03 Jun 2018 13:13:10: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 03 Jun 2018 13:13:10: #2 number of paired peaks: 826 INFO @ Sun, 03 Jun 2018 13:13:10: #2.2 Generate R script for model : SRX4085414.20_model.r WARNING @ Sun, 03 Jun 2018 13:13:10: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Sun, 03 Jun 2018 13:13:10: start model_add_line... WARNING @ Sun, 03 Jun 2018 13:13:10: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:13:10: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 03 Jun 2018 13:13:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:13:10: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:13:10: start X-correlation... INFO @ Sun, 03 Jun 2018 13:13:10: end of X-cor INFO @ Sun, 03 Jun 2018 13:13:10: #2 finished! INFO @ Sun, 03 Jun 2018 13:13:10: #2 predicted fragment length is 80 bps INFO @ Sun, 03 Jun 2018 13:13:10: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 03 Jun 2018 13:13:10: #2.2 Generate R script for model : SRX4085414.05_model.r WARNING @ Sun, 03 Jun 2018 13:13:10: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:13:10: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 03 Jun 2018 13:13:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:13:10: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:22: #4 Write output xls file... SRX4085414.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:22: #4 Write peak in narrowPeak format file... SRX4085414.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:22: #4 Write summits bed file... SRX4085414.10_summits.bed INFO @ Sun, 03 Jun 2018 13:13:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2344 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:13:25: #4 Write output xls file... SRX4085414.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:25: #4 Write peak in narrowPeak format file... SRX4085414.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:25: #4 Write summits bed file... SRX4085414.20_summits.bed INFO @ Sun, 03 Jun 2018 13:13:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:13:25: #4 Write output xls file... SRX4085414.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:25: #4 Write peak in narrowPeak format file... SRX4085414.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:25: #4 Write summits bed file... SRX4085414.05_summits.bed INFO @ Sun, 03 Jun 2018 13:13:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4368 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。