Job ID = 10714496 sra ファイルのダウンロード中... Completed: 1222349K bytes transferred in 15 seconds (628262K 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 18770721 spots for /home/okishinya/chipatlas/results/ce10/SRX4085413/SRR7167442.sra Written 18770721 spots for /home/okishinya/chipatlas/results/ce10/SRX4085413/SRR7167442.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:28 18770721 reads; of these: 18770721 (100.00%) were paired; of these: 10794397 (57.51%) aligned concordantly 0 times 6543975 (34.86%) aligned concordantly exactly 1 time 1432349 (7.63%) aligned concordantly >1 times ---- 10794397 pairs aligned concordantly 0 times; of these: 418582 (3.88%) aligned discordantly 1 time ---- 10375815 pairs aligned 0 times concordantly or discordantly; of these: 20751630 mates make up the pairs; of these: 14381663 (69.30%) aligned 0 times 5678055 (27.36%) aligned exactly 1 time 691912 (3.33%) aligned >1 times 61.69% overall alignment rate Time searching: 00:14:28 Overall time: 00:14:28 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 12 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] 1114437 / 8228836 = 0.1354 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 13:17:16: # Command line: callpeak -t SRX4085413.bam -f BAM -g ce -n SRX4085413.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085413.20 # format = BAM # ChIP-seq file = ['SRX4085413.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 13:17:16: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:17:16: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:17:16: # Command line: callpeak -t SRX4085413.bam -f BAM -g ce -n SRX4085413.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085413.05 # format = BAM # ChIP-seq file = ['SRX4085413.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 13:17:16: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:17:16: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:17:16: # Command line: callpeak -t SRX4085413.bam -f BAM -g ce -n SRX4085413.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085413.10 # format = BAM # ChIP-seq file = ['SRX4085413.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 13:17:16: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:17:16: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:17:22: 1000000 INFO @ Sun, 03 Jun 2018 13:17:23: 1000000 INFO @ Sun, 03 Jun 2018 13:17:23: 1000000 INFO @ Sun, 03 Jun 2018 13:17:29: 2000000 INFO @ Sun, 03 Jun 2018 13:17:31: 2000000 INFO @ Sun, 03 Jun 2018 13:17:31: 2000000 INFO @ Sun, 03 Jun 2018 13:17:36: 3000000 INFO @ Sun, 03 Jun 2018 13:17:38: 3000000 INFO @ Sun, 03 Jun 2018 13:17:38: 3000000 INFO @ Sun, 03 Jun 2018 13:17:42: 4000000 INFO @ Sun, 03 Jun 2018 13:17:46: 4000000 INFO @ Sun, 03 Jun 2018 13:17:46: 4000000 INFO @ Sun, 03 Jun 2018 13:17:49: 5000000 INFO @ Sun, 03 Jun 2018 13:17:53: 5000000 INFO @ Sun, 03 Jun 2018 13:17:53: 5000000 INFO @ Sun, 03 Jun 2018 13:17:56: 6000000 INFO @ Sun, 03 Jun 2018 13:18:01: 6000000 INFO @ Sun, 03 Jun 2018 13:18:01: 6000000 INFO @ Sun, 03 Jun 2018 13:18:02: 7000000 INFO @ Sun, 03 Jun 2018 13:18:08: 7000000 INFO @ Sun, 03 Jun 2018 13:18:08: 7000000 INFO @ Sun, 03 Jun 2018 13:18:09: 8000000 INFO @ Sun, 03 Jun 2018 13:18:15: 9000000 INFO @ Sun, 03 Jun 2018 13:18:16: 8000000 INFO @ Sun, 03 Jun 2018 13:18:16: 8000000 INFO @ Sun, 03 Jun 2018 13:18:22: 10000000 INFO @ Sun, 03 Jun 2018 13:18:23: 9000000 INFO @ Sun, 03 Jun 2018 13:18:23: 9000000 INFO @ Sun, 03 Jun 2018 13:18:29: 11000000 INFO @ Sun, 03 Jun 2018 13:18:31: 10000000 INFO @ Sun, 03 Jun 2018 13:18:31: 10000000 INFO @ Sun, 03 Jun 2018 13:18:35: 12000000 INFO @ Sun, 03 Jun 2018 13:18:38: 11000000 INFO @ Sun, 03 Jun 2018 13:18:38: 11000000 INFO @ Sun, 03 Jun 2018 13:18:42: 13000000 INFO @ Sun, 03 Jun 2018 13:18:46: 12000000 INFO @ Sun, 03 Jun 2018 13:18:46: 12000000 INFO @ Sun, 03 Jun 2018 13:18:48: 14000000 INFO @ Sun, 03 Jun 2018 13:18:53: 13000000 INFO @ Sun, 03 Jun 2018 13:18:53: 13000000 INFO @ Sun, 03 Jun 2018 13:18:55: 15000000 INFO @ Sun, 03 Jun 2018 13:19:01: 14000000 INFO @ Sun, 03 Jun 2018 13:19:01: 14000000 INFO @ Sun, 03 Jun 2018 13:19:02: 16000000 INFO @ Sun, 03 Jun 2018 13:19:08: 15000000 INFO @ Sun, 03 Jun 2018 13:19:08: 15000000 INFO @ Sun, 03 Jun 2018 13:19:08: 17000000 INFO @ Sun, 03 Jun 2018 13:19:15: 18000000 INFO @ Sun, 03 Jun 2018 13:19:15: 16000000 INFO @ Sun, 03 Jun 2018 13:19:15: 16000000 INFO @ Sun, 03 Jun 2018 13:19:21: 19000000 INFO @ Sun, 03 Jun 2018 13:19:23: 17000000 INFO @ Sun, 03 Jun 2018 13:19:23: 17000000 INFO @ Sun, 03 Jun 2018 13:19:27: 20000000 INFO @ Sun, 03 Jun 2018 13:19:30: 18000000 INFO @ Sun, 03 Jun 2018 13:19:30: 18000000 INFO @ Sun, 03 Jun 2018 13:19:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:32: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:32: #1 total tags in treatment: 6894591 INFO @ Sun, 03 Jun 2018 13:19:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:32: #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 13:19:32: #1 tags after filtering in treatment: 5599346 INFO @ Sun, 03 Jun 2018 13:19:32: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:19:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:33: #2 number of paired peaks: 1242 INFO @ Sun, 03 Jun 2018 13:19:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:33: #2 predicted fragment length is 83 bps INFO @ Sun, 03 Jun 2018 13:19:33: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 03 Jun 2018 13:19:33: #2.2 Generate R script for model : SRX4085413.10_model.r WARNING @ Sun, 03 Jun 2018 13:19:33: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:33: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 03 Jun 2018 13:19:33: #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 13:19:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:37: 19000000 INFO @ Sun, 03 Jun 2018 13:19:37: 19000000 INFO @ Sun, 03 Jun 2018 13:19:44: 20000000 INFO @ Sun, 03 Jun 2018 13:19:44: 20000000 INFO @ Sun, 03 Jun 2018 13:19:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:50: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:50: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:50: #1 total tags in treatment: 6894591 INFO @ Sun, 03 Jun 2018 13:19:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:50: #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 13:19:50: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:50: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:50: #1 total tags in treatment: 6894591 INFO @ Sun, 03 Jun 2018 13:19:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:50: #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 13:19:50: #1 tags after filtering in treatment: 5599346 INFO @ Sun, 03 Jun 2018 13:19:50: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:19:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:50: #1 tags after filtering in treatment: 5599346 INFO @ Sun, 03 Jun 2018 13:19:50: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:19:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:50: #2 number of paired peaks: 1242 INFO @ Sun, 03 Jun 2018 13:19:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:50: #2 number of paired peaks: 1242 INFO @ Sun, 03 Jun 2018 13:19:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:50: #2 predicted fragment length is 83 bps INFO @ Sun, 03 Jun 2018 13:19:50: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 03 Jun 2018 13:19:50: #2.2 Generate R script for model : SRX4085413.20_model.r INFO @ Sun, 03 Jun 2018 13:19:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:50: #2 predicted fragment length is 83 bps INFO @ Sun, 03 Jun 2018 13:19:50: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 03 Jun 2018 13:19:50: #2.2 Generate R script for model : SRX4085413.05_model.r WARNING @ Sun, 03 Jun 2018 13:19:50: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:50: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 03 Jun 2018 13:19:50: #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 13:19:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:50: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Jun 2018 13:19:50: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:19:50: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 03 Jun 2018 13:19:50: #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 13:19:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:54: #4 Write output xls file... SRX4085413.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:54: #4 Write peak in narrowPeak format file... SRX4085413.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:54: #4 Write summits bed file... SRX4085413.10_summits.bed INFO @ Sun, 03 Jun 2018 13:19:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4638 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:20:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:11: #4 Write output xls file... SRX4085413.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:20:11: #4 Write peak in narrowPeak format file... SRX4085413.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:20:11: #4 Write summits bed file... SRX4085413.20_summits.bed INFO @ Sun, 03 Jun 2018 13:20:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2431 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:20:12: #4 Write output xls file... SRX4085413.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:20:12: #4 Write peak in narrowPeak format file... SRX4085413.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:20:12: #4 Write summits bed file... SRX4085413.05_summits.bed INFO @ Sun, 03 Jun 2018 13:20:12: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7556 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。