Job ID = 10714485 sra ファイルのダウンロード中... Completed: 1545570K bytes transferred in 24 seconds (514177K 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 21354776 spots for /home/okishinya/chipatlas/results/ce10/SRX4085401/SRR7167430.sra Written 21354776 spots for /home/okishinya/chipatlas/results/ce10/SRX4085401/SRR7167430.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: 00:19:39 21354776 reads; of these: 21354776 (100.00%) were paired; of these: 1246180 (5.84%) aligned concordantly 0 times 18187548 (85.17%) aligned concordantly exactly 1 time 1921048 (9.00%) aligned concordantly >1 times ---- 1246180 pairs aligned concordantly 0 times; of these: 76266 (6.12%) aligned discordantly 1 time ---- 1169914 pairs aligned 0 times concordantly or discordantly; of these: 2339828 mates make up the pairs; of these: 1758932 (75.17%) aligned 0 times 474716 (20.29%) aligned exactly 1 time 106180 (4.54%) aligned >1 times 95.88% overall alignment rate Time searching: 00:19:39 Overall time: 00:19:39 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 20 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] 11304635 / 20164955 = 0.5606 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 13:16:43: # Command line: callpeak -t SRX4085401.bam -f BAM -g ce -n SRX4085401.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085401.10 # format = BAM # ChIP-seq file = ['SRX4085401.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 13:16:43: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:16:43: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:16:43: # Command line: callpeak -t SRX4085401.bam -f BAM -g ce -n SRX4085401.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085401.20 # format = BAM # ChIP-seq file = ['SRX4085401.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 13:16:43: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:16:43: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:16:43: # Command line: callpeak -t SRX4085401.bam -f BAM -g ce -n SRX4085401.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085401.05 # format = BAM # ChIP-seq file = ['SRX4085401.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 13:16:43: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:16:43: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:16:50: 1000000 INFO @ Sun, 03 Jun 2018 13:16:50: 1000000 INFO @ Sun, 03 Jun 2018 13:16:50: 1000000 INFO @ Sun, 03 Jun 2018 13:16:56: 2000000 INFO @ Sun, 03 Jun 2018 13:16:57: 2000000 INFO @ Sun, 03 Jun 2018 13:16:57: 2000000 INFO @ Sun, 03 Jun 2018 13:17:02: 3000000 INFO @ Sun, 03 Jun 2018 13:17:03: 3000000 INFO @ Sun, 03 Jun 2018 13:17:03: 3000000 INFO @ Sun, 03 Jun 2018 13:17:09: 4000000 INFO @ Sun, 03 Jun 2018 13:17:10: 4000000 INFO @ Sun, 03 Jun 2018 13:17:10: 4000000 INFO @ Sun, 03 Jun 2018 13:17:15: 5000000 INFO @ Sun, 03 Jun 2018 13:17:16: 5000000 INFO @ Sun, 03 Jun 2018 13:17:17: 5000000 INFO @ Sun, 03 Jun 2018 13:17:22: 6000000 INFO @ Sun, 03 Jun 2018 13:17:23: 6000000 INFO @ Sun, 03 Jun 2018 13:17:23: 6000000 INFO @ Sun, 03 Jun 2018 13:17:28: 7000000 INFO @ Sun, 03 Jun 2018 13:17:30: 7000000 INFO @ Sun, 03 Jun 2018 13:17:30: 7000000 INFO @ Sun, 03 Jun 2018 13:17:35: 8000000 INFO @ Sun, 03 Jun 2018 13:17:37: 8000000 INFO @ Sun, 03 Jun 2018 13:17:37: 8000000 INFO @ Sun, 03 Jun 2018 13:17:41: 9000000 INFO @ Sun, 03 Jun 2018 13:17:44: 9000000 INFO @ Sun, 03 Jun 2018 13:17:44: 9000000 INFO @ Sun, 03 Jun 2018 13:17:47: 10000000 INFO @ Sun, 03 Jun 2018 13:17:51: 10000000 INFO @ Sun, 03 Jun 2018 13:17:51: 10000000 INFO @ Sun, 03 Jun 2018 13:17:54: 11000000 INFO @ Sun, 03 Jun 2018 13:17:58: 11000000 INFO @ Sun, 03 Jun 2018 13:17:59: 11000000 INFO @ Sun, 03 Jun 2018 13:18:00: 12000000 INFO @ Sun, 03 Jun 2018 13:18:05: 12000000 INFO @ Sun, 03 Jun 2018 13:18:06: 12000000 INFO @ Sun, 03 Jun 2018 13:18:07: 13000000 INFO @ Sun, 03 Jun 2018 13:18:11: 13000000 INFO @ Sun, 03 Jun 2018 13:18:13: 13000000 INFO @ Sun, 03 Jun 2018 13:18:13: 14000000 INFO @ Sun, 03 Jun 2018 13:18:18: 14000000 INFO @ Sun, 03 Jun 2018 13:18:19: 14000000 INFO @ Sun, 03 Jun 2018 13:18:20: 15000000 INFO @ Sun, 03 Jun 2018 13:18:25: 15000000 INFO @ Sun, 03 Jun 2018 13:18:26: 16000000 INFO @ Sun, 03 Jun 2018 13:18:26: 15000000 INFO @ Sun, 03 Jun 2018 13:18:32: 16000000 INFO @ Sun, 03 Jun 2018 13:18:33: 17000000 INFO @ Sun, 03 Jun 2018 13:18:33: 16000000 INFO @ Sun, 03 Jun 2018 13:18:38: 17000000 INFO @ Sun, 03 Jun 2018 13:18:39: 18000000 INFO @ Sun, 03 Jun 2018 13:18:40: 17000000 INFO @ Sun, 03 Jun 2018 13:18:41: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:41: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:41: #1 total tags in treatment: 8832506 INFO @ Sun, 03 Jun 2018 13:18:41: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:41: #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 13:18:41: #1 tags after filtering in treatment: 7189991 INFO @ Sun, 03 Jun 2018 13:18:41: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:18:41: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:42: #2 number of paired peaks: 672 WARNING @ Sun, 03 Jun 2018 13:18:42: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:42: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:42: #2 predicted fragment length is 118 bps INFO @ Sun, 03 Jun 2018 13:18:42: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 03 Jun 2018 13:18:42: #2.2 Generate R script for model : SRX4085401.05_model.r INFO @ Sun, 03 Jun 2018 13:18:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:18:45: 18000000 INFO @ Sun, 03 Jun 2018 13:18:47: 18000000 INFO @ Sun, 03 Jun 2018 13:18:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:47: #1 total tags in treatment: 8832506 INFO @ Sun, 03 Jun 2018 13:18:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:47: #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 13:18:47: #1 tags after filtering in treatment: 7189991 INFO @ Sun, 03 Jun 2018 13:18:47: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:18:47: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:47: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:48: #2 number of paired peaks: 672 WARNING @ Sun, 03 Jun 2018 13:18:48: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:48: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:48: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:48: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:48: #2 predicted fragment length is 118 bps INFO @ Sun, 03 Jun 2018 13:18:48: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 03 Jun 2018 13:18:48: #2.2 Generate R script for model : SRX4085401.10_model.r INFO @ Sun, 03 Jun 2018 13:18:48: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:18:49: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:18:49: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:18:49: #1 total tags in treatment: 8832506 INFO @ Sun, 03 Jun 2018 13:18:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:18:49: #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 13:18:49: #1 tags after filtering in treatment: 7189991 INFO @ Sun, 03 Jun 2018 13:18:49: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:18:49: #1 finished! INFO @ Sun, 03 Jun 2018 13:18:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:18:50: #2 number of paired peaks: 672 WARNING @ Sun, 03 Jun 2018 13:18:50: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Sun, 03 Jun 2018 13:18:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:18:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:18:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:18:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:18:50: #2 predicted fragment length is 118 bps INFO @ Sun, 03 Jun 2018 13:18:50: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 03 Jun 2018 13:18:50: #2.2 Generate R script for model : SRX4085401.20_model.r INFO @ Sun, 03 Jun 2018 13:18:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:01: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:05: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:10: #4 Write output xls file... SRX4085401.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:10: #4 Write peak in narrowPeak format file... SRX4085401.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:10: #4 Write summits bed file... SRX4085401.05_summits.bed INFO @ Sun, 03 Jun 2018 13:19:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3518 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:16: #4 Write output xls file... SRX4085401.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:16: #4 Write peak in narrowPeak format file... SRX4085401.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:16: #4 Write summits bed file... SRX4085401.10_summits.bed INFO @ Sun, 03 Jun 2018 13:19:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2098 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:17: #4 Write output xls file... SRX4085401.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:17: #4 Write peak in narrowPeak format file... SRX4085401.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:17: #4 Write summits bed file... SRX4085401.20_summits.bed INFO @ Sun, 03 Jun 2018 13:19:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1100 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。