Job ID = 10714435 sra ファイルのダウンロード中... Completed: 1555886K bytes transferred in 30 seconds (419633K 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 21977351 spots for /home/okishinya/chipatlas/results/ce10/SRX4085351/SRR7167380.sra Written 21977351 spots for /home/okishinya/chipatlas/results/ce10/SRX4085351/SRR7167380.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: 00:21:00 21977351 reads; of these: 21977351 (100.00%) were paired; of these: 5778318 (26.29%) aligned concordantly 0 times 14129719 (64.29%) aligned concordantly exactly 1 time 2069314 (9.42%) aligned concordantly >1 times ---- 5778318 pairs aligned concordantly 0 times; of these: 444377 (7.69%) aligned discordantly 1 time ---- 5333941 pairs aligned 0 times concordantly or discordantly; of these: 10667882 mates make up the pairs; of these: 6902273 (64.70%) aligned 0 times 3162336 (29.64%) aligned exactly 1 time 603273 (5.66%) aligned >1 times 84.30% overall alignment rate Time searching: 00:21:00 Overall time: 00:21:00 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 16 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] 8158331 / 16299228 = 0.5005 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 13:06:43: # Command line: callpeak -t SRX4085351.bam -f BAM -g ce -n SRX4085351.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085351.05 # format = BAM # ChIP-seq file = ['SRX4085351.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 13:06:43: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:06:43: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:06:43: # Command line: callpeak -t SRX4085351.bam -f BAM -g ce -n SRX4085351.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085351.20 # format = BAM # ChIP-seq file = ['SRX4085351.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 13:06:43: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:06:43: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:06:43: # Command line: callpeak -t SRX4085351.bam -f BAM -g ce -n SRX4085351.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085351.10 # format = BAM # ChIP-seq file = ['SRX4085351.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 13:06:43: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:06:43: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:06:50: 1000000 INFO @ Sun, 03 Jun 2018 13:06:50: 1000000 INFO @ Sun, 03 Jun 2018 13:06:50: 1000000 INFO @ Sun, 03 Jun 2018 13:06:57: 2000000 INFO @ Sun, 03 Jun 2018 13:06:57: 2000000 INFO @ Sun, 03 Jun 2018 13:06:57: 2000000 INFO @ Sun, 03 Jun 2018 13:07:03: 3000000 INFO @ Sun, 03 Jun 2018 13:07:04: 3000000 INFO @ Sun, 03 Jun 2018 13:07:04: 3000000 INFO @ Sun, 03 Jun 2018 13:07:10: 4000000 INFO @ Sun, 03 Jun 2018 13:07:11: 4000000 INFO @ Sun, 03 Jun 2018 13:07:11: 4000000 INFO @ Sun, 03 Jun 2018 13:07:16: 5000000 INFO @ Sun, 03 Jun 2018 13:07:18: 5000000 INFO @ Sun, 03 Jun 2018 13:07:18: 5000000 INFO @ Sun, 03 Jun 2018 13:07:23: 6000000 INFO @ Sun, 03 Jun 2018 13:07:25: 6000000 INFO @ Sun, 03 Jun 2018 13:07:25: 6000000 INFO @ Sun, 03 Jun 2018 13:07:29: 7000000 INFO @ Sun, 03 Jun 2018 13:07:31: 7000000 INFO @ Sun, 03 Jun 2018 13:07:31: 7000000 INFO @ Sun, 03 Jun 2018 13:07:36: 8000000 INFO @ Sun, 03 Jun 2018 13:07:38: 8000000 INFO @ Sun, 03 Jun 2018 13:07:38: 8000000 INFO @ Sun, 03 Jun 2018 13:07:42: 9000000 INFO @ Sun, 03 Jun 2018 13:07:44: 9000000 INFO @ Sun, 03 Jun 2018 13:07:44: 9000000 INFO @ Sun, 03 Jun 2018 13:07:48: 10000000 INFO @ Sun, 03 Jun 2018 13:07:51: 10000000 INFO @ Sun, 03 Jun 2018 13:07:51: 10000000 INFO @ Sun, 03 Jun 2018 13:07:54: 11000000 INFO @ Sun, 03 Jun 2018 13:07:58: 11000000 INFO @ Sun, 03 Jun 2018 13:07:58: 11000000 INFO @ Sun, 03 Jun 2018 13:08:01: 12000000 INFO @ Sun, 03 Jun 2018 13:08:04: 12000000 INFO @ Sun, 03 Jun 2018 13:08:04: 12000000 INFO @ Sun, 03 Jun 2018 13:08:07: 13000000 INFO @ Sun, 03 Jun 2018 13:08:11: 13000000 INFO @ Sun, 03 Jun 2018 13:08:11: 13000000 INFO @ Sun, 03 Jun 2018 13:08:13: 14000000 INFO @ Sun, 03 Jun 2018 13:08:17: 14000000 INFO @ Sun, 03 Jun 2018 13:08:17: 14000000 INFO @ Sun, 03 Jun 2018 13:08:20: 15000000 INFO @ Sun, 03 Jun 2018 13:08:23: 15000000 INFO @ Sun, 03 Jun 2018 13:08:23: 15000000 INFO @ Sun, 03 Jun 2018 13:08:26: 16000000 INFO @ Sun, 03 Jun 2018 13:08:30: 16000000 INFO @ Sun, 03 Jun 2018 13:08:30: 16000000 INFO @ Sun, 03 Jun 2018 13:08:32: 17000000 INFO @ Sun, 03 Jun 2018 13:08:36: 17000000 INFO @ Sun, 03 Jun 2018 13:08:36: 17000000 INFO @ Sun, 03 Jun 2018 13:08:38: 18000000 INFO @ Sun, 03 Jun 2018 13:08:43: 18000000 INFO @ Sun, 03 Jun 2018 13:08:43: 18000000 INFO @ Sun, 03 Jun 2018 13:08:44: 19000000 INFO @ Sun, 03 Jun 2018 13:08:50: 19000000 INFO @ Sun, 03 Jun 2018 13:08:50: 19000000 INFO @ Sun, 03 Jun 2018 13:08:50: 20000000 INFO @ Sun, 03 Jun 2018 13:08:55: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:08:55: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:08:55: #1 total tags in treatment: 8085270 INFO @ Sun, 03 Jun 2018 13:08:55: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:08:55: #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 13:08:55: #1 tags after filtering in treatment: 6868601 INFO @ Sun, 03 Jun 2018 13:08:55: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:08:55: #1 finished! INFO @ Sun, 03 Jun 2018 13:08:55: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:08:55: #2 number of paired peaks: 544 WARNING @ Sun, 03 Jun 2018 13:08:55: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 03 Jun 2018 13:08:55: start model_add_line... INFO @ Sun, 03 Jun 2018 13:08:55: start X-correlation... INFO @ Sun, 03 Jun 2018 13:08:55: end of X-cor INFO @ Sun, 03 Jun 2018 13:08:55: #2 finished! INFO @ Sun, 03 Jun 2018 13:08:55: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:08:55: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 03 Jun 2018 13:08:55: #2.2 Generate R script for model : SRX4085351.10_model.r INFO @ Sun, 03 Jun 2018 13:08:55: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:08:56: 20000000 INFO @ Sun, 03 Jun 2018 13:08:56: 20000000 INFO @ Sun, 03 Jun 2018 13:09:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:09:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:09:01: #1 total tags in treatment: 8085270 INFO @ Sun, 03 Jun 2018 13:09:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:09:01: #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 13:09:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:09:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:09:01: #1 total tags in treatment: 8085270 INFO @ Sun, 03 Jun 2018 13:09:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:09:01: #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 13:09:01: #1 tags after filtering in treatment: 6868601 INFO @ Sun, 03 Jun 2018 13:09:01: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:09:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:09:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:09:01: #1 tags after filtering in treatment: 6868601 INFO @ Sun, 03 Jun 2018 13:09:01: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 03 Jun 2018 13:09:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:09:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:09:01: #2 number of paired peaks: 544 WARNING @ Sun, 03 Jun 2018 13:09:01: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 03 Jun 2018 13:09:01: start model_add_line... INFO @ Sun, 03 Jun 2018 13:09:01: #2 number of paired peaks: 544 WARNING @ Sun, 03 Jun 2018 13:09:01: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 03 Jun 2018 13:09:01: start model_add_line... INFO @ Sun, 03 Jun 2018 13:09:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:09:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:09:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:09:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:09:01: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:09:01: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 03 Jun 2018 13:09:01: #2.2 Generate R script for model : SRX4085351.20_model.r INFO @ Sun, 03 Jun 2018 13:09:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:09:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:09:01: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:09:01: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 03 Jun 2018 13:09:01: #2.2 Generate R script for model : SRX4085351.05_model.r INFO @ Sun, 03 Jun 2018 13:09:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:09:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:09:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:09:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:09:18: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:09:20: #4 Write output xls file... SRX4085351.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:09:20: #4 Write peak in narrowPeak format file... SRX4085351.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:09:20: #4 Write summits bed file... SRX4085351.10_summits.bed INFO @ Sun, 03 Jun 2018 13:09:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1457 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:09:26: #4 Write output xls file... SRX4085351.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:09:26: #4 Write peak in narrowPeak format file... SRX4085351.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:09:26: #4 Write summits bed file... SRX4085351.20_summits.bed INFO @ Sun, 03 Jun 2018 13:09:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (787 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:09:26: #4 Write output xls file... SRX4085351.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:09:26: #4 Write peak in narrowPeak format file... SRX4085351.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:09:26: #4 Write summits bed file... SRX4085351.05_summits.bed INFO @ Sun, 03 Jun 2018 13:09:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2255 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。