Job ID = 10714457 sra ファイルのダウンロード中... Completed: 848760K bytes transferred in 11 seconds (631052K 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 13330407 spots for /home/okishinya/chipatlas/results/ce10/SRX4085373/SRR7167402.sra Written 13330407 spots for /home/okishinya/chipatlas/results/ce10/SRX4085373/SRR7167402.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: 00:09:04 13330407 reads; of these: 13330407 (100.00%) were paired; of these: 7119842 (53.41%) aligned concordantly 0 times 5366509 (40.26%) aligned concordantly exactly 1 time 844056 (6.33%) aligned concordantly >1 times ---- 7119842 pairs aligned concordantly 0 times; of these: 303261 (4.26%) aligned discordantly 1 time ---- 6816581 pairs aligned 0 times concordantly or discordantly; of these: 13633162 mates make up the pairs; of these: 11109263 (81.49%) aligned 0 times 2156186 (15.82%) aligned exactly 1 time 367713 (2.70%) aligned >1 times 58.33% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 534456 / 6400159 = 0.0835 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 12:53:59: # Command line: callpeak -t SRX4085373.bam -f BAM -g ce -n SRX4085373.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085373.05 # format = BAM # ChIP-seq file = ['SRX4085373.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 12:53:59: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:53:59: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:53:59: # Command line: callpeak -t SRX4085373.bam -f BAM -g ce -n SRX4085373.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085373.10 # format = BAM # ChIP-seq file = ['SRX4085373.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 12:53:59: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:53:59: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:53:59: # Command line: callpeak -t SRX4085373.bam -f BAM -g ce -n SRX4085373.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085373.20 # format = BAM # ChIP-seq file = ['SRX4085373.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 12:53:59: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:53:59: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:06: 1000000 INFO @ Sun, 03 Jun 2018 12:54:06: 1000000 INFO @ Sun, 03 Jun 2018 12:54:06: 1000000 INFO @ Sun, 03 Jun 2018 12:54:12: 2000000 INFO @ Sun, 03 Jun 2018 12:54:12: 2000000 INFO @ Sun, 03 Jun 2018 12:54:13: 2000000 INFO @ Sun, 03 Jun 2018 12:54:19: 3000000 INFO @ Sun, 03 Jun 2018 12:54:19: 3000000 INFO @ Sun, 03 Jun 2018 12:54:20: 3000000 INFO @ Sun, 03 Jun 2018 12:54:26: 4000000 INFO @ Sun, 03 Jun 2018 12:54:26: 4000000 INFO @ Sun, 03 Jun 2018 12:54:27: 4000000 INFO @ Sun, 03 Jun 2018 12:54:33: 5000000 INFO @ Sun, 03 Jun 2018 12:54:33: 5000000 INFO @ Sun, 03 Jun 2018 12:54:34: 5000000 INFO @ Sun, 03 Jun 2018 12:54:39: 6000000 INFO @ Sun, 03 Jun 2018 12:54:39: 6000000 INFO @ Sun, 03 Jun 2018 12:54:41: 6000000 INFO @ Sun, 03 Jun 2018 12:54:46: 7000000 INFO @ Sun, 03 Jun 2018 12:54:46: 7000000 INFO @ Sun, 03 Jun 2018 12:54:49: 7000000 INFO @ Sun, 03 Jun 2018 12:54:53: 8000000 INFO @ Sun, 03 Jun 2018 12:54:53: 8000000 INFO @ Sun, 03 Jun 2018 12:54:56: 8000000 INFO @ Sun, 03 Jun 2018 12:55:00: 9000000 INFO @ Sun, 03 Jun 2018 12:55:00: 9000000 INFO @ Sun, 03 Jun 2018 12:55:03: 9000000 INFO @ Sun, 03 Jun 2018 12:55:07: 10000000 INFO @ Sun, 03 Jun 2018 12:55:07: 10000000 INFO @ Sun, 03 Jun 2018 12:55:10: 10000000 INFO @ Sun, 03 Jun 2018 12:55:13: 11000000 INFO @ Sun, 03 Jun 2018 12:55:13: 11000000 INFO @ Sun, 03 Jun 2018 12:55:17: 11000000 INFO @ Sun, 03 Jun 2018 12:55:20: 12000000 INFO @ Sun, 03 Jun 2018 12:55:20: 12000000 INFO @ Sun, 03 Jun 2018 12:55:25: 12000000 INFO @ Sun, 03 Jun 2018 12:55:27: 13000000 INFO @ Sun, 03 Jun 2018 12:55:27: 13000000 INFO @ Sun, 03 Jun 2018 12:55:32: 13000000 INFO @ Sun, 03 Jun 2018 12:55:34: 14000000 INFO @ Sun, 03 Jun 2018 12:55:34: 14000000 INFO @ Sun, 03 Jun 2018 12:55:37: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:37: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:37: #1 total tags in treatment: 5692959 INFO @ Sun, 03 Jun 2018 12:55:37: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:37: #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 12:55:37: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:37: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:37: #1 total tags in treatment: 5692959 INFO @ Sun, 03 Jun 2018 12:55:37: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:37: #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 12:55:38: #1 tags after filtering in treatment: 5337169 INFO @ Sun, 03 Jun 2018 12:55:38: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 12:55:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:38: #1 tags after filtering in treatment: 5337169 INFO @ Sun, 03 Jun 2018 12:55:38: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 12:55:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:38: #2 number of paired peaks: 287 WARNING @ Sun, 03 Jun 2018 12:55:38: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:38: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:38: #2 number of paired peaks: 287 WARNING @ Sun, 03 Jun 2018 12:55:38: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:38: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:38: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:38: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:38: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:38: #2 predicted fragment length is 133 bps INFO @ Sun, 03 Jun 2018 12:55:38: #2 alternative fragment length(s) may be 4,93,133 bps INFO @ Sun, 03 Jun 2018 12:55:38: #2.2 Generate R script for model : SRX4085373.05_model.r INFO @ Sun, 03 Jun 2018 12:55:38: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:38: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:38: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:38: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:38: #2 predicted fragment length is 133 bps INFO @ Sun, 03 Jun 2018 12:55:38: #2 alternative fragment length(s) may be 4,93,133 bps INFO @ Sun, 03 Jun 2018 12:55:38: #2.2 Generate R script for model : SRX4085373.10_model.r INFO @ Sun, 03 Jun 2018 12:55:38: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:39: 14000000 INFO @ Sun, 03 Jun 2018 12:55:42: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:42: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:42: #1 total tags in treatment: 5692959 INFO @ Sun, 03 Jun 2018 12:55:42: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:42: #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 12:55:42: #1 tags after filtering in treatment: 5337169 INFO @ Sun, 03 Jun 2018 12:55:42: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 12:55:42: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:42: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:42: #2 number of paired peaks: 287 WARNING @ Sun, 03 Jun 2018 12:55:42: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:42: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:42: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:42: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:42: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:42: #2 predicted fragment length is 133 bps INFO @ Sun, 03 Jun 2018 12:55:42: #2 alternative fragment length(s) may be 4,93,133 bps INFO @ Sun, 03 Jun 2018 12:55:42: #2.2 Generate R script for model : SRX4085373.20_model.r INFO @ Sun, 03 Jun 2018 12:55:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:55:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:55:55: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:55:57: #4 Write output xls file... SRX4085373.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:55:57: #4 Write peak in narrowPeak format file... SRX4085373.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:55:57: #4 Write summits bed file... SRX4085373.10_summits.bed INFO @ Sun, 03 Jun 2018 12:55:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:55:58: #4 Write output xls file... SRX4085373.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:55:58: #4 Write peak in narrowPeak format file... SRX4085373.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:55:58: #4 Write summits bed file... SRX4085373.05_summits.bed INFO @ Sun, 03 Jun 2018 12:55:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:56:01: #4 Write output xls file... SRX4085373.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:01: #4 Write peak in narrowPeak format file... SRX4085373.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:01: #4 Write summits bed file... SRX4085373.20_summits.bed INFO @ Sun, 03 Jun 2018 12:56:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。