Job ID = 10714440 sra ファイルのダウンロード中... Completed: 865838K bytes transferred in 16 seconds (437973K 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 12039430 spots for /home/okishinya/chipatlas/results/ce10/SRX4085356/SRR7167385.sra Written 12039430 spots for /home/okishinya/chipatlas/results/ce10/SRX4085356/SRR7167385.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: 00:12:39 12039430 reads; of these: 12039430 (100.00%) were paired; of these: 556974 (4.63%) aligned concordantly 0 times 10053898 (83.51%) aligned concordantly exactly 1 time 1428558 (11.87%) aligned concordantly >1 times ---- 556974 pairs aligned concordantly 0 times; of these: 46199 (8.29%) aligned discordantly 1 time ---- 510775 pairs aligned 0 times concordantly or discordantly; of these: 1021550 mates make up the pairs; of these: 566544 (55.46%) aligned 0 times 358636 (35.11%) aligned exactly 1 time 96370 (9.43%) aligned >1 times 97.65% overall alignment rate Time searching: 00:12:39 Overall time: 00:12:39 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 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] 3802654 / 11512842 = 0.3303 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 12:56:24: # Command line: callpeak -t SRX4085356.bam -f BAM -g ce -n SRX4085356.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085356.10 # format = BAM # ChIP-seq file = ['SRX4085356.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 12:56:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:56:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:56:24: # Command line: callpeak -t SRX4085356.bam -f BAM -g ce -n SRX4085356.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085356.05 # format = BAM # ChIP-seq file = ['SRX4085356.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 12:56:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:56:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:56:24: # Command line: callpeak -t SRX4085356.bam -f BAM -g ce -n SRX4085356.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085356.20 # format = BAM # ChIP-seq file = ['SRX4085356.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 12:56:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:56:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:56:32: 1000000 INFO @ Sun, 03 Jun 2018 12:56:33: 1000000 INFO @ Sun, 03 Jun 2018 12:56:33: 1000000 INFO @ Sun, 03 Jun 2018 12:56:39: 2000000 INFO @ Sun, 03 Jun 2018 12:56:42: 2000000 INFO @ Sun, 03 Jun 2018 12:56:42: 2000000 INFO @ Sun, 03 Jun 2018 12:56:46: 3000000 INFO @ Sun, 03 Jun 2018 12:56:50: 3000000 INFO @ Sun, 03 Jun 2018 12:56:50: 3000000 INFO @ Sun, 03 Jun 2018 12:56:53: 4000000 INFO @ Sun, 03 Jun 2018 12:56:58: 4000000 INFO @ Sun, 03 Jun 2018 12:56:58: 4000000 INFO @ Sun, 03 Jun 2018 12:57:00: 5000000 INFO @ Sun, 03 Jun 2018 12:57:05: 5000000 INFO @ Sun, 03 Jun 2018 12:57:05: 5000000 INFO @ Sun, 03 Jun 2018 12:57:07: 6000000 INFO @ Sun, 03 Jun 2018 12:57:13: 6000000 INFO @ Sun, 03 Jun 2018 12:57:13: 6000000 INFO @ Sun, 03 Jun 2018 12:57:13: 7000000 INFO @ Sun, 03 Jun 2018 12:57:20: 8000000 INFO @ Sun, 03 Jun 2018 12:57:20: 7000000 INFO @ Sun, 03 Jun 2018 12:57:20: 7000000 INFO @ Sun, 03 Jun 2018 12:57:27: 9000000 INFO @ Sun, 03 Jun 2018 12:57:28: 8000000 INFO @ Sun, 03 Jun 2018 12:57:28: 8000000 INFO @ Sun, 03 Jun 2018 12:57:34: 10000000 INFO @ Sun, 03 Jun 2018 12:57:35: 9000000 INFO @ Sun, 03 Jun 2018 12:57:35: 9000000 INFO @ Sun, 03 Jun 2018 12:57:40: 11000000 INFO @ Sun, 03 Jun 2018 12:57:43: 10000000 INFO @ Sun, 03 Jun 2018 12:57:43: 10000000 INFO @ Sun, 03 Jun 2018 12:57:47: 12000000 INFO @ Sun, 03 Jun 2018 12:57:50: 11000000 INFO @ Sun, 03 Jun 2018 12:57:50: 11000000 INFO @ Sun, 03 Jun 2018 12:57:54: 13000000 INFO @ Sun, 03 Jun 2018 12:57:58: 12000000 INFO @ Sun, 03 Jun 2018 12:57:58: 12000000 INFO @ Sun, 03 Jun 2018 12:58:01: 14000000 INFO @ Sun, 03 Jun 2018 12:58:05: 13000000 INFO @ Sun, 03 Jun 2018 12:58:06: 13000000 INFO @ Sun, 03 Jun 2018 12:58:08: 15000000 INFO @ Sun, 03 Jun 2018 12:58:13: 14000000 INFO @ Sun, 03 Jun 2018 12:58:13: 14000000 INFO @ Sun, 03 Jun 2018 12:58:14: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:58:14: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:58:14: #1 total tags in treatment: 7688246 INFO @ Sun, 03 Jun 2018 12:58:14: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:58:14: #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 12:58:14: #1 tags after filtering in treatment: 6770792 INFO @ Sun, 03 Jun 2018 12:58:14: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 12:58:14: #1 finished! INFO @ Sun, 03 Jun 2018 12:58:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:58:15: #2 number of paired peaks: 380 WARNING @ Sun, 03 Jun 2018 12:58:15: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Sun, 03 Jun 2018 12:58:15: start model_add_line... INFO @ Sun, 03 Jun 2018 12:58:15: start X-correlation... INFO @ Sun, 03 Jun 2018 12:58:15: end of X-cor INFO @ Sun, 03 Jun 2018 12:58:15: #2 finished! INFO @ Sun, 03 Jun 2018 12:58:15: #2 predicted fragment length is 165 bps INFO @ Sun, 03 Jun 2018 12:58:15: #2 alternative fragment length(s) may be 4,141,149,165 bps INFO @ Sun, 03 Jun 2018 12:58:15: #2.2 Generate R script for model : SRX4085356.05_model.r INFO @ Sun, 03 Jun 2018 12:58:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:58:21: 15000000 INFO @ Sun, 03 Jun 2018 12:58:21: 15000000 INFO @ Sun, 03 Jun 2018 12:58:27: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:58:27: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:58:27: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:58:27: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:58:27: #1 total tags in treatment: 7688246 INFO @ Sun, 03 Jun 2018 12:58:27: #1 total tags in treatment: 7688246 INFO @ Sun, 03 Jun 2018 12:58:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:58:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:58:27: #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 12:58:27: #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 12:58:27: #1 tags after filtering in treatment: 6770792 INFO @ Sun, 03 Jun 2018 12:58:27: #1 tags after filtering in treatment: 6770792 INFO @ Sun, 03 Jun 2018 12:58:27: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 12:58:27: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 12:58:27: #1 finished! INFO @ Sun, 03 Jun 2018 12:58:27: #1 finished! INFO @ Sun, 03 Jun 2018 12:58:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:58:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:58:28: #2 number of paired peaks: 380 WARNING @ Sun, 03 Jun 2018 12:58:28: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Sun, 03 Jun 2018 12:58:28: start model_add_line... INFO @ Sun, 03 Jun 2018 12:58:28: #2 number of paired peaks: 380 WARNING @ Sun, 03 Jun 2018 12:58:28: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Sun, 03 Jun 2018 12:58:28: start model_add_line... INFO @ Sun, 03 Jun 2018 12:58:28: start X-correlation... INFO @ Sun, 03 Jun 2018 12:58:28: end of X-cor INFO @ Sun, 03 Jun 2018 12:58:28: #2 finished! INFO @ Sun, 03 Jun 2018 12:58:28: #2 predicted fragment length is 165 bps INFO @ Sun, 03 Jun 2018 12:58:28: #2 alternative fragment length(s) may be 4,141,149,165 bps INFO @ Sun, 03 Jun 2018 12:58:28: #2.2 Generate R script for model : SRX4085356.20_model.r INFO @ Sun, 03 Jun 2018 12:58:28: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:58:28: start X-correlation... INFO @ Sun, 03 Jun 2018 12:58:28: end of X-cor INFO @ Sun, 03 Jun 2018 12:58:28: #2 finished! INFO @ Sun, 03 Jun 2018 12:58:28: #2 predicted fragment length is 165 bps INFO @ Sun, 03 Jun 2018 12:58:28: #2 alternative fragment length(s) may be 4,141,149,165 bps INFO @ Sun, 03 Jun 2018 12:58:28: #2.2 Generate R script for model : SRX4085356.10_model.r INFO @ Sun, 03 Jun 2018 12:58:28: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:58:31: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:39: #4 Write output xls file... SRX4085356.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:39: #4 Write peak in narrowPeak format file... SRX4085356.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:39: #4 Write summits bed file... SRX4085356.05_summits.bed INFO @ Sun, 03 Jun 2018 12:58:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1016 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:43: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:44: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:52: #4 Write output xls file... SRX4085356.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:52: #4 Write peak in narrowPeak format file... SRX4085356.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:52: #4 Write summits bed file... SRX4085356.20_summits.bed INFO @ Sun, 03 Jun 2018 12:58:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (263 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:52: #4 Write output xls file... SRX4085356.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:52: #4 Write peak in narrowPeak format file... SRX4085356.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:52: #4 Write summits bed file... SRX4085356.10_summits.bed INFO @ Sun, 03 Jun 2018 12:58:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。