Job ID = 10714477 sra ファイルのダウンロード中... Completed: 2020595K bytes transferred in 43 seconds (378711K 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 29930971 spots for /home/okishinya/chipatlas/results/ce10/SRX4085393/SRR7167422.sra Written 29930971 spots for /home/okishinya/chipatlas/results/ce10/SRX4085393/SRR7167422.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: 00:27:07 29930971 reads; of these: 29930971 (100.00%) were paired; of these: 2546414 (8.51%) aligned concordantly 0 times 25262406 (84.40%) aligned concordantly exactly 1 time 2122151 (7.09%) aligned concordantly >1 times ---- 2546414 pairs aligned concordantly 0 times; of these: 169104 (6.64%) aligned discordantly 1 time ---- 2377310 pairs aligned 0 times concordantly or discordantly; of these: 4754620 mates make up the pairs; of these: 3809284 (80.12%) aligned 0 times 752505 (15.83%) aligned exactly 1 time 192831 (4.06%) aligned >1 times 93.64% overall alignment rate Time searching: 00:27:07 Overall time: 00:27:07 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 24 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] 22232383 / 27480566 = 0.8090 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 13:23:30: # Command line: callpeak -t SRX4085393.bam -f BAM -g ce -n SRX4085393.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085393.20 # format = BAM # ChIP-seq file = ['SRX4085393.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 13:23:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:23:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:23:30: # Command line: callpeak -t SRX4085393.bam -f BAM -g ce -n SRX4085393.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085393.10 # format = BAM # ChIP-seq file = ['SRX4085393.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 13:23:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:23:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:23:30: # Command line: callpeak -t SRX4085393.bam -f BAM -g ce -n SRX4085393.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085393.05 # format = BAM # ChIP-seq file = ['SRX4085393.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 13:23:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:23:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:23:37: 1000000 INFO @ Sun, 03 Jun 2018 13:23:37: 1000000 INFO @ Sun, 03 Jun 2018 13:23:37: 1000000 INFO @ Sun, 03 Jun 2018 13:23:44: 2000000 INFO @ Sun, 03 Jun 2018 13:23:44: 2000000 INFO @ Sun, 03 Jun 2018 13:23:44: 2000000 INFO @ Sun, 03 Jun 2018 13:23:51: 3000000 INFO @ Sun, 03 Jun 2018 13:23:51: 3000000 INFO @ Sun, 03 Jun 2018 13:23:51: 3000000 INFO @ Sun, 03 Jun 2018 13:23:58: 4000000 INFO @ Sun, 03 Jun 2018 13:23:58: 4000000 INFO @ Sun, 03 Jun 2018 13:23:58: 4000000 INFO @ Sun, 03 Jun 2018 13:24:05: 5000000 INFO @ Sun, 03 Jun 2018 13:24:05: 5000000 INFO @ Sun, 03 Jun 2018 13:24:05: 5000000 INFO @ Sun, 03 Jun 2018 13:24:12: 6000000 INFO @ Sun, 03 Jun 2018 13:24:12: 6000000 INFO @ Sun, 03 Jun 2018 13:24:12: 6000000 INFO @ Sun, 03 Jun 2018 13:24:19: 7000000 INFO @ Sun, 03 Jun 2018 13:24:19: 7000000 INFO @ Sun, 03 Jun 2018 13:24:19: 7000000 INFO @ Sun, 03 Jun 2018 13:24:26: 8000000 INFO @ Sun, 03 Jun 2018 13:24:26: 8000000 INFO @ Sun, 03 Jun 2018 13:24:26: 8000000 INFO @ Sun, 03 Jun 2018 13:24:34: 9000000 INFO @ Sun, 03 Jun 2018 13:24:34: 9000000 INFO @ Sun, 03 Jun 2018 13:24:34: 9000000 INFO @ Sun, 03 Jun 2018 13:24:41: 10000000 INFO @ Sun, 03 Jun 2018 13:24:41: 10000000 INFO @ Sun, 03 Jun 2018 13:24:41: 10000000 INFO @ Sun, 03 Jun 2018 13:24:48: 11000000 INFO @ Sun, 03 Jun 2018 13:24:48: 11000000 INFO @ Sun, 03 Jun 2018 13:24:48: 11000000 INFO @ Sun, 03 Jun 2018 13:24:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:52: #1 total tags in treatment: 5223388 INFO @ Sun, 03 Jun 2018 13:24:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:52: #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 13:24:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:52: #1 total tags in treatment: 5223388 INFO @ Sun, 03 Jun 2018 13:24:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:52: #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 13:24:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:52: #1 total tags in treatment: 5223388 INFO @ Sun, 03 Jun 2018 13:24:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:52: #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 13:24:52: #1 tags after filtering in treatment: 4147074 INFO @ Sun, 03 Jun 2018 13:24:52: #1 Redundant rate of treatment: 0.21 INFO @ Sun, 03 Jun 2018 13:24:52: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:52: #1 tags after filtering in treatment: 4147074 INFO @ Sun, 03 Jun 2018 13:24:52: #1 Redundant rate of treatment: 0.21 INFO @ Sun, 03 Jun 2018 13:24:52: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:52: #1 tags after filtering in treatment: 4147074 INFO @ Sun, 03 Jun 2018 13:24:52: #1 Redundant rate of treatment: 0.21 INFO @ Sun, 03 Jun 2018 13:24:52: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:52: #2 number of paired peaks: 603 WARNING @ Sun, 03 Jun 2018 13:24:52: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:52: #2 number of paired peaks: 603 WARNING @ Sun, 03 Jun 2018 13:24:52: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:52: #2 number of paired peaks: 603 WARNING @ Sun, 03 Jun 2018 13:24:52: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:52: #2 predicted fragment length is 161 bps INFO @ Sun, 03 Jun 2018 13:24:52: #2 alternative fragment length(s) may be 4,161 bps INFO @ Sun, 03 Jun 2018 13:24:52: #2.2 Generate R script for model : SRX4085393.10_model.r INFO @ Sun, 03 Jun 2018 13:24:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:24:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:52: #2 predicted fragment length is 161 bps INFO @ Sun, 03 Jun 2018 13:24:52: #2 alternative fragment length(s) may be 4,161 bps INFO @ Sun, 03 Jun 2018 13:24:52: #2.2 Generate R script for model : SRX4085393.20_model.r INFO @ Sun, 03 Jun 2018 13:24:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:52: #2 predicted fragment length is 161 bps INFO @ Sun, 03 Jun 2018 13:24:52: #2 alternative fragment length(s) may be 4,161 bps INFO @ Sun, 03 Jun 2018 13:24:52: #2.2 Generate R script for model : SRX4085393.05_model.r INFO @ Sun, 03 Jun 2018 13:24:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:24:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:25:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:08: #4 Write output xls file... SRX4085393.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:08: #4 Write peak in narrowPeak format file... SRX4085393.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:08: #4 Write summits bed file... SRX4085393.20_summits.bed INFO @ Sun, 03 Jun 2018 13:25:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:25:10: #4 Write output xls file... SRX4085393.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:10: #4 Write peak in narrowPeak format file... SRX4085393.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:10: #4 Write summits bed file... SRX4085393.10_summits.bed INFO @ Sun, 03 Jun 2018 13:25:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (316 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:25:10: #4 Write output xls file... SRX4085393.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:10: #4 Write peak in narrowPeak format file... SRX4085393.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:10: #4 Write summits bed file... SRX4085393.05_summits.bed INFO @ Sun, 03 Jun 2018 13:25:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (513 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。