Job ID = 10714466 sra ファイルのダウンロード中... Completed: 611651K bytes transferred in 18 seconds (274292K 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 9786578 spots for /home/okishinya/chipatlas/results/ce10/SRX4085382/SRR7167411.sra Written 9786578 spots for /home/okishinya/chipatlas/results/ce10/SRX4085382/SRR7167411.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: 00:05:58 9786578 reads; of these: 9786578 (100.00%) were paired; of these: 8215811 (83.95%) aligned concordantly 0 times 1346378 (13.76%) aligned concordantly exactly 1 time 224389 (2.29%) aligned concordantly >1 times ---- 8215811 pairs aligned concordantly 0 times; of these: 238458 (2.90%) aligned discordantly 1 time ---- 7977353 pairs aligned 0 times concordantly or discordantly; of these: 15954706 mates make up the pairs; of these: 11857938 (74.32%) aligned 0 times 3566522 (22.35%) aligned exactly 1 time 530246 (3.32%) aligned >1 times 39.42% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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_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] 101151 / 1680710 = 0.0602 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 12:49:09: # Command line: callpeak -t SRX4085382.bam -f BAM -g ce -n SRX4085382.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085382.05 # format = BAM # ChIP-seq file = ['SRX4085382.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 12:49:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:49:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:49:09: # Command line: callpeak -t SRX4085382.bam -f BAM -g ce -n SRX4085382.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085382.10 # format = BAM # ChIP-seq file = ['SRX4085382.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 12:49:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:49:09: # Command line: callpeak -t SRX4085382.bam -f BAM -g ce -n SRX4085382.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085382.20 # format = BAM # ChIP-seq file = ['SRX4085382.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 12:49:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:49:09: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:49:09: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:49:15: 1000000 INFO @ Sun, 03 Jun 2018 12:49:15: 1000000 INFO @ Sun, 03 Jun 2018 12:49:15: 1000000 INFO @ Sun, 03 Jun 2018 12:49:21: 2000000 INFO @ Sun, 03 Jun 2018 12:49:21: 2000000 INFO @ Sun, 03 Jun 2018 12:49:22: 2000000 INFO @ Sun, 03 Jun 2018 12:49:27: 3000000 INFO @ Sun, 03 Jun 2018 12:49:28: 3000000 INFO @ Sun, 03 Jun 2018 12:49:28: 3000000 INFO @ Sun, 03 Jun 2018 12:49:34: 4000000 INFO @ Sun, 03 Jun 2018 12:49:34: 4000000 INFO @ Sun, 03 Jun 2018 12:49:35: 4000000 INFO @ Sun, 03 Jun 2018 12:49:40: 5000000 INFO @ Sun, 03 Jun 2018 12:49:40: 5000000 INFO @ Sun, 03 Jun 2018 12:49:42: 5000000 INFO @ Sun, 03 Jun 2018 12:49:46: 6000000 INFO @ Sun, 03 Jun 2018 12:49:47: 6000000 INFO @ Sun, 03 Jun 2018 12:49:49: 6000000 INFO @ Sun, 03 Jun 2018 12:49:52: 7000000 INFO @ Sun, 03 Jun 2018 12:49:55: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:49:55: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:49:55: #1 total tags in treatment: 1475612 INFO @ Sun, 03 Jun 2018 12:49:55: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:49:55: #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 12:49:55: #1 tags after filtering in treatment: 1432339 INFO @ Sun, 03 Jun 2018 12:49:55: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 03 Jun 2018 12:49:55: #1 finished! INFO @ Sun, 03 Jun 2018 12:49:55: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:49:55: 7000000 INFO @ Sun, 03 Jun 2018 12:49:55: #2 number of paired peaks: 352 WARNING @ Sun, 03 Jun 2018 12:49:55: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sun, 03 Jun 2018 12:49:55: start model_add_line... INFO @ Sun, 03 Jun 2018 12:49:55: start X-correlation... INFO @ Sun, 03 Jun 2018 12:49:55: end of X-cor INFO @ Sun, 03 Jun 2018 12:49:55: #2 finished! INFO @ Sun, 03 Jun 2018 12:49:55: #2 predicted fragment length is 152 bps INFO @ Sun, 03 Jun 2018 12:49:55: #2 alternative fragment length(s) may be 127,152 bps INFO @ Sun, 03 Jun 2018 12:49:55: #2.2 Generate R script for model : SRX4085382.20_model.r INFO @ Sun, 03 Jun 2018 12:49:55: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:49:57: 7000000 INFO @ Sun, 03 Jun 2018 12:49:59: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:49:59: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:49:59: #1 total tags in treatment: 1475612 INFO @ Sun, 03 Jun 2018 12:49:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:49:59: #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 12:49:59: #1 tags after filtering in treatment: 1432339 INFO @ Sun, 03 Jun 2018 12:49:59: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 03 Jun 2018 12:49:59: #1 finished! INFO @ Sun, 03 Jun 2018 12:49:59: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:49:59: #2 number of paired peaks: 352 WARNING @ Sun, 03 Jun 2018 12:49:59: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sun, 03 Jun 2018 12:49:59: start model_add_line... INFO @ Sun, 03 Jun 2018 12:49:59: start X-correlation... INFO @ Sun, 03 Jun 2018 12:49:59: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:49:59: end of X-cor INFO @ Sun, 03 Jun 2018 12:49:59: #2 finished! INFO @ Sun, 03 Jun 2018 12:49:59: #2 predicted fragment length is 152 bps INFO @ Sun, 03 Jun 2018 12:49:59: #2 alternative fragment length(s) may be 127,152 bps INFO @ Sun, 03 Jun 2018 12:49:59: #2.2 Generate R script for model : SRX4085382.05_model.r INFO @ Sun, 03 Jun 2018 12:49:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:50:00: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:50:00: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:50:00: #1 total tags in treatment: 1475612 INFO @ Sun, 03 Jun 2018 12:50:00: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:50:00: #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 12:50:00: #1 tags after filtering in treatment: 1432339 INFO @ Sun, 03 Jun 2018 12:50:00: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 03 Jun 2018 12:50:00: #1 finished! INFO @ Sun, 03 Jun 2018 12:50:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:50:00: #2 number of paired peaks: 352 WARNING @ Sun, 03 Jun 2018 12:50:00: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sun, 03 Jun 2018 12:50:00: start model_add_line... INFO @ Sun, 03 Jun 2018 12:50:00: start X-correlation... INFO @ Sun, 03 Jun 2018 12:50:00: end of X-cor INFO @ Sun, 03 Jun 2018 12:50:00: #2 finished! INFO @ Sun, 03 Jun 2018 12:50:00: #2 predicted fragment length is 152 bps INFO @ Sun, 03 Jun 2018 12:50:00: #2 alternative fragment length(s) may be 127,152 bps INFO @ Sun, 03 Jun 2018 12:50:00: #2.2 Generate R script for model : SRX4085382.10_model.r INFO @ Sun, 03 Jun 2018 12:50:00: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:50:01: #4 Write output xls file... SRX4085382.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:50:01: #4 Write peak in narrowPeak format file... SRX4085382.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:50:01: #4 Write summits bed file... SRX4085382.20_summits.bed INFO @ Sun, 03 Jun 2018 12:50:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:50:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:50:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:50:04: #4 Write output xls file... SRX4085382.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:50:04: #4 Write peak in narrowPeak format file... SRX4085382.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:50:04: #4 Write summits bed file... SRX4085382.05_summits.bed INFO @ Sun, 03 Jun 2018 12:50:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:50:06: #4 Write output xls file... SRX4085382.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:50:06: #4 Write peak in narrowPeak format file... SRX4085382.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:50:06: #4 Write summits bed file... SRX4085382.10_summits.bed INFO @ Sun, 03 Jun 2018 12:50:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (109 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。