Job ID = 10714508 sra ファイルのダウンロード中... Completed: 862914K bytes transferred in 9 seconds (734976K 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 13497903 spots for /home/okishinya/chipatlas/results/ce10/SRX4085424/SRR7167453.sra Written 13497903 spots for /home/okishinya/chipatlas/results/ce10/SRX4085424/SRR7167453.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: 00:08:53 13497903 reads; of these: 13497903 (100.00%) were paired; of these: 10267950 (76.07%) aligned concordantly 0 times 2808709 (20.81%) aligned concordantly exactly 1 time 421244 (3.12%) aligned concordantly >1 times ---- 10267950 pairs aligned concordantly 0 times; of these: 214057 (2.08%) aligned discordantly 1 time ---- 10053893 pairs aligned 0 times concordantly or discordantly; of these: 20107786 mates make up the pairs; of these: 14137369 (70.31%) aligned 0 times 5320414 (26.46%) aligned exactly 1 time 650003 (3.23%) aligned >1 times 47.63% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 182734 / 3328206 = 0.0549 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 13:15:49: # Command line: callpeak -t SRX4085424.bam -f BAM -g ce -n SRX4085424.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085424.05 # format = BAM # ChIP-seq file = ['SRX4085424.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 13:15:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:49: # Command line: callpeak -t SRX4085424.bam -f BAM -g ce -n SRX4085424.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085424.10 # format = BAM # ChIP-seq file = ['SRX4085424.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 13:15:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:49: # Command line: callpeak -t SRX4085424.bam -f BAM -g ce -n SRX4085424.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085424.20 # format = BAM # ChIP-seq file = ['SRX4085424.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 13:15:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:55: 1000000 INFO @ Sun, 03 Jun 2018 13:15:56: 1000000 INFO @ Sun, 03 Jun 2018 13:15:56: 1000000 INFO @ Sun, 03 Jun 2018 13:16:01: 2000000 INFO @ Sun, 03 Jun 2018 13:16:02: 2000000 INFO @ Sun, 03 Jun 2018 13:16:02: 2000000 INFO @ Sun, 03 Jun 2018 13:16:06: 3000000 INFO @ Sun, 03 Jun 2018 13:16:09: 3000000 INFO @ Sun, 03 Jun 2018 13:16:09: 3000000 INFO @ Sun, 03 Jun 2018 13:16:12: 4000000 INFO @ Sun, 03 Jun 2018 13:16:15: 4000000 INFO @ Sun, 03 Jun 2018 13:16:15: 4000000 INFO @ Sun, 03 Jun 2018 13:16:18: 5000000 INFO @ Sun, 03 Jun 2018 13:16:22: 5000000 INFO @ Sun, 03 Jun 2018 13:16:22: 5000000 INFO @ Sun, 03 Jun 2018 13:16:23: 6000000 INFO @ Sun, 03 Jun 2018 13:16:29: 6000000 INFO @ Sun, 03 Jun 2018 13:16:29: 6000000 INFO @ Sun, 03 Jun 2018 13:16:29: 7000000 INFO @ Sun, 03 Jun 2018 13:16:35: 8000000 INFO @ Sun, 03 Jun 2018 13:16:35: 7000000 INFO @ Sun, 03 Jun 2018 13:16:35: 7000000 INFO @ Sun, 03 Jun 2018 13:16:41: 9000000 INFO @ Sun, 03 Jun 2018 13:16:41: 8000000 INFO @ Sun, 03 Jun 2018 13:16:41: 8000000 INFO @ Sun, 03 Jun 2018 13:16:46: 10000000 INFO @ Sun, 03 Jun 2018 13:16:47: 9000000 INFO @ Sun, 03 Jun 2018 13:16:47: 9000000 INFO @ Sun, 03 Jun 2018 13:16:52: 11000000 INFO @ Sun, 03 Jun 2018 13:16:54: 10000000 INFO @ Sun, 03 Jun 2018 13:16:54: 10000000 INFO @ Sun, 03 Jun 2018 13:16:58: 12000000 INFO @ Sun, 03 Jun 2018 13:17:00: 11000000 INFO @ Sun, 03 Jun 2018 13:17:00: 11000000 INFO @ Sun, 03 Jun 2018 13:17:00: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:17:00: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:17:00: #1 total tags in treatment: 3050449 INFO @ Sun, 03 Jun 2018 13:17:00: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:17:00: #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 13:17:00: #1 tags after filtering in treatment: 2866080 INFO @ Sun, 03 Jun 2018 13:17:00: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 13:17:00: #1 finished! INFO @ Sun, 03 Jun 2018 13:17:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:17:00: #2 number of paired peaks: 271 WARNING @ Sun, 03 Jun 2018 13:17:00: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 03 Jun 2018 13:17:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:17:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:17:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:17:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:17:01: #2 predicted fragment length is 162 bps INFO @ Sun, 03 Jun 2018 13:17:01: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 03 Jun 2018 13:17:01: #2.2 Generate R script for model : SRX4085424.05_model.r INFO @ Sun, 03 Jun 2018 13:17:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:17:06: 12000000 INFO @ Sun, 03 Jun 2018 13:17:06: 12000000 INFO @ Sun, 03 Jun 2018 13:17:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:17:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:17:09: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:17:09: #1 total tags in treatment: 3050449 INFO @ Sun, 03 Jun 2018 13:17:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:17:09: #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 13:17:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:17:09: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:17:09: #1 total tags in treatment: 3050449 INFO @ Sun, 03 Jun 2018 13:17:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:17:09: #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 13:17:09: #1 tags after filtering in treatment: 2866080 INFO @ Sun, 03 Jun 2018 13:17:09: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 13:17:09: #1 finished! INFO @ Sun, 03 Jun 2018 13:17:09: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:17:09: #1 tags after filtering in treatment: 2866080 INFO @ Sun, 03 Jun 2018 13:17:09: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 13:17:09: #1 finished! INFO @ Sun, 03 Jun 2018 13:17:09: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:17:09: #2 number of paired peaks: 271 WARNING @ Sun, 03 Jun 2018 13:17:09: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 03 Jun 2018 13:17:09: start model_add_line... INFO @ Sun, 03 Jun 2018 13:17:09: #2 number of paired peaks: 271 WARNING @ Sun, 03 Jun 2018 13:17:09: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Sun, 03 Jun 2018 13:17:09: start model_add_line... INFO @ Sun, 03 Jun 2018 13:17:09: start X-correlation... INFO @ Sun, 03 Jun 2018 13:17:09: start X-correlation... INFO @ Sun, 03 Jun 2018 13:17:09: end of X-cor INFO @ Sun, 03 Jun 2018 13:17:09: #2 finished! INFO @ Sun, 03 Jun 2018 13:17:09: #2 predicted fragment length is 162 bps INFO @ Sun, 03 Jun 2018 13:17:09: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 03 Jun 2018 13:17:09: #2.2 Generate R script for model : SRX4085424.20_model.r INFO @ Sun, 03 Jun 2018 13:17:09: end of X-cor INFO @ Sun, 03 Jun 2018 13:17:09: #2 finished! INFO @ Sun, 03 Jun 2018 13:17:09: #2 predicted fragment length is 162 bps INFO @ Sun, 03 Jun 2018 13:17:09: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 03 Jun 2018 13:17:09: #2.2 Generate R script for model : SRX4085424.10_model.r INFO @ Sun, 03 Jun 2018 13:17:09: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:17:09: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:17:12: #4 Write output xls file... SRX4085424.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:17:12: #4 Write peak in narrowPeak format file... SRX4085424.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:17:12: #4 Write summits bed file... SRX4085424.05_summits.bed INFO @ Sun, 03 Jun 2018 13:17:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (656 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:17:16: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:17:16: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:17:20: #4 Write output xls file... SRX4085424.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:17:20: #4 Write peak in narrowPeak format file... SRX4085424.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:17:20: #4 Write summits bed file... SRX4085424.20_summits.bed INFO @ Sun, 03 Jun 2018 13:17:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:17:20: #4 Write output xls file... SRX4085424.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:17:20: #4 Write peak in narrowPeak format file... SRX4085424.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:17:20: #4 Write summits bed file... SRX4085424.10_summits.bed INFO @ Sun, 03 Jun 2018 13:17:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (206 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。