Job ID = 9370015 sra ファイルのダウンロード中... Completed: 859256K bytes transferred in 16 seconds (436646K bits/sec), in 1 file, 2 directories. 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... Written 6426854 spots for /home/okishinya/chipatlas/results/ce10/SRX2035137/SRR4044261.sra Written 6426854 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:08 6426854 reads; of these: 6426854 (100.00%) were paired; of these: 1717889 (26.73%) aligned concordantly 0 times 4125127 (64.19%) aligned concordantly exactly 1 time 583838 (9.08%) aligned concordantly >1 times ---- 1717889 pairs aligned concordantly 0 times; of these: 331287 (19.28%) aligned discordantly 1 time ---- 1386602 pairs aligned 0 times concordantly or discordantly; of these: 2773204 mates make up the pairs; of these: 2631177 (94.88%) aligned 0 times 61398 (2.21%) aligned exactly 1 time 80629 (2.91%) aligned >1 times 79.53% overall alignment rate Time searching: 00:17:09 Overall time: 00:17:09 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] 331644 / 5035083 = 0.0659 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 @ Fri, 04 Aug 2017 12:13:41: # Command line: callpeak -t SRX2035137.bam -f BAM -g ce -n SRX2035137.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2035137.05 # format = BAM # ChIP-seq file = ['SRX2035137.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 @ Fri, 04 Aug 2017 12:13:41: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:13:41: # Command line: callpeak -t SRX2035137.bam -f BAM -g ce -n SRX2035137.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2035137.10 # format = BAM # ChIP-seq file = ['SRX2035137.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 @ Fri, 04 Aug 2017 12:13:41: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:13:41: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:13:41: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:13:41: # Command line: callpeak -t SRX2035137.bam -f BAM -g ce -n SRX2035137.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2035137.20 # format = BAM # ChIP-seq file = ['SRX2035137.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 @ Fri, 04 Aug 2017 12:13:41: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:13:41: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:13:57: 1000000 INFO @ Fri, 04 Aug 2017 12:13:57: 1000000 INFO @ Fri, 04 Aug 2017 12:13:58: 1000000 INFO @ Fri, 04 Aug 2017 12:14:12: 2000000 INFO @ Fri, 04 Aug 2017 12:14:13: 2000000 INFO @ Fri, 04 Aug 2017 12:14:14: 2000000 INFO @ Fri, 04 Aug 2017 12:14:26: 3000000 INFO @ Fri, 04 Aug 2017 12:14:27: 3000000 INFO @ Fri, 04 Aug 2017 12:14:31: 3000000 INFO @ Fri, 04 Aug 2017 12:14:39: 4000000 INFO @ Fri, 04 Aug 2017 12:14:41: 4000000 INFO @ Fri, 04 Aug 2017 12:14:49: 4000000 INFO @ Fri, 04 Aug 2017 12:14:51: 5000000 INFO @ Fri, 04 Aug 2017 12:14:56: 5000000 INFO @ Fri, 04 Aug 2017 12:15:03: 6000000 INFO @ Fri, 04 Aug 2017 12:15:07: 5000000 INFO @ Fri, 04 Aug 2017 12:15:10: 6000000 INFO @ Fri, 04 Aug 2017 12:15:15: 7000000 INFO @ Fri, 04 Aug 2017 12:15:25: 7000000 INFO @ Fri, 04 Aug 2017 12:15:25: 6000000 INFO @ Fri, 04 Aug 2017 12:15:26: 8000000 INFO @ Fri, 04 Aug 2017 12:15:38: 9000000 INFO @ Fri, 04 Aug 2017 12:15:39: 8000000 INFO @ Fri, 04 Aug 2017 12:15:43: 7000000 INFO @ Fri, 04 Aug 2017 12:15:45: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:15:45: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:15:45: #1 total tags in treatment: 4383666 INFO @ Fri, 04 Aug 2017 12:15:45: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:15:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:15:45: #1 tags after filtering in treatment: 4064534 INFO @ Fri, 04 Aug 2017 12:15:45: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 Aug 2017 12:15:45: #1 finished! INFO @ Fri, 04 Aug 2017 12:15:45: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:15:46: #2 number of paired peaks: 3297 INFO @ Fri, 04 Aug 2017 12:15:46: start model_add_line... INFO @ Fri, 04 Aug 2017 12:15:46: start X-correlation... INFO @ Fri, 04 Aug 2017 12:15:46: end of X-cor INFO @ Fri, 04 Aug 2017 12:15:46: #2 finished! INFO @ Fri, 04 Aug 2017 12:15:46: #2 predicted fragment length is 267 bps INFO @ Fri, 04 Aug 2017 12:15:46: #2 alternative fragment length(s) may be 267 bps INFO @ Fri, 04 Aug 2017 12:15:46: #2.2 Generate R script for model : SRX2035137.20_model.r INFO @ Fri, 04 Aug 2017 12:15:46: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:15:53: 9000000 INFO @ Fri, 04 Aug 2017 12:15:59: 8000000 INFO @ Fri, 04 Aug 2017 12:16:03: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:16:03: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:16:03: #1 total tags in treatment: 4383666 INFO @ Fri, 04 Aug 2017 12:16:03: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:16:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:16:03: #1 tags after filtering in treatment: 4064534 INFO @ Fri, 04 Aug 2017 12:16:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 Aug 2017 12:16:03: #1 finished! INFO @ Fri, 04 Aug 2017 12:16:03: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:16:03: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:16:04: #2 number of paired peaks: 3297 INFO @ Fri, 04 Aug 2017 12:16:04: start model_add_line... INFO @ Fri, 04 Aug 2017 12:16:04: start X-correlation... INFO @ Fri, 04 Aug 2017 12:16:04: end of X-cor INFO @ Fri, 04 Aug 2017 12:16:04: #2 finished! INFO @ Fri, 04 Aug 2017 12:16:04: #2 predicted fragment length is 267 bps INFO @ Fri, 04 Aug 2017 12:16:04: #2 alternative fragment length(s) may be 267 bps INFO @ Fri, 04 Aug 2017 12:16:04: #2.2 Generate R script for model : SRX2035137.05_model.r INFO @ Fri, 04 Aug 2017 12:16:04: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:16:12: #4 Write output xls file... SRX2035137.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:16:12: #4 Write peak in narrowPeak format file... SRX2035137.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:16:12: #4 Write summits bed file... SRX2035137.20_summits.bed INFO @ Fri, 04 Aug 2017 12:16:12: Done! pass1 - making usageList (6 chroms): 7 millis pass2 - checking and writing primary data (2005 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:16:15: 9000000 INFO @ Fri, 04 Aug 2017 12:16:20: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:16:24: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:16:24: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:16:24: #1 total tags in treatment: 4383666 INFO @ Fri, 04 Aug 2017 12:16:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:16:25: #1 tags after filtering in treatment: 4064534 INFO @ Fri, 04 Aug 2017 12:16:25: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 Aug 2017 12:16:25: #1 finished! INFO @ Fri, 04 Aug 2017 12:16:25: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:16:25: #2 number of paired peaks: 3297 INFO @ Fri, 04 Aug 2017 12:16:25: start model_add_line... INFO @ Fri, 04 Aug 2017 12:16:25: start X-correlation... INFO @ Fri, 04 Aug 2017 12:16:25: end of X-cor INFO @ Fri, 04 Aug 2017 12:16:25: #2 finished! INFO @ Fri, 04 Aug 2017 12:16:25: #2 predicted fragment length is 267 bps INFO @ Fri, 04 Aug 2017 12:16:25: #2 alternative fragment length(s) may be 267 bps INFO @ Fri, 04 Aug 2017 12:16:25: #2.2 Generate R script for model : SRX2035137.10_model.r INFO @ Fri, 04 Aug 2017 12:16:25: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:16:27: #4 Write output xls file... SRX2035137.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:16:27: #4 Write peak in narrowPeak format file... SRX2035137.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:16:27: #4 Write summits bed file... SRX2035137.05_summits.bed INFO @ Fri, 04 Aug 2017 12:16:28: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (3160 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:16:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:16:54: #4 Write output xls file... SRX2035137.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:16:54: #4 Write peak in narrowPeak format file... SRX2035137.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:16:54: #4 Write summits bed file... SRX2035137.10_summits.bed INFO @ Fri, 04 Aug 2017 12:16:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2545 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。