Job ID = 10714500 sra ファイルのダウンロード中... Completed: 907374K bytes transferred in 25 seconds (295658K 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 14395633 spots for /home/okishinya/chipatlas/results/ce10/SRX4085417/SRR7167446.sra Written 14395633 spots for /home/okishinya/chipatlas/results/ce10/SRX4085417/SRR7167446.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:30 14395633 reads; of these: 14395633 (100.00%) were paired; of these: 11446419 (79.51%) aligned concordantly 0 times 2501889 (17.38%) aligned concordantly exactly 1 time 447325 (3.11%) aligned concordantly >1 times ---- 11446419 pairs aligned concordantly 0 times; of these: 343921 (3.00%) aligned discordantly 1 time ---- 11102498 pairs aligned 0 times concordantly or discordantly; of these: 22204996 mates make up the pairs; of these: 16140937 (72.69%) aligned 0 times 5229142 (23.55%) aligned exactly 1 time 834917 (3.76%) aligned >1 times 43.94% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 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] 147728 / 3127519 = 0.0472 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 13:12:02: # Command line: callpeak -t SRX4085417.bam -f BAM -g ce -n SRX4085417.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085417.20 # format = BAM # ChIP-seq file = ['SRX4085417.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 13:12:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:12:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:12:02: # Command line: callpeak -t SRX4085417.bam -f BAM -g ce -n SRX4085417.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085417.10 # format = BAM # ChIP-seq file = ['SRX4085417.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 13:12:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:12:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:12:02: # Command line: callpeak -t SRX4085417.bam -f BAM -g ce -n SRX4085417.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085417.05 # format = BAM # ChIP-seq file = ['SRX4085417.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 13:12:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:12:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:12:08: 1000000 INFO @ Sun, 03 Jun 2018 13:12:09: 1000000 INFO @ Sun, 03 Jun 2018 13:12:09: 1000000 INFO @ Sun, 03 Jun 2018 13:12:14: 2000000 INFO @ Sun, 03 Jun 2018 13:12:15: 2000000 INFO @ Sun, 03 Jun 2018 13:12:15: 2000000 INFO @ Sun, 03 Jun 2018 13:12:21: 3000000 INFO @ Sun, 03 Jun 2018 13:12:21: 3000000 INFO @ Sun, 03 Jun 2018 13:12:21: 3000000 INFO @ Sun, 03 Jun 2018 13:12:27: 4000000 INFO @ Sun, 03 Jun 2018 13:12:27: 4000000 INFO @ Sun, 03 Jun 2018 13:12:28: 4000000 INFO @ Sun, 03 Jun 2018 13:12:33: 5000000 INFO @ Sun, 03 Jun 2018 13:12:34: 5000000 INFO @ Sun, 03 Jun 2018 13:12:34: 5000000 INFO @ Sun, 03 Jun 2018 13:12:39: 6000000 INFO @ Sun, 03 Jun 2018 13:12:40: 6000000 INFO @ Sun, 03 Jun 2018 13:12:40: 6000000 INFO @ Sun, 03 Jun 2018 13:12:45: 7000000 INFO @ Sun, 03 Jun 2018 13:12:46: 7000000 INFO @ Sun, 03 Jun 2018 13:12:47: 7000000 INFO @ Sun, 03 Jun 2018 13:12:51: 8000000 INFO @ Sun, 03 Jun 2018 13:12:52: 8000000 INFO @ Sun, 03 Jun 2018 13:12:53: 8000000 INFO @ Sun, 03 Jun 2018 13:12:57: 9000000 INFO @ Sun, 03 Jun 2018 13:12:59: 9000000 INFO @ Sun, 03 Jun 2018 13:12:59: 9000000 INFO @ Sun, 03 Jun 2018 13:13:03: 10000000 INFO @ Sun, 03 Jun 2018 13:13:05: 10000000 INFO @ Sun, 03 Jun 2018 13:13:06: 10000000 INFO @ Sun, 03 Jun 2018 13:13:10: 11000000 INFO @ Sun, 03 Jun 2018 13:13:11: 11000000 INFO @ Sun, 03 Jun 2018 13:13:12: 11000000 INFO @ Sun, 03 Jun 2018 13:13:16: 12000000 INFO @ Sun, 03 Jun 2018 13:13:17: 12000000 INFO @ Sun, 03 Jun 2018 13:13:18: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:13:18: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:13:18: #1 total tags in treatment: 2808865 INFO @ Sun, 03 Jun 2018 13:13:18: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:13:18: #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 13:13:18: #1 tags after filtering in treatment: 2689510 INFO @ Sun, 03 Jun 2018 13:13:18: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 03 Jun 2018 13:13:18: #1 finished! INFO @ Sun, 03 Jun 2018 13:13:18: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:13:18: #2 number of paired peaks: 363 WARNING @ Sun, 03 Jun 2018 13:13:18: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 03 Jun 2018 13:13:18: start model_add_line... INFO @ Sun, 03 Jun 2018 13:13:18: start X-correlation... INFO @ Sun, 03 Jun 2018 13:13:18: end of X-cor INFO @ Sun, 03 Jun 2018 13:13:18: #2 finished! INFO @ Sun, 03 Jun 2018 13:13:18: #2 predicted fragment length is 194 bps INFO @ Sun, 03 Jun 2018 13:13:18: #2 alternative fragment length(s) may be 95,128,165,194,225 bps INFO @ Sun, 03 Jun 2018 13:13:18: #2.2 Generate R script for model : SRX4085417.05_model.r INFO @ Sun, 03 Jun 2018 13:13:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:13:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:13:18: 12000000 INFO @ Sun, 03 Jun 2018 13:13:19: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:13:19: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:13:19: #1 total tags in treatment: 2808865 INFO @ Sun, 03 Jun 2018 13:13:19: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:13:19: #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 13:13:19: #1 tags after filtering in treatment: 2689510 INFO @ Sun, 03 Jun 2018 13:13:19: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 03 Jun 2018 13:13:19: #1 finished! INFO @ Sun, 03 Jun 2018 13:13:19: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:13:20: #2 number of paired peaks: 363 WARNING @ Sun, 03 Jun 2018 13:13:20: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 03 Jun 2018 13:13:20: start model_add_line... INFO @ Sun, 03 Jun 2018 13:13:20: start X-correlation... INFO @ Sun, 03 Jun 2018 13:13:20: end of X-cor INFO @ Sun, 03 Jun 2018 13:13:20: #2 finished! INFO @ Sun, 03 Jun 2018 13:13:20: #2 predicted fragment length is 194 bps INFO @ Sun, 03 Jun 2018 13:13:20: #2 alternative fragment length(s) may be 95,128,165,194,225 bps INFO @ Sun, 03 Jun 2018 13:13:20: #2.2 Generate R script for model : SRX4085417.20_model.r INFO @ Sun, 03 Jun 2018 13:13:20: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:13:21: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:13:21: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:13:21: #1 total tags in treatment: 2808865 INFO @ Sun, 03 Jun 2018 13:13:21: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:13:21: #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 13:13:21: #1 tags after filtering in treatment: 2689510 INFO @ Sun, 03 Jun 2018 13:13:21: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 03 Jun 2018 13:13:21: #1 finished! INFO @ Sun, 03 Jun 2018 13:13:21: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:13:21: #2 number of paired peaks: 363 WARNING @ Sun, 03 Jun 2018 13:13:21: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 03 Jun 2018 13:13:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:13:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:13:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:13:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:13:21: #2 predicted fragment length is 194 bps INFO @ Sun, 03 Jun 2018 13:13:21: #2 alternative fragment length(s) may be 95,128,165,194,225 bps INFO @ Sun, 03 Jun 2018 13:13:21: #2.2 Generate R script for model : SRX4085417.10_model.r INFO @ Sun, 03 Jun 2018 13:13:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:13:25: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:29: #4 Write output xls file... SRX4085417.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:29: #4 Write peak in narrowPeak format file... SRX4085417.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:29: #4 Write summits bed file... SRX4085417.05_summits.bed INFO @ Sun, 03 Jun 2018 13:13:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:13:30: #4 Write output xls file... SRX4085417.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:30: #4 Write peak in narrowPeak format file... SRX4085417.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:30: #4 Write summits bed file... SRX4085417.20_summits.bed INFO @ Sun, 03 Jun 2018 13:13:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:13:31: #4 Write output xls file... SRX4085417.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:31: #4 Write peak in narrowPeak format file... SRX4085417.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:31: #4 Write summits bed file... SRX4085417.10_summits.bed INFO @ Sun, 03 Jun 2018 13:13:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (151 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。