Job ID = 10714432 sra ファイルのダウンロード中... Completed: 1076153K bytes transferred in 28 seconds (304677K 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 15383484 spots for /home/okishinya/chipatlas/results/ce10/SRX4085348/SRR7167377.sra Written 15383484 spots for /home/okishinya/chipatlas/results/ce10/SRX4085348/SRR7167377.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: 00:14:45 15383484 reads; of these: 15383484 (100.00%) were paired; of these: 1376826 (8.95%) aligned concordantly 0 times 12277207 (79.81%) aligned concordantly exactly 1 time 1729451 (11.24%) aligned concordantly >1 times ---- 1376826 pairs aligned concordantly 0 times; of these: 90444 (6.57%) aligned discordantly 1 time ---- 1286382 pairs aligned 0 times concordantly or discordantly; of these: 2572764 mates make up the pairs; of these: 1664021 (64.68%) aligned 0 times 765891 (29.77%) aligned exactly 1 time 142852 (5.55%) aligned >1 times 94.59% overall alignment rate Time searching: 00:14:45 Overall time: 00:14:45 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 12 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] 2455564 / 14076260 = 0.1744 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 12:54:04: # Command line: callpeak -t SRX4085348.bam -f BAM -g ce -n SRX4085348.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085348.20 # format = BAM # ChIP-seq file = ['SRX4085348.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 12:54:04: # Command line: callpeak -t SRX4085348.bam -f BAM -g ce -n SRX4085348.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085348.05 # format = BAM # ChIP-seq file = ['SRX4085348.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 12:54:04: # Command line: callpeak -t SRX4085348.bam -f BAM -g ce -n SRX4085348.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085348.10 # format = BAM # ChIP-seq file = ['SRX4085348.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 12:54:04: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:04: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:04: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:04: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:04: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:04: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:10: 1000000 INFO @ Sun, 03 Jun 2018 12:54:10: 1000000 INFO @ Sun, 03 Jun 2018 12:54:10: 1000000 INFO @ Sun, 03 Jun 2018 12:54:16: 2000000 INFO @ Sun, 03 Jun 2018 12:54:16: 2000000 INFO @ Sun, 03 Jun 2018 12:54:16: 2000000 INFO @ Sun, 03 Jun 2018 12:54:23: 3000000 INFO @ Sun, 03 Jun 2018 12:54:23: 3000000 INFO @ Sun, 03 Jun 2018 12:54:23: 3000000 INFO @ Sun, 03 Jun 2018 12:54:29: 4000000 INFO @ Sun, 03 Jun 2018 12:54:29: 4000000 INFO @ Sun, 03 Jun 2018 12:54:29: 4000000 INFO @ Sun, 03 Jun 2018 12:54:35: 5000000 INFO @ Sun, 03 Jun 2018 12:54:35: 5000000 INFO @ Sun, 03 Jun 2018 12:54:36: 5000000 INFO @ Sun, 03 Jun 2018 12:54:42: 6000000 INFO @ Sun, 03 Jun 2018 12:54:42: 6000000 INFO @ Sun, 03 Jun 2018 12:54:42: 6000000 INFO @ Sun, 03 Jun 2018 12:54:48: 7000000 INFO @ Sun, 03 Jun 2018 12:54:48: 7000000 INFO @ Sun, 03 Jun 2018 12:54:48: 7000000 INFO @ Sun, 03 Jun 2018 12:54:54: 8000000 INFO @ Sun, 03 Jun 2018 12:54:54: 8000000 INFO @ Sun, 03 Jun 2018 12:54:55: 8000000 INFO @ Sun, 03 Jun 2018 12:55:01: 9000000 INFO @ Sun, 03 Jun 2018 12:55:01: 9000000 INFO @ Sun, 03 Jun 2018 12:55:01: 9000000 INFO @ Sun, 03 Jun 2018 12:55:07: 10000000 INFO @ Sun, 03 Jun 2018 12:55:07: 10000000 INFO @ Sun, 03 Jun 2018 12:55:07: 10000000 INFO @ Sun, 03 Jun 2018 12:55:13: 11000000 INFO @ Sun, 03 Jun 2018 12:55:13: 11000000 INFO @ Sun, 03 Jun 2018 12:55:13: 11000000 INFO @ Sun, 03 Jun 2018 12:55:19: 12000000 INFO @ Sun, 03 Jun 2018 12:55:20: 12000000 INFO @ Sun, 03 Jun 2018 12:55:20: 12000000 INFO @ Sun, 03 Jun 2018 12:55:26: 13000000 INFO @ Sun, 03 Jun 2018 12:55:26: 13000000 INFO @ Sun, 03 Jun 2018 12:55:26: 13000000 INFO @ Sun, 03 Jun 2018 12:55:32: 14000000 INFO @ Sun, 03 Jun 2018 12:55:32: 14000000 INFO @ Sun, 03 Jun 2018 12:55:32: 14000000 INFO @ Sun, 03 Jun 2018 12:55:38: 15000000 INFO @ Sun, 03 Jun 2018 12:55:38: 15000000 INFO @ Sun, 03 Jun 2018 12:55:39: 15000000 INFO @ Sun, 03 Jun 2018 12:55:44: 16000000 INFO @ Sun, 03 Jun 2018 12:55:45: 16000000 INFO @ Sun, 03 Jun 2018 12:55:45: 16000000 INFO @ Sun, 03 Jun 2018 12:55:50: 17000000 INFO @ Sun, 03 Jun 2018 12:55:51: 17000000 INFO @ Sun, 03 Jun 2018 12:55:51: 17000000 INFO @ Sun, 03 Jun 2018 12:55:56: 18000000 INFO @ Sun, 03 Jun 2018 12:55:57: 18000000 INFO @ Sun, 03 Jun 2018 12:55:57: 18000000 INFO @ Sun, 03 Jun 2018 12:56:03: 19000000 INFO @ Sun, 03 Jun 2018 12:56:04: 19000000 INFO @ Sun, 03 Jun 2018 12:56:04: 19000000 INFO @ Sun, 03 Jun 2018 12:56:09: 20000000 INFO @ Sun, 03 Jun 2018 12:56:10: 20000000 INFO @ Sun, 03 Jun 2018 12:56:10: 20000000 INFO @ Sun, 03 Jun 2018 12:56:15: 21000000 INFO @ Sun, 03 Jun 2018 12:56:16: 21000000 INFO @ Sun, 03 Jun 2018 12:56:16: 21000000 INFO @ Sun, 03 Jun 2018 12:56:21: 22000000 INFO @ Sun, 03 Jun 2018 12:56:22: 22000000 INFO @ Sun, 03 Jun 2018 12:56:22: 22000000 INFO @ Sun, 03 Jun 2018 12:56:27: 23000000 INFO @ Sun, 03 Jun 2018 12:56:29: 23000000 INFO @ Sun, 03 Jun 2018 12:56:29: 23000000 INFO @ Sun, 03 Jun 2018 12:56:33: 24000000 INFO @ Sun, 03 Jun 2018 12:56:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:56:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:56:34: #1 total tags in treatment: 11558755 INFO @ Sun, 03 Jun 2018 12:56:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:56:34: #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 12:56:34: #1 tags after filtering in treatment: 10215630 INFO @ Sun, 03 Jun 2018 12:56:34: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 12:56:34: #1 finished! INFO @ Sun, 03 Jun 2018 12:56:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:56:35: 24000000 INFO @ Sun, 03 Jun 2018 12:56:35: 24000000 INFO @ Sun, 03 Jun 2018 12:56:35: #2 number of paired peaks: 248 WARNING @ Sun, 03 Jun 2018 12:56:35: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 03 Jun 2018 12:56:35: start model_add_line... INFO @ Sun, 03 Jun 2018 12:56:36: start X-correlation... INFO @ Sun, 03 Jun 2018 12:56:36: end of X-cor INFO @ Sun, 03 Jun 2018 12:56:36: #2 finished! INFO @ Sun, 03 Jun 2018 12:56:36: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 12:56:36: #2 alternative fragment length(s) may be 4,107,142 bps INFO @ Sun, 03 Jun 2018 12:56:36: #2.2 Generate R script for model : SRX4085348.05_model.r INFO @ Sun, 03 Jun 2018 12:56:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:36: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:56:36: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:56:36: #1 total tags in treatment: 11558755 INFO @ Sun, 03 Jun 2018 12:56:36: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:56:36: #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 12:56:36: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:56:36: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:56:36: #1 total tags in treatment: 11558755 INFO @ Sun, 03 Jun 2018 12:56:36: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:56:36: #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 12:56:36: #1 tags after filtering in treatment: 10215630 INFO @ Sun, 03 Jun 2018 12:56:36: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 12:56:36: #1 finished! INFO @ Sun, 03 Jun 2018 12:56:36: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:56:36: #1 tags after filtering in treatment: 10215630 INFO @ Sun, 03 Jun 2018 12:56:36: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 12:56:36: #1 finished! INFO @ Sun, 03 Jun 2018 12:56:36: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:56:37: #2 number of paired peaks: 248 WARNING @ Sun, 03 Jun 2018 12:56:37: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 03 Jun 2018 12:56:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:56:37: #2 number of paired peaks: 248 WARNING @ Sun, 03 Jun 2018 12:56:37: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 03 Jun 2018 12:56:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:56:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:56:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:56:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:56:37: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 12:56:37: #2 alternative fragment length(s) may be 4,107,142 bps INFO @ Sun, 03 Jun 2018 12:56:37: #2.2 Generate R script for model : SRX4085348.10_model.r INFO @ Sun, 03 Jun 2018 12:56:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:56:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:56:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:56:37: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 12:56:37: #2 alternative fragment length(s) may be 4,107,142 bps INFO @ Sun, 03 Jun 2018 12:56:37: #2.2 Generate R script for model : SRX4085348.20_model.r INFO @ Sun, 03 Jun 2018 12:56:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:59: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:57:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:57:08: #4 Write output xls file... SRX4085348.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:57:08: #4 Write peak in narrowPeak format file... SRX4085348.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:57:08: #4 Write summits bed file... SRX4085348.05_summits.bed INFO @ Sun, 03 Jun 2018 12:57:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:57:11: #4 Write output xls file... SRX4085348.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:57:11: #4 Write peak in narrowPeak format file... SRX4085348.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:57:11: #4 Write summits bed file... SRX4085348.20_summits.bed INFO @ Sun, 03 Jun 2018 12:57:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:57:11: #4 Write output xls file... SRX4085348.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:57:11: #4 Write peak in narrowPeak format file... SRX4085348.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:57:11: #4 Write summits bed file... SRX4085348.10_summits.bed INFO @ Sun, 03 Jun 2018 12:57:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。