Job ID = 10714487 sra ファイルのダウンロード中... Completed: 6219705K bytes transferred in 92 seconds (550646K 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 85721229 spots for /home/okishinya/chipatlas/results/ce10/SRX4085403/SRR7167432.sra Written 85721229 spots for /home/okishinya/chipatlas/results/ce10/SRX4085403/SRR7167432.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: 01:18:33 85721229 reads; of these: 85721229 (100.00%) were paired; of these: 5547154 (6.47%) aligned concordantly 0 times 72812453 (84.94%) aligned concordantly exactly 1 time 7361622 (8.59%) aligned concordantly >1 times ---- 5547154 pairs aligned concordantly 0 times; of these: 410750 (7.40%) aligned discordantly 1 time ---- 5136404 pairs aligned 0 times concordantly or discordantly; of these: 10272808 mates make up the pairs; of these: 7597903 (73.96%) aligned 0 times 2218190 (21.59%) aligned exactly 1 time 456715 (4.45%) aligned >1 times 95.57% overall alignment rate Time searching: 01:18:33 Overall time: 01:18:33 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 68 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] 66382738 / 80475733 = 0.8249 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 14:46:17: # Command line: callpeak -t SRX4085403.bam -f BAM -g ce -n SRX4085403.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085403.05 # format = BAM # ChIP-seq file = ['SRX4085403.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 14:46:17: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:46:17: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:46:17: # Command line: callpeak -t SRX4085403.bam -f BAM -g ce -n SRX4085403.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085403.20 # format = BAM # ChIP-seq file = ['SRX4085403.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 14:46:17: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:46:17: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:46:17: # Command line: callpeak -t SRX4085403.bam -f BAM -g ce -n SRX4085403.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085403.10 # format = BAM # ChIP-seq file = ['SRX4085403.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 14:46:17: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:46:17: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:46:24: 1000000 INFO @ Sun, 03 Jun 2018 14:46:24: 1000000 INFO @ Sun, 03 Jun 2018 14:46:24: 1000000 INFO @ Sun, 03 Jun 2018 14:46:31: 2000000 INFO @ Sun, 03 Jun 2018 14:46:31: 2000000 INFO @ Sun, 03 Jun 2018 14:46:32: 2000000 INFO @ Sun, 03 Jun 2018 14:46:38: 3000000 INFO @ Sun, 03 Jun 2018 14:46:38: 3000000 INFO @ Sun, 03 Jun 2018 14:46:40: 3000000 INFO @ Sun, 03 Jun 2018 14:46:46: 4000000 INFO @ Sun, 03 Jun 2018 14:46:46: 4000000 INFO @ Sun, 03 Jun 2018 14:46:47: 4000000 INFO @ Sun, 03 Jun 2018 14:46:53: 5000000 INFO @ Sun, 03 Jun 2018 14:46:53: 5000000 INFO @ Sun, 03 Jun 2018 14:46:55: 5000000 INFO @ Sun, 03 Jun 2018 14:47:00: 6000000 INFO @ Sun, 03 Jun 2018 14:47:00: 6000000 INFO @ Sun, 03 Jun 2018 14:47:02: 6000000 INFO @ Sun, 03 Jun 2018 14:47:07: 7000000 INFO @ Sun, 03 Jun 2018 14:47:07: 7000000 INFO @ Sun, 03 Jun 2018 14:47:10: 7000000 INFO @ Sun, 03 Jun 2018 14:47:14: 8000000 INFO @ Sun, 03 Jun 2018 14:47:14: 8000000 INFO @ Sun, 03 Jun 2018 14:47:17: 8000000 INFO @ Sun, 03 Jun 2018 14:47:21: 9000000 INFO @ Sun, 03 Jun 2018 14:47:21: 9000000 INFO @ Sun, 03 Jun 2018 14:47:25: 9000000 INFO @ Sun, 03 Jun 2018 14:47:29: 10000000 INFO @ Sun, 03 Jun 2018 14:47:29: 10000000 INFO @ Sun, 03 Jun 2018 14:47:33: 10000000 INFO @ Sun, 03 Jun 2018 14:47:36: 11000000 INFO @ Sun, 03 Jun 2018 14:47:36: 11000000 INFO @ Sun, 03 Jun 2018 14:47:40: 11000000 INFO @ Sun, 03 Jun 2018 14:47:43: 12000000 INFO @ Sun, 03 Jun 2018 14:47:43: 12000000 INFO @ Sun, 03 Jun 2018 14:47:48: 12000000 INFO @ Sun, 03 Jun 2018 14:47:50: 13000000 INFO @ Sun, 03 Jun 2018 14:47:50: 13000000 INFO @ Sun, 03 Jun 2018 14:47:55: 13000000 INFO @ Sun, 03 Jun 2018 14:47:58: 14000000 INFO @ Sun, 03 Jun 2018 14:47:58: 14000000 INFO @ Sun, 03 Jun 2018 14:48:03: 14000000 INFO @ Sun, 03 Jun 2018 14:48:05: 15000000 INFO @ Sun, 03 Jun 2018 14:48:05: 15000000 INFO @ Sun, 03 Jun 2018 14:48:11: 15000000 INFO @ Sun, 03 Jun 2018 14:48:12: 16000000 INFO @ Sun, 03 Jun 2018 14:48:12: 16000000 INFO @ Sun, 03 Jun 2018 14:48:18: 16000000 INFO @ Sun, 03 Jun 2018 14:48:19: 17000000 INFO @ Sun, 03 Jun 2018 14:48:19: 17000000 INFO @ Sun, 03 Jun 2018 14:48:26: 17000000 INFO @ Sun, 03 Jun 2018 14:48:26: 18000000 INFO @ Sun, 03 Jun 2018 14:48:26: 18000000 INFO @ Sun, 03 Jun 2018 14:48:33: 18000000 INFO @ Sun, 03 Jun 2018 14:48:33: 19000000 INFO @ Sun, 03 Jun 2018 14:48:33: 19000000 INFO @ Sun, 03 Jun 2018 14:48:41: 19000000 INFO @ Sun, 03 Jun 2018 14:48:41: 20000000 INFO @ Sun, 03 Jun 2018 14:48:41: 20000000 INFO @ Sun, 03 Jun 2018 14:48:48: 21000000 INFO @ Sun, 03 Jun 2018 14:48:48: 21000000 INFO @ Sun, 03 Jun 2018 14:48:48: 20000000 INFO @ Sun, 03 Jun 2018 14:48:56: 22000000 INFO @ Sun, 03 Jun 2018 14:48:56: 22000000 INFO @ Sun, 03 Jun 2018 14:48:56: 21000000 INFO @ Sun, 03 Jun 2018 14:49:03: 23000000 INFO @ Sun, 03 Jun 2018 14:49:03: 23000000 INFO @ Sun, 03 Jun 2018 14:49:03: 22000000 INFO @ Sun, 03 Jun 2018 14:49:11: 24000000 INFO @ Sun, 03 Jun 2018 14:49:11: 24000000 INFO @ Sun, 03 Jun 2018 14:49:11: 23000000 INFO @ Sun, 03 Jun 2018 14:49:18: 25000000 INFO @ Sun, 03 Jun 2018 14:49:18: 25000000 INFO @ Sun, 03 Jun 2018 14:49:18: 24000000 INFO @ Sun, 03 Jun 2018 14:49:25: 26000000 INFO @ Sun, 03 Jun 2018 14:49:25: 26000000 INFO @ Sun, 03 Jun 2018 14:49:26: 25000000 INFO @ Sun, 03 Jun 2018 14:49:33: 27000000 INFO @ Sun, 03 Jun 2018 14:49:33: 27000000 INFO @ Sun, 03 Jun 2018 14:49:33: 26000000 INFO @ Sun, 03 Jun 2018 14:49:40: 28000000 INFO @ Sun, 03 Jun 2018 14:49:40: 28000000 INFO @ Sun, 03 Jun 2018 14:49:40: 27000000 INFO @ Sun, 03 Jun 2018 14:49:47: 29000000 INFO @ Sun, 03 Jun 2018 14:49:47: 29000000 INFO @ Sun, 03 Jun 2018 14:49:48: 28000000 INFO @ Sun, 03 Jun 2018 14:49:54: 30000000 INFO @ Sun, 03 Jun 2018 14:49:54: 30000000 INFO @ Sun, 03 Jun 2018 14:49:55: 29000000 INFO @ Sun, 03 Jun 2018 14:50:01: 31000000 INFO @ Sun, 03 Jun 2018 14:50:01: 31000000 INFO @ Sun, 03 Jun 2018 14:50:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:50:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:50:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:50:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:50:01: #1 total tags in treatment: 14030379 INFO @ Sun, 03 Jun 2018 14:50:01: #1 total tags in treatment: 14030379 INFO @ Sun, 03 Jun 2018 14:50:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:50:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:50:01: #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 14:50:01: #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 14:50:02: #1 tags after filtering in treatment: 10518885 INFO @ Sun, 03 Jun 2018 14:50:02: #1 tags after filtering in treatment: 10518885 INFO @ Sun, 03 Jun 2018 14:50:02: #1 Redundant rate of treatment: 0.25 INFO @ Sun, 03 Jun 2018 14:50:02: #1 Redundant rate of treatment: 0.25 INFO @ Sun, 03 Jun 2018 14:50:02: #1 finished! INFO @ Sun, 03 Jun 2018 14:50:02: #1 finished! INFO @ Sun, 03 Jun 2018 14:50:02: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:50:02: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:50:02: 30000000 INFO @ Sun, 03 Jun 2018 14:50:02: #2 number of paired peaks: 761 WARNING @ Sun, 03 Jun 2018 14:50:02: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Sun, 03 Jun 2018 14:50:02: start model_add_line... INFO @ Sun, 03 Jun 2018 14:50:03: #2 number of paired peaks: 761 WARNING @ Sun, 03 Jun 2018 14:50:03: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Sun, 03 Jun 2018 14:50:03: start model_add_line... INFO @ Sun, 03 Jun 2018 14:50:03: start X-correlation... INFO @ Sun, 03 Jun 2018 14:50:03: end of X-cor INFO @ Sun, 03 Jun 2018 14:50:03: #2 finished! INFO @ Sun, 03 Jun 2018 14:50:03: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 14:50:03: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 03 Jun 2018 14:50:03: #2.2 Generate R script for model : SRX4085403.05_model.r INFO @ Sun, 03 Jun 2018 14:50:03: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:50:03: start X-correlation... INFO @ Sun, 03 Jun 2018 14:50:03: end of X-cor INFO @ Sun, 03 Jun 2018 14:50:03: #2 finished! INFO @ Sun, 03 Jun 2018 14:50:03: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 14:50:03: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 03 Jun 2018 14:50:03: #2.2 Generate R script for model : SRX4085403.20_model.r INFO @ Sun, 03 Jun 2018 14:50:03: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:50:09: 31000000 INFO @ Sun, 03 Jun 2018 14:50:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:50:09: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:50:09: #1 total tags in treatment: 14030379 INFO @ Sun, 03 Jun 2018 14:50:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:50:09: #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 14:50:10: #1 tags after filtering in treatment: 10518885 INFO @ Sun, 03 Jun 2018 14:50:10: #1 Redundant rate of treatment: 0.25 INFO @ Sun, 03 Jun 2018 14:50:10: #1 finished! INFO @ Sun, 03 Jun 2018 14:50:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:50:10: #2 number of paired peaks: 761 WARNING @ Sun, 03 Jun 2018 14:50:10: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Sun, 03 Jun 2018 14:50:10: start model_add_line... INFO @ Sun, 03 Jun 2018 14:50:11: start X-correlation... INFO @ Sun, 03 Jun 2018 14:50:11: end of X-cor INFO @ Sun, 03 Jun 2018 14:50:11: #2 finished! INFO @ Sun, 03 Jun 2018 14:50:11: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 14:50:11: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 03 Jun 2018 14:50:11: #2.2 Generate R script for model : SRX4085403.10_model.r INFO @ Sun, 03 Jun 2018 14:50:11: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:50:25: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:50:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:50:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:50:38: #4 Write output xls file... SRX4085403.05_peaks.xls INFO @ Sun, 03 Jun 2018 14:50:38: #4 Write peak in narrowPeak format file... SRX4085403.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:50:38: #4 Write summits bed file... SRX4085403.05_summits.bed INFO @ Sun, 03 Jun 2018 14:50:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4913 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 14:50:40: #4 Write output xls file... SRX4085403.20_peaks.xls INFO @ Sun, 03 Jun 2018 14:50:40: #4 Write peak in narrowPeak format file... SRX4085403.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:50:40: #4 Write summits bed file... SRX4085403.20_summits.bed INFO @ Sun, 03 Jun 2018 14:50:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1753 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 14:50:47: #4 Write output xls file... SRX4085403.10_peaks.xls INFO @ Sun, 03 Jun 2018 14:50:47: #4 Write peak in narrowPeak format file... SRX4085403.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:50:47: #4 Write summits bed file... SRX4085403.10_summits.bed INFO @ Sun, 03 Jun 2018 14:50:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3089 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。