Job ID = 10714423 sra ファイルのダウンロード中... Completed: 1871111K bytes transferred in 45 seconds (333297K 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 26268412 spots for /home/okishinya/chipatlas/results/ce10/SRX4085339/SRR7167368.sra Written 26268412 spots for /home/okishinya/chipatlas/results/ce10/SRX4085339/SRR7167368.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: 00:27:05 26268412 reads; of these: 26268412 (100.00%) were paired; of these: 1947764 (7.41%) aligned concordantly 0 times 21625637 (82.33%) aligned concordantly exactly 1 time 2695011 (10.26%) aligned concordantly >1 times ---- 1947764 pairs aligned concordantly 0 times; of these: 155203 (7.97%) aligned discordantly 1 time ---- 1792561 pairs aligned 0 times concordantly or discordantly; of these: 3585122 mates make up the pairs; of these: 2412607 (67.29%) aligned 0 times 974841 (27.19%) aligned exactly 1 time 197674 (5.51%) aligned >1 times 95.41% overall alignment rate Time searching: 00:27:05 Overall time: 00:27:05 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 24 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] 10576553 / 24447186 = 0.4326 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 13:12:06: # Command line: callpeak -t SRX4085339.bam -f BAM -g ce -n SRX4085339.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085339.10 # format = BAM # ChIP-seq file = ['SRX4085339.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 13:12:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:12:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:12:06: # Command line: callpeak -t SRX4085339.bam -f BAM -g ce -n SRX4085339.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085339.05 # format = BAM # ChIP-seq file = ['SRX4085339.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 13:12:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:12:06: # Command line: callpeak -t SRX4085339.bam -f BAM -g ce -n SRX4085339.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085339.20 # format = BAM # ChIP-seq file = ['SRX4085339.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 13:12:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:12:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:12:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:12:12: 1000000 INFO @ Sun, 03 Jun 2018 13:12:12: 1000000 INFO @ Sun, 03 Jun 2018 13:12:13: 1000000 INFO @ Sun, 03 Jun 2018 13:12:18: 2000000 INFO @ Sun, 03 Jun 2018 13:12:18: 2000000 INFO @ Sun, 03 Jun 2018 13:12:19: 2000000 INFO @ Sun, 03 Jun 2018 13:12:24: 3000000 INFO @ Sun, 03 Jun 2018 13:12:24: 3000000 INFO @ Sun, 03 Jun 2018 13:12:25: 3000000 INFO @ Sun, 03 Jun 2018 13:12:31: 4000000 INFO @ Sun, 03 Jun 2018 13:12:31: 4000000 INFO @ Sun, 03 Jun 2018 13:12:31: 4000000 INFO @ Sun, 03 Jun 2018 13:12:37: 5000000 INFO @ Sun, 03 Jun 2018 13:12:37: 5000000 INFO @ Sun, 03 Jun 2018 13:12:37: 5000000 INFO @ Sun, 03 Jun 2018 13:12:43: 6000000 INFO @ Sun, 03 Jun 2018 13:12:43: 6000000 INFO @ Sun, 03 Jun 2018 13:12:44: 6000000 INFO @ Sun, 03 Jun 2018 13:12:49: 7000000 INFO @ Sun, 03 Jun 2018 13:12:49: 7000000 INFO @ Sun, 03 Jun 2018 13:12:50: 7000000 INFO @ Sun, 03 Jun 2018 13:12:55: 8000000 INFO @ Sun, 03 Jun 2018 13:12:55: 8000000 INFO @ Sun, 03 Jun 2018 13:12:56: 8000000 INFO @ Sun, 03 Jun 2018 13:13:01: 9000000 INFO @ Sun, 03 Jun 2018 13:13:01: 9000000 INFO @ Sun, 03 Jun 2018 13:13:02: 9000000 INFO @ Sun, 03 Jun 2018 13:13:07: 10000000 INFO @ Sun, 03 Jun 2018 13:13:07: 10000000 INFO @ Sun, 03 Jun 2018 13:13:08: 10000000 INFO @ Sun, 03 Jun 2018 13:13:13: 11000000 INFO @ Sun, 03 Jun 2018 13:13:13: 11000000 INFO @ Sun, 03 Jun 2018 13:13:14: 11000000 INFO @ Sun, 03 Jun 2018 13:13:19: 12000000 INFO @ Sun, 03 Jun 2018 13:13:19: 12000000 INFO @ Sun, 03 Jun 2018 13:13:20: 12000000 INFO @ Sun, 03 Jun 2018 13:13:25: 13000000 INFO @ Sun, 03 Jun 2018 13:13:25: 13000000 INFO @ Sun, 03 Jun 2018 13:13:26: 13000000 INFO @ Sun, 03 Jun 2018 13:13:30: 14000000 INFO @ Sun, 03 Jun 2018 13:13:30: 14000000 INFO @ Sun, 03 Jun 2018 13:13:32: 14000000 INFO @ Sun, 03 Jun 2018 13:13:36: 15000000 INFO @ Sun, 03 Jun 2018 13:13:36: 15000000 INFO @ Sun, 03 Jun 2018 13:13:38: 15000000 INFO @ Sun, 03 Jun 2018 13:13:42: 16000000 INFO @ Sun, 03 Jun 2018 13:13:42: 16000000 INFO @ Sun, 03 Jun 2018 13:13:44: 16000000 INFO @ Sun, 03 Jun 2018 13:13:48: 17000000 INFO @ Sun, 03 Jun 2018 13:13:48: 17000000 INFO @ Sun, 03 Jun 2018 13:13:50: 17000000 INFO @ Sun, 03 Jun 2018 13:13:55: 18000000 INFO @ Sun, 03 Jun 2018 13:13:55: 18000000 INFO @ Sun, 03 Jun 2018 13:13:56: 18000000 INFO @ Sun, 03 Jun 2018 13:14:00: 19000000 INFO @ Sun, 03 Jun 2018 13:14:00: 19000000 INFO @ Sun, 03 Jun 2018 13:14:02: 19000000 INFO @ Sun, 03 Jun 2018 13:14:06: 20000000 INFO @ Sun, 03 Jun 2018 13:14:06: 20000000 INFO @ Sun, 03 Jun 2018 13:14:08: 20000000 INFO @ Sun, 03 Jun 2018 13:14:13: 21000000 INFO @ Sun, 03 Jun 2018 13:14:13: 21000000 INFO @ Sun, 03 Jun 2018 13:14:14: 21000000 INFO @ Sun, 03 Jun 2018 13:14:18: 22000000 INFO @ Sun, 03 Jun 2018 13:14:18: 22000000 INFO @ Sun, 03 Jun 2018 13:14:20: 22000000 INFO @ Sun, 03 Jun 2018 13:14:24: 23000000 INFO @ Sun, 03 Jun 2018 13:14:24: 23000000 INFO @ Sun, 03 Jun 2018 13:14:26: 23000000 INFO @ Sun, 03 Jun 2018 13:14:30: 24000000 INFO @ Sun, 03 Jun 2018 13:14:30: 24000000 INFO @ Sun, 03 Jun 2018 13:14:33: 24000000 INFO @ Sun, 03 Jun 2018 13:14:36: 25000000 INFO @ Sun, 03 Jun 2018 13:14:36: 25000000 INFO @ Sun, 03 Jun 2018 13:14:39: 25000000 INFO @ Sun, 03 Jun 2018 13:14:42: 26000000 INFO @ Sun, 03 Jun 2018 13:14:42: 26000000 INFO @ Sun, 03 Jun 2018 13:14:45: 26000000 INFO @ Sun, 03 Jun 2018 13:14:48: 27000000 INFO @ Sun, 03 Jun 2018 13:14:48: 27000000 INFO @ Sun, 03 Jun 2018 13:14:51: 27000000 INFO @ Sun, 03 Jun 2018 13:14:54: 28000000 INFO @ Sun, 03 Jun 2018 13:14:54: 28000000 INFO @ Sun, 03 Jun 2018 13:14:57: 28000000 INFO @ Sun, 03 Jun 2018 13:14:59: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:59: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:59: #1 total tags in treatment: 13779877 INFO @ Sun, 03 Jun 2018 13:14:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:59: #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 13:14:59: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:59: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:59: #1 total tags in treatment: 13779877 INFO @ Sun, 03 Jun 2018 13:14:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:59: #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 13:15:00: #1 tags after filtering in treatment: 11952360 INFO @ Sun, 03 Jun 2018 13:15:00: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:15:00: #1 finished! INFO @ Sun, 03 Jun 2018 13:15:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:15:00: #1 tags after filtering in treatment: 11952360 INFO @ Sun, 03 Jun 2018 13:15:00: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:15:00: #1 finished! INFO @ Sun, 03 Jun 2018 13:15:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:15:01: #2 number of paired peaks: 316 WARNING @ Sun, 03 Jun 2018 13:15:01: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 03 Jun 2018 13:15:01: start model_add_line... INFO @ Sun, 03 Jun 2018 13:15:01: #2 number of paired peaks: 316 WARNING @ Sun, 03 Jun 2018 13:15:01: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 03 Jun 2018 13:15:01: start model_add_line... INFO @ Sun, 03 Jun 2018 13:15:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:15:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:15:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:15:01: #2 predicted fragment length is 142 bps INFO @ Sun, 03 Jun 2018 13:15:01: #2 alternative fragment length(s) may be 4,123,142 bps INFO @ Sun, 03 Jun 2018 13:15:01: #2.2 Generate R script for model : SRX4085339.05_model.r INFO @ Sun, 03 Jun 2018 13:15:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:15:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:15:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:15:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:15:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:15:01: #2 predicted fragment length is 142 bps INFO @ Sun, 03 Jun 2018 13:15:01: #2 alternative fragment length(s) may be 4,123,142 bps INFO @ Sun, 03 Jun 2018 13:15:01: #2.2 Generate R script for model : SRX4085339.20_model.r INFO @ Sun, 03 Jun 2018 13:15:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:15:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:15:03: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:15:03: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:15:03: #1 total tags in treatment: 13779877 INFO @ Sun, 03 Jun 2018 13:15:03: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:15:03: #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 13:15:03: #1 tags after filtering in treatment: 11952360 INFO @ Sun, 03 Jun 2018 13:15:03: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:15:03: #1 finished! INFO @ Sun, 03 Jun 2018 13:15:03: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:15:04: #2 number of paired peaks: 316 WARNING @ Sun, 03 Jun 2018 13:15:04: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 03 Jun 2018 13:15:04: start model_add_line... INFO @ Sun, 03 Jun 2018 13:15:04: start X-correlation... INFO @ Sun, 03 Jun 2018 13:15:04: end of X-cor INFO @ Sun, 03 Jun 2018 13:15:04: #2 finished! INFO @ Sun, 03 Jun 2018 13:15:04: #2 predicted fragment length is 142 bps INFO @ Sun, 03 Jun 2018 13:15:04: #2 alternative fragment length(s) may be 4,123,142 bps INFO @ Sun, 03 Jun 2018 13:15:04: #2.2 Generate R script for model : SRX4085339.10_model.r INFO @ Sun, 03 Jun 2018 13:15:04: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:15:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:15:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:15:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:15:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:15:38: #4 Write output xls file... SRX4085339.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:15:38: #4 Write peak in narrowPeak format file... SRX4085339.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:15:38: #4 Write summits bed file... SRX4085339.20_summits.bed INFO @ Sun, 03 Jun 2018 13:15:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:15:39: #4 Write output xls file... SRX4085339.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:15:39: #4 Write peak in narrowPeak format file... SRX4085339.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:15:39: #4 Write summits bed file... SRX4085339.05_summits.bed INFO @ Sun, 03 Jun 2018 13:15:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (626 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:15:41: #4 Write output xls file... SRX4085339.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:15:41: #4 Write peak in narrowPeak format file... SRX4085339.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:15:41: #4 Write summits bed file... SRX4085339.10_summits.bed INFO @ Sun, 03 Jun 2018 13:15:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (390 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。