Job ID = 10714444 sra ファイルのダウンロード中... Completed: 1424760K bytes transferred in 19 seconds (604280K 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 19703192 spots for /home/okishinya/chipatlas/results/ce10/SRX4085360/SRR7167389.sra Written 19703192 spots for /home/okishinya/chipatlas/results/ce10/SRX4085360/SRR7167389.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: 00:20:54 19703192 reads; of these: 19703192 (100.00%) were paired; of these: 1150406 (5.84%) aligned concordantly 0 times 16150413 (81.97%) aligned concordantly exactly 1 time 2402373 (12.19%) aligned concordantly >1 times ---- 1150406 pairs aligned concordantly 0 times; of these: 556090 (48.34%) aligned discordantly 1 time ---- 594316 pairs aligned 0 times concordantly or discordantly; of these: 1188632 mates make up the pairs; of these: 529812 (44.57%) aligned 0 times 385926 (32.47%) aligned exactly 1 time 272894 (22.96%) aligned >1 times 98.66% overall alignment rate Time searching: 00:20:54 Overall time: 00:20:54 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 16 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] 2387774 / 18667204 = 0.1279 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 13:11:49: # Command line: callpeak -t SRX4085360.bam -f BAM -g ce -n SRX4085360.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085360.05 # format = BAM # ChIP-seq file = ['SRX4085360.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 13:11:49: # Command line: callpeak -t SRX4085360.bam -f BAM -g ce -n SRX4085360.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085360.10 # format = BAM # ChIP-seq file = ['SRX4085360.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 13:11:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:11:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:11:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:49: # Command line: callpeak -t SRX4085360.bam -f BAM -g ce -n SRX4085360.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085360.20 # format = BAM # ChIP-seq file = ['SRX4085360.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 13:11:49: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:11:49: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:55: 1000000 INFO @ Sun, 03 Jun 2018 13:11:55: 1000000 INFO @ Sun, 03 Jun 2018 13:11:55: 1000000 INFO @ Sun, 03 Jun 2018 13:12:02: 2000000 INFO @ Sun, 03 Jun 2018 13:12:02: 2000000 INFO @ Sun, 03 Jun 2018 13:12:02: 2000000 INFO @ Sun, 03 Jun 2018 13:12:08: 3000000 INFO @ Sun, 03 Jun 2018 13:12:08: 3000000 INFO @ Sun, 03 Jun 2018 13:12:08: 3000000 INFO @ Sun, 03 Jun 2018 13:12:14: 4000000 INFO @ Sun, 03 Jun 2018 13:12:14: 4000000 INFO @ Sun, 03 Jun 2018 13:12:14: 4000000 INFO @ Sun, 03 Jun 2018 13:12:21: 5000000 INFO @ Sun, 03 Jun 2018 13:12:21: 5000000 INFO @ Sun, 03 Jun 2018 13:12:21: 5000000 INFO @ Sun, 03 Jun 2018 13:12:27: 6000000 INFO @ Sun, 03 Jun 2018 13:12:27: 6000000 INFO @ Sun, 03 Jun 2018 13:12:27: 6000000 INFO @ Sun, 03 Jun 2018 13:12:32: 7000000 INFO @ Sun, 03 Jun 2018 13:12:33: 7000000 INFO @ Sun, 03 Jun 2018 13:12:33: 7000000 INFO @ Sun, 03 Jun 2018 13:12:38: 8000000 INFO @ Sun, 03 Jun 2018 13:12:38: 8000000 INFO @ Sun, 03 Jun 2018 13:12:38: 8000000 INFO @ Sun, 03 Jun 2018 13:12:43: 9000000 INFO @ Sun, 03 Jun 2018 13:12:44: 9000000 INFO @ Sun, 03 Jun 2018 13:12:44: 9000000 INFO @ Sun, 03 Jun 2018 13:12:49: 10000000 INFO @ Sun, 03 Jun 2018 13:12:50: 10000000 INFO @ Sun, 03 Jun 2018 13:12:50: 10000000 INFO @ Sun, 03 Jun 2018 13:12:54: 11000000 INFO @ Sun, 03 Jun 2018 13:12:56: 11000000 INFO @ Sun, 03 Jun 2018 13:12:56: 11000000 INFO @ Sun, 03 Jun 2018 13:13:00: 12000000 INFO @ Sun, 03 Jun 2018 13:13:02: 12000000 INFO @ Sun, 03 Jun 2018 13:13:02: 12000000 INFO @ Sun, 03 Jun 2018 13:13:05: 13000000 INFO @ Sun, 03 Jun 2018 13:13:07: 13000000 INFO @ Sun, 03 Jun 2018 13:13:07: 13000000 INFO @ Sun, 03 Jun 2018 13:13:11: 14000000 INFO @ Sun, 03 Jun 2018 13:13:13: 14000000 INFO @ Sun, 03 Jun 2018 13:13:13: 14000000 INFO @ Sun, 03 Jun 2018 13:13:16: 15000000 INFO @ Sun, 03 Jun 2018 13:13:19: 15000000 INFO @ Sun, 03 Jun 2018 13:13:19: 15000000 INFO @ Sun, 03 Jun 2018 13:13:22: 16000000 INFO @ Sun, 03 Jun 2018 13:13:24: 16000000 INFO @ Sun, 03 Jun 2018 13:13:24: 16000000 INFO @ Sun, 03 Jun 2018 13:13:27: 17000000 INFO @ Sun, 03 Jun 2018 13:13:30: 17000000 INFO @ Sun, 03 Jun 2018 13:13:30: 17000000 INFO @ Sun, 03 Jun 2018 13:13:33: 18000000 INFO @ Sun, 03 Jun 2018 13:13:36: 18000000 INFO @ Sun, 03 Jun 2018 13:13:36: 18000000 INFO @ Sun, 03 Jun 2018 13:13:38: 19000000 INFO @ Sun, 03 Jun 2018 13:13:41: 19000000 INFO @ Sun, 03 Jun 2018 13:13:42: 19000000 INFO @ Sun, 03 Jun 2018 13:13:44: 20000000 INFO @ Sun, 03 Jun 2018 13:13:47: 20000000 INFO @ Sun, 03 Jun 2018 13:13:47: 20000000 INFO @ Sun, 03 Jun 2018 13:13:50: 21000000 INFO @ Sun, 03 Jun 2018 13:13:53: 21000000 INFO @ Sun, 03 Jun 2018 13:13:53: 21000000 INFO @ Sun, 03 Jun 2018 13:13:55: 22000000 INFO @ Sun, 03 Jun 2018 13:13:59: 22000000 INFO @ Sun, 03 Jun 2018 13:13:59: 22000000 INFO @ Sun, 03 Jun 2018 13:14:01: 23000000 INFO @ Sun, 03 Jun 2018 13:14:05: 23000000 INFO @ Sun, 03 Jun 2018 13:14:05: 23000000 INFO @ Sun, 03 Jun 2018 13:14:06: 24000000 INFO @ Sun, 03 Jun 2018 13:14:10: 24000000 INFO @ Sun, 03 Jun 2018 13:14:11: 24000000 INFO @ Sun, 03 Jun 2018 13:14:11: 25000000 INFO @ Sun, 03 Jun 2018 13:14:16: 25000000 INFO @ Sun, 03 Jun 2018 13:14:16: 25000000 INFO @ Sun, 03 Jun 2018 13:14:17: 26000000 INFO @ Sun, 03 Jun 2018 13:14:22: 26000000 INFO @ Sun, 03 Jun 2018 13:14:22: 27000000 INFO @ Sun, 03 Jun 2018 13:14:22: 26000000 INFO @ Sun, 03 Jun 2018 13:14:28: 28000000 INFO @ Sun, 03 Jun 2018 13:14:28: 27000000 INFO @ Sun, 03 Jun 2018 13:14:28: 27000000 INFO @ Sun, 03 Jun 2018 13:14:33: 29000000 INFO @ Sun, 03 Jun 2018 13:14:34: 28000000 INFO @ Sun, 03 Jun 2018 13:14:34: 28000000 INFO @ Sun, 03 Jun 2018 13:14:39: 30000000 INFO @ Sun, 03 Jun 2018 13:14:40: 29000000 INFO @ Sun, 03 Jun 2018 13:14:40: 29000000 INFO @ Sun, 03 Jun 2018 13:14:44: 31000000 INFO @ Sun, 03 Jun 2018 13:14:46: 30000000 INFO @ Sun, 03 Jun 2018 13:14:46: 30000000 INFO @ Sun, 03 Jun 2018 13:14:50: 32000000 INFO @ Sun, 03 Jun 2018 13:14:52: 31000000 INFO @ Sun, 03 Jun 2018 13:14:52: 31000000 INFO @ Sun, 03 Jun 2018 13:14:55: 33000000 INFO @ Sun, 03 Jun 2018 13:14:58: 32000000 INFO @ Sun, 03 Jun 2018 13:14:58: 32000000 INFO @ Sun, 03 Jun 2018 13:15:01: 34000000 INFO @ Sun, 03 Jun 2018 13:15:02: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:15:02: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:15:02: #1 total tags in treatment: 16176650 INFO @ Sun, 03 Jun 2018 13:15:02: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:15:02: #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 13:15:02: #1 tags after filtering in treatment: 13850313 INFO @ Sun, 03 Jun 2018 13:15:02: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:15:02: #1 finished! INFO @ Sun, 03 Jun 2018 13:15:02: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:15:03: #2 number of paired peaks: 214 WARNING @ Sun, 03 Jun 2018 13:15:03: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sun, 03 Jun 2018 13:15:03: start model_add_line... INFO @ Sun, 03 Jun 2018 13:15:03: start X-correlation... INFO @ Sun, 03 Jun 2018 13:15:03: end of X-cor INFO @ Sun, 03 Jun 2018 13:15:03: #2 finished! INFO @ Sun, 03 Jun 2018 13:15:03: #2 predicted fragment length is 104 bps INFO @ Sun, 03 Jun 2018 13:15:03: #2 alternative fragment length(s) may be 3,77,104,128,148 bps INFO @ Sun, 03 Jun 2018 13:15:03: #2.2 Generate R script for model : SRX4085360.10_model.r INFO @ Sun, 03 Jun 2018 13:15:03: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:15:04: 33000000 INFO @ Sun, 03 Jun 2018 13:15:04: 33000000 INFO @ Sun, 03 Jun 2018 13:15:09: 34000000 INFO @ Sun, 03 Jun 2018 13:15:10: 34000000 INFO @ Sun, 03 Jun 2018 13:15:10: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:15:10: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:15:10: #1 total tags in treatment: 16176650 INFO @ Sun, 03 Jun 2018 13:15:10: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:15:10: #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 13:15:10: #1 tags after filtering in treatment: 13850313 INFO @ Sun, 03 Jun 2018 13:15:10: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:15:10: #1 finished! INFO @ Sun, 03 Jun 2018 13:15:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:15:10: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:15:10: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:15:10: #1 total tags in treatment: 16176650 INFO @ Sun, 03 Jun 2018 13:15:10: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:15:10: #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 13:15:11: #1 tags after filtering in treatment: 13850313 INFO @ Sun, 03 Jun 2018 13:15:11: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:15:11: #1 finished! INFO @ Sun, 03 Jun 2018 13:15:11: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:15:11: #2 number of paired peaks: 214 WARNING @ Sun, 03 Jun 2018 13:15:11: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sun, 03 Jun 2018 13:15:11: start model_add_line... INFO @ Sun, 03 Jun 2018 13:15:11: start X-correlation... INFO @ Sun, 03 Jun 2018 13:15:11: end of X-cor INFO @ Sun, 03 Jun 2018 13:15:11: #2 finished! INFO @ Sun, 03 Jun 2018 13:15:11: #2 predicted fragment length is 104 bps INFO @ Sun, 03 Jun 2018 13:15:11: #2 alternative fragment length(s) may be 3,77,104,128,148 bps INFO @ Sun, 03 Jun 2018 13:15:11: #2.2 Generate R script for model : SRX4085360.20_model.r INFO @ Sun, 03 Jun 2018 13:15:11: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:15:12: #2 number of paired peaks: 214 WARNING @ Sun, 03 Jun 2018 13:15:12: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sun, 03 Jun 2018 13:15:12: start model_add_line... INFO @ Sun, 03 Jun 2018 13:15:12: start X-correlation... INFO @ Sun, 03 Jun 2018 13:15:12: end of X-cor INFO @ Sun, 03 Jun 2018 13:15:12: #2 finished! INFO @ Sun, 03 Jun 2018 13:15:12: #2 predicted fragment length is 104 bps INFO @ Sun, 03 Jun 2018 13:15:12: #2 alternative fragment length(s) may be 3,77,104,128,148 bps INFO @ Sun, 03 Jun 2018 13:15:12: #2.2 Generate R script for model : SRX4085360.05_model.r INFO @ Sun, 03 Jun 2018 13:15:12: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:15:30: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:15:38: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:15:40: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:15:44: #4 Write output xls file... SRX4085360.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:15:44: #4 Write peak in narrowPeak format file... SRX4085360.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:15:44: #4 Write summits bed file... SRX4085360.10_summits.bed INFO @ Sun, 03 Jun 2018 13:15:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:15:53: #4 Write output xls file... SRX4085360.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:15:53: #4 Write peak in narrowPeak format file... SRX4085360.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:15:53: #4 Write summits bed file... SRX4085360.20_summits.bed INFO @ Sun, 03 Jun 2018 13:15:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (295 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:15:55: #4 Write output xls file... SRX4085360.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:15:55: #4 Write peak in narrowPeak format file... SRX4085360.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:15:55: #4 Write summits bed file... SRX4085360.05_summits.bed INFO @ Sun, 03 Jun 2018 13:15:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2110 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。