Job ID = 10714476 sra ファイルのダウンロード中... Completed: 1896287K bytes transferred in 36 seconds (424886K 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 28117009 spots for /home/okishinya/chipatlas/results/ce10/SRX4085392/SRR7167421.sra Written 28117009 spots for /home/okishinya/chipatlas/results/ce10/SRX4085392/SRR7167421.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: 00:25:25 28117009 reads; of these: 28117009 (100.00%) were paired; of these: 1918465 (6.82%) aligned concordantly 0 times 24203589 (86.08%) aligned concordantly exactly 1 time 1994955 (7.10%) aligned concordantly >1 times ---- 1918465 pairs aligned concordantly 0 times; of these: 192013 (10.01%) aligned discordantly 1 time ---- 1726452 pairs aligned 0 times concordantly or discordantly; of these: 3452904 mates make up the pairs; of these: 2398601 (69.47%) aligned 0 times 849620 (24.61%) aligned exactly 1 time 204683 (5.93%) aligned >1 times 95.73% overall alignment rate Time searching: 00:25:25 Overall time: 00:25:25 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] 17318572 / 26314039 = 0.6581 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 13:22:13: # Command line: callpeak -t SRX4085392.bam -f BAM -g ce -n SRX4085392.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085392.20 # format = BAM # ChIP-seq file = ['SRX4085392.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 13:22:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:22:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:22:13: # Command line: callpeak -t SRX4085392.bam -f BAM -g ce -n SRX4085392.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085392.10 # format = BAM # ChIP-seq file = ['SRX4085392.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 13:22:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:22:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:22:13: # Command line: callpeak -t SRX4085392.bam -f BAM -g ce -n SRX4085392.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085392.05 # format = BAM # ChIP-seq file = ['SRX4085392.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 13:22:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:22:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:22:19: 1000000 INFO @ Sun, 03 Jun 2018 13:22:19: 1000000 INFO @ Sun, 03 Jun 2018 13:22:19: 1000000 INFO @ Sun, 03 Jun 2018 13:22:25: 2000000 INFO @ Sun, 03 Jun 2018 13:22:25: 2000000 INFO @ Sun, 03 Jun 2018 13:22:25: 2000000 INFO @ Sun, 03 Jun 2018 13:22:31: 3000000 INFO @ Sun, 03 Jun 2018 13:22:31: 3000000 INFO @ Sun, 03 Jun 2018 13:22:32: 3000000 INFO @ Sun, 03 Jun 2018 13:22:36: 4000000 INFO @ Sun, 03 Jun 2018 13:22:37: 4000000 INFO @ Sun, 03 Jun 2018 13:22:38: 4000000 INFO @ Sun, 03 Jun 2018 13:22:42: 5000000 INFO @ Sun, 03 Jun 2018 13:22:43: 5000000 INFO @ Sun, 03 Jun 2018 13:22:44: 5000000 INFO @ Sun, 03 Jun 2018 13:22:48: 6000000 INFO @ Sun, 03 Jun 2018 13:22:50: 6000000 INFO @ Sun, 03 Jun 2018 13:22:51: 6000000 INFO @ Sun, 03 Jun 2018 13:22:54: 7000000 INFO @ Sun, 03 Jun 2018 13:22:56: 7000000 INFO @ Sun, 03 Jun 2018 13:22:57: 7000000 INFO @ Sun, 03 Jun 2018 13:23:00: 8000000 INFO @ Sun, 03 Jun 2018 13:23:02: 8000000 INFO @ Sun, 03 Jun 2018 13:23:04: 8000000 INFO @ Sun, 03 Jun 2018 13:23:06: 9000000 INFO @ Sun, 03 Jun 2018 13:23:08: 9000000 INFO @ Sun, 03 Jun 2018 13:23:10: 9000000 INFO @ Sun, 03 Jun 2018 13:23:11: 10000000 INFO @ Sun, 03 Jun 2018 13:23:14: 10000000 INFO @ Sun, 03 Jun 2018 13:23:16: 10000000 INFO @ Sun, 03 Jun 2018 13:23:17: 11000000 INFO @ Sun, 03 Jun 2018 13:23:21: 11000000 INFO @ Sun, 03 Jun 2018 13:23:23: 11000000 INFO @ Sun, 03 Jun 2018 13:23:23: 12000000 INFO @ Sun, 03 Jun 2018 13:23:27: 12000000 INFO @ Sun, 03 Jun 2018 13:23:29: 13000000 INFO @ Sun, 03 Jun 2018 13:23:29: 12000000 INFO @ Sun, 03 Jun 2018 13:23:33: 13000000 INFO @ Sun, 03 Jun 2018 13:23:35: 14000000 INFO @ Sun, 03 Jun 2018 13:23:36: 13000000 INFO @ Sun, 03 Jun 2018 13:23:39: 14000000 INFO @ Sun, 03 Jun 2018 13:23:40: 15000000 INFO @ Sun, 03 Jun 2018 13:23:42: 14000000 INFO @ Sun, 03 Jun 2018 13:23:45: 15000000 INFO @ Sun, 03 Jun 2018 13:23:47: 16000000 INFO @ Sun, 03 Jun 2018 13:23:48: 15000000 INFO @ Sun, 03 Jun 2018 13:23:52: 16000000 INFO @ Sun, 03 Jun 2018 13:23:53: 17000000 INFO @ Sun, 03 Jun 2018 13:23:54: 16000000 INFO @ Sun, 03 Jun 2018 13:23:58: 17000000 INFO @ Sun, 03 Jun 2018 13:23:58: 18000000 INFO @ Sun, 03 Jun 2018 13:24:00: 17000000 INFO @ Sun, 03 Jun 2018 13:24:03: 18000000 INFO @ Sun, 03 Jun 2018 13:24:04: 19000000 INFO @ Sun, 03 Jun 2018 13:24:05: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:05: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:05: #1 total tags in treatment: 8949814 INFO @ Sun, 03 Jun 2018 13:24:05: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:05: #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 13:24:05: #1 tags after filtering in treatment: 7371187 INFO @ Sun, 03 Jun 2018 13:24:05: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 13:24:05: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:05: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:06: 18000000 INFO @ Sun, 03 Jun 2018 13:24:06: #2 number of paired peaks: 429 WARNING @ Sun, 03 Jun 2018 13:24:06: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:06: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:06: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:06: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:06: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:06: #2 predicted fragment length is 147 bps INFO @ Sun, 03 Jun 2018 13:24:06: #2 alternative fragment length(s) may be 4,131,147 bps INFO @ Sun, 03 Jun 2018 13:24:06: #2.2 Generate R script for model : SRX4085392.20_model.r INFO @ Sun, 03 Jun 2018 13:24:06: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:24:09: 19000000 INFO @ Sun, 03 Jun 2018 13:24:10: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:10: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:10: #1 total tags in treatment: 8949814 INFO @ Sun, 03 Jun 2018 13:24:10: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:10: #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 13:24:10: #1 tags after filtering in treatment: 7371187 INFO @ Sun, 03 Jun 2018 13:24:10: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 13:24:10: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:11: #2 number of paired peaks: 429 WARNING @ Sun, 03 Jun 2018 13:24:11: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:11: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:11: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:11: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:11: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:11: #2 predicted fragment length is 147 bps INFO @ Sun, 03 Jun 2018 13:24:11: #2 alternative fragment length(s) may be 4,131,147 bps INFO @ Sun, 03 Jun 2018 13:24:11: #2.2 Generate R script for model : SRX4085392.05_model.r INFO @ Sun, 03 Jun 2018 13:24:11: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:24:11: 19000000 INFO @ Sun, 03 Jun 2018 13:24:12: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:12: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:12: #1 total tags in treatment: 8949814 INFO @ Sun, 03 Jun 2018 13:24:12: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:12: #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 13:24:12: #1 tags after filtering in treatment: 7371187 INFO @ Sun, 03 Jun 2018 13:24:12: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 13:24:12: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:12: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:13: #2 number of paired peaks: 429 WARNING @ Sun, 03 Jun 2018 13:24:13: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:13: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:13: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:13: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:13: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:13: #2 predicted fragment length is 147 bps INFO @ Sun, 03 Jun 2018 13:24:13: #2 alternative fragment length(s) may be 4,131,147 bps INFO @ Sun, 03 Jun 2018 13:24:13: #2.2 Generate R script for model : SRX4085392.10_model.r INFO @ Sun, 03 Jun 2018 13:24:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:24:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:24:28: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:24:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:24:31: #4 Write output xls file... SRX4085392.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:24:31: #4 Write peak in narrowPeak format file... SRX4085392.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:24:31: #4 Write summits bed file... SRX4085392.20_summits.bed INFO @ Sun, 03 Jun 2018 13:24:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:24:36: #4 Write output xls file... SRX4085392.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:24:36: #4 Write peak in narrowPeak format file... SRX4085392.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:24:36: #4 Write summits bed file... SRX4085392.05_summits.bed INFO @ Sun, 03 Jun 2018 13:24:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (419 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:24:39: #4 Write output xls file... SRX4085392.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:24:39: #4 Write peak in narrowPeak format file... SRX4085392.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:24:39: #4 Write summits bed file... SRX4085392.10_summits.bed INFO @ Sun, 03 Jun 2018 13:24:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (283 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。