Job ID = 10714425 sra ファイルのダウンロード中... Completed: 1890495K bytes transferred in 47 seconds (325918K 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 26582614 spots for /home/okishinya/chipatlas/results/ce10/SRX4085341/SRR7167370.sra Written 26582614 spots for /home/okishinya/chipatlas/results/ce10/SRX4085341/SRR7167370.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: 00:28:57 26582614 reads; of these: 26582614 (100.00%) were paired; of these: 2079567 (7.82%) aligned concordantly 0 times 21431572 (80.62%) aligned concordantly exactly 1 time 3071475 (11.55%) aligned concordantly >1 times ---- 2079567 pairs aligned concordantly 0 times; of these: 205809 (9.90%) aligned discordantly 1 time ---- 1873758 pairs aligned 0 times concordantly or discordantly; of these: 3747516 mates make up the pairs; of these: 2084481 (55.62%) aligned 0 times 1381958 (36.88%) aligned exactly 1 time 281077 (7.50%) aligned >1 times 96.08% overall alignment rate Time searching: 00:28:57 Overall time: 00:28:57 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] 6136622 / 24642834 = 0.2490 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 13:15:37: # Command line: callpeak -t SRX4085341.bam -f BAM -g ce -n SRX4085341.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085341.20 # format = BAM # ChIP-seq file = ['SRX4085341.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 13:15:37: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:37: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:37: # Command line: callpeak -t SRX4085341.bam -f BAM -g ce -n SRX4085341.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085341.10 # format = BAM # ChIP-seq file = ['SRX4085341.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 13:15:37: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:37: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:37: # Command line: callpeak -t SRX4085341.bam -f BAM -g ce -n SRX4085341.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085341.05 # format = BAM # ChIP-seq file = ['SRX4085341.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 13:15:37: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:37: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:44: 1000000 INFO @ Sun, 03 Jun 2018 13:15:44: 1000000 INFO @ Sun, 03 Jun 2018 13:15:44: 1000000 INFO @ Sun, 03 Jun 2018 13:15:50: 2000000 INFO @ Sun, 03 Jun 2018 13:15:51: 2000000 INFO @ Sun, 03 Jun 2018 13:15:51: 2000000 INFO @ Sun, 03 Jun 2018 13:15:57: 3000000 INFO @ Sun, 03 Jun 2018 13:15:58: 3000000 INFO @ Sun, 03 Jun 2018 13:15:58: 3000000 INFO @ Sun, 03 Jun 2018 13:16:03: 4000000 INFO @ Sun, 03 Jun 2018 13:16:04: 4000000 INFO @ Sun, 03 Jun 2018 13:16:04: 4000000 INFO @ Sun, 03 Jun 2018 13:16:09: 5000000 INFO @ Sun, 03 Jun 2018 13:16:11: 5000000 INFO @ Sun, 03 Jun 2018 13:16:11: 5000000 INFO @ Sun, 03 Jun 2018 13:16:16: 6000000 INFO @ Sun, 03 Jun 2018 13:16:18: 6000000 INFO @ Sun, 03 Jun 2018 13:16:18: 6000000 INFO @ Sun, 03 Jun 2018 13:16:22: 7000000 INFO @ Sun, 03 Jun 2018 13:16:25: 7000000 INFO @ Sun, 03 Jun 2018 13:16:25: 7000000 INFO @ Sun, 03 Jun 2018 13:16:29: 8000000 INFO @ Sun, 03 Jun 2018 13:16:31: 8000000 INFO @ Sun, 03 Jun 2018 13:16:32: 8000000 INFO @ Sun, 03 Jun 2018 13:16:36: 9000000 INFO @ Sun, 03 Jun 2018 13:16:38: 9000000 INFO @ Sun, 03 Jun 2018 13:16:40: 9000000 INFO @ Sun, 03 Jun 2018 13:16:43: 10000000 INFO @ Sun, 03 Jun 2018 13:16:45: 10000000 INFO @ Sun, 03 Jun 2018 13:16:46: 10000000 INFO @ Sun, 03 Jun 2018 13:16:51: 11000000 INFO @ Sun, 03 Jun 2018 13:16:52: 11000000 INFO @ Sun, 03 Jun 2018 13:16:53: 11000000 INFO @ Sun, 03 Jun 2018 13:16:59: 12000000 INFO @ Sun, 03 Jun 2018 13:17:00: 12000000 INFO @ Sun, 03 Jun 2018 13:17:00: 12000000 INFO @ Sun, 03 Jun 2018 13:17:06: 13000000 INFO @ Sun, 03 Jun 2018 13:17:06: 13000000 INFO @ Sun, 03 Jun 2018 13:17:07: 13000000 INFO @ Sun, 03 Jun 2018 13:17:12: 14000000 INFO @ Sun, 03 Jun 2018 13:17:13: 14000000 INFO @ Sun, 03 Jun 2018 13:17:14: 14000000 INFO @ Sun, 03 Jun 2018 13:17:20: 15000000 INFO @ Sun, 03 Jun 2018 13:17:20: 15000000 INFO @ Sun, 03 Jun 2018 13:17:22: 15000000 INFO @ Sun, 03 Jun 2018 13:17:26: 16000000 INFO @ Sun, 03 Jun 2018 13:17:27: 16000000 INFO @ Sun, 03 Jun 2018 13:17:29: 16000000 INFO @ Sun, 03 Jun 2018 13:17:32: 17000000 INFO @ Sun, 03 Jun 2018 13:17:35: 17000000 INFO @ Sun, 03 Jun 2018 13:17:36: 17000000 INFO @ Sun, 03 Jun 2018 13:17:40: 18000000 INFO @ Sun, 03 Jun 2018 13:17:43: 18000000 INFO @ Sun, 03 Jun 2018 13:17:43: 18000000 INFO @ Sun, 03 Jun 2018 13:17:47: 19000000 INFO @ Sun, 03 Jun 2018 13:17:49: 19000000 INFO @ Sun, 03 Jun 2018 13:17:50: 19000000 INFO @ Sun, 03 Jun 2018 13:17:55: 20000000 INFO @ Sun, 03 Jun 2018 13:17:56: 20000000 INFO @ Sun, 03 Jun 2018 13:17:58: 20000000 INFO @ Sun, 03 Jun 2018 13:18:02: 21000000 INFO @ Sun, 03 Jun 2018 13:18:03: 21000000 INFO @ Sun, 03 Jun 2018 13:18:05: 21000000 INFO @ Sun, 03 Jun 2018 13:18:09: 22000000 INFO @ Sun, 03 Jun 2018 13:18:10: 22000000 INFO @ Sun, 03 Jun 2018 13:18:13: 22000000 INFO @ Sun, 03 Jun 2018 13:18:16: 23000000 INFO @ Sun, 03 Jun 2018 13:18:18: 23000000 INFO @ Sun, 03 Jun 2018 13:18:21: 23000000 INFO @ Sun, 03 Jun 2018 13:18:23: 24000000 INFO @ Sun, 03 Jun 2018 13:18:26: 24000000 INFO @ Sun, 03 Jun 2018 13:18:30: 24000000 INFO @ Sun, 03 Jun 2018 13:18:32: 25000000 INFO @ Sun, 03 Jun 2018 13:18:35: 25000000 INFO @ Sun, 03 Jun 2018 13:18:38: 25000000 INFO @ Sun, 03 Jun 2018 13:18:40: 26000000 INFO @ Sun, 03 Jun 2018 13:18:42: 26000000 INFO @ Sun, 03 Jun 2018 13:18:45: 26000000 INFO @ Sun, 03 Jun 2018 13:18:47: 27000000 INFO @ Sun, 03 Jun 2018 13:18:49: 27000000 INFO @ Sun, 03 Jun 2018 13:18:51: 27000000 INFO @ Sun, 03 Jun 2018 13:18:54: 28000000 INFO @ Sun, 03 Jun 2018 13:18:56: 28000000 INFO @ Sun, 03 Jun 2018 13:18:57: 28000000 INFO @ Sun, 03 Jun 2018 13:19:01: 29000000 INFO @ Sun, 03 Jun 2018 13:19:04: 29000000 INFO @ Sun, 03 Jun 2018 13:19:04: 29000000 INFO @ Sun, 03 Jun 2018 13:19:09: 30000000 INFO @ Sun, 03 Jun 2018 13:19:10: 30000000 INFO @ Sun, 03 Jun 2018 13:19:11: 30000000 INFO @ Sun, 03 Jun 2018 13:19:16: 31000000 INFO @ Sun, 03 Jun 2018 13:19:16: 31000000 INFO @ Sun, 03 Jun 2018 13:19:18: 31000000 INFO @ Sun, 03 Jun 2018 13:19:23: 32000000 INFO @ Sun, 03 Jun 2018 13:19:23: 32000000 INFO @ Sun, 03 Jun 2018 13:19:25: 32000000 INFO @ Sun, 03 Jun 2018 13:19:29: 33000000 INFO @ Sun, 03 Jun 2018 13:19:31: 33000000 INFO @ Sun, 03 Jun 2018 13:19:32: 33000000 INFO @ Sun, 03 Jun 2018 13:19:35: 34000000 INFO @ Sun, 03 Jun 2018 13:19:38: 34000000 INFO @ Sun, 03 Jun 2018 13:19:40: 34000000 INFO @ Sun, 03 Jun 2018 13:19:41: 35000000 INFO @ Sun, 03 Jun 2018 13:19:46: 35000000 INFO @ Sun, 03 Jun 2018 13:19:47: 36000000 INFO @ Sun, 03 Jun 2018 13:19:47: 35000000 INFO @ Sun, 03 Jun 2018 13:19:53: 36000000 INFO @ Sun, 03 Jun 2018 13:19:54: 37000000 INFO @ Sun, 03 Jun 2018 13:19:55: 36000000 INFO @ Sun, 03 Jun 2018 13:20:00: 38000000 INFO @ Sun, 03 Jun 2018 13:20:00: 37000000 INFO @ Sun, 03 Jun 2018 13:20:02: 37000000 INFO @ Sun, 03 Jun 2018 13:20:05: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:20:05: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:20:05: #1 total tags in treatment: 18386910 INFO @ Sun, 03 Jun 2018 13:20:05: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:20:05: #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 13:20:05: #1 tags after filtering in treatment: 15840074 INFO @ Sun, 03 Jun 2018 13:20:05: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:20:05: #1 finished! INFO @ Sun, 03 Jun 2018 13:20:05: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:20:06: #2 number of paired peaks: 193 WARNING @ Sun, 03 Jun 2018 13:20:06: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sun, 03 Jun 2018 13:20:06: start model_add_line... INFO @ Sun, 03 Jun 2018 13:20:06: start X-correlation... INFO @ Sun, 03 Jun 2018 13:20:06: end of X-cor INFO @ Sun, 03 Jun 2018 13:20:06: #2 finished! INFO @ Sun, 03 Jun 2018 13:20:06: #2 predicted fragment length is 106 bps INFO @ Sun, 03 Jun 2018 13:20:06: #2 alternative fragment length(s) may be 3,83,106 bps INFO @ Sun, 03 Jun 2018 13:20:06: #2.2 Generate R script for model : SRX4085341.05_model.r INFO @ Sun, 03 Jun 2018 13:20:06: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:20:07: 38000000 INFO @ Sun, 03 Jun 2018 13:20:09: 38000000 INFO @ Sun, 03 Jun 2018 13:20:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:20:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:20:13: #1 total tags in treatment: 18386910 INFO @ Sun, 03 Jun 2018 13:20:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:20:13: #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 13:20:13: #1 tags after filtering in treatment: 15840074 INFO @ Sun, 03 Jun 2018 13:20:13: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:20:13: #1 finished! INFO @ Sun, 03 Jun 2018 13:20:13: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:20:14: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:20:14: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:20:14: #1 total tags in treatment: 18386910 INFO @ Sun, 03 Jun 2018 13:20:14: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:20:14: #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 13:20:14: #2 number of paired peaks: 193 WARNING @ Sun, 03 Jun 2018 13:20:14: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sun, 03 Jun 2018 13:20:14: start model_add_line... INFO @ Sun, 03 Jun 2018 13:20:14: #1 tags after filtering in treatment: 15840074 INFO @ Sun, 03 Jun 2018 13:20:14: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:20:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:20:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:20:14: start X-correlation... INFO @ Sun, 03 Jun 2018 13:20:14: end of X-cor INFO @ Sun, 03 Jun 2018 13:20:14: #2 finished! INFO @ Sun, 03 Jun 2018 13:20:14: #2 predicted fragment length is 106 bps INFO @ Sun, 03 Jun 2018 13:20:14: #2 alternative fragment length(s) may be 3,83,106 bps INFO @ Sun, 03 Jun 2018 13:20:14: #2.2 Generate R script for model : SRX4085341.20_model.r INFO @ Sun, 03 Jun 2018 13:20:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:20:15: #2 number of paired peaks: 193 WARNING @ Sun, 03 Jun 2018 13:20:15: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sun, 03 Jun 2018 13:20:15: start model_add_line... INFO @ Sun, 03 Jun 2018 13:20:16: start X-correlation... INFO @ Sun, 03 Jun 2018 13:20:16: end of X-cor INFO @ Sun, 03 Jun 2018 13:20:16: #2 finished! INFO @ Sun, 03 Jun 2018 13:20:16: #2 predicted fragment length is 106 bps INFO @ Sun, 03 Jun 2018 13:20:16: #2 alternative fragment length(s) may be 3,83,106 bps INFO @ Sun, 03 Jun 2018 13:20:16: #2.2 Generate R script for model : SRX4085341.10_model.r INFO @ Sun, 03 Jun 2018 13:20:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:20:36: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:50: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:20:53: #4 Write output xls file... SRX4085341.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:20:53: #4 Write peak in narrowPeak format file... SRX4085341.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:20:53: #4 Write summits bed file... SRX4085341.05_summits.bed INFO @ Sun, 03 Jun 2018 13:20:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1107 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:21:01: #4 Write output xls file... SRX4085341.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:21:01: #4 Write peak in narrowPeak format file... SRX4085341.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:21:01: #4 Write summits bed file... SRX4085341.20_summits.bed INFO @ Sun, 03 Jun 2018 13:21:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:21:06: #4 Write output xls file... SRX4085341.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:21:06: #4 Write peak in narrowPeak format file... SRX4085341.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:21:06: #4 Write summits bed file... SRX4085341.10_summits.bed INFO @ Sun, 03 Jun 2018 13:21:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (713 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。