Job ID = 10714525 sra ファイルのダウンロード中... Completed: 1735288K bytes transferred in 22 seconds (632811K 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 26010822 spots for /home/okishinya/chipatlas/results/ce10/SRX4085440/SRR7167469.sra Written 26010822 spots for /home/okishinya/chipatlas/results/ce10/SRX4085440/SRR7167469.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: 00:23:21 26010822 reads; of these: 26010822 (100.00%) were paired; of these: 8306937 (31.94%) aligned concordantly 0 times 14688793 (56.47%) aligned concordantly exactly 1 time 3015092 (11.59%) aligned concordantly >1 times ---- 8306937 pairs aligned concordantly 0 times; of these: 390835 (4.70%) aligned discordantly 1 time ---- 7916102 pairs aligned 0 times concordantly or discordantly; of these: 15832204 mates make up the pairs; of these: 12485008 (78.86%) aligned 0 times 2872821 (18.15%) aligned exactly 1 time 474375 (3.00%) aligned >1 times 76.00% overall alignment rate Time searching: 00:23:21 Overall time: 00:23:21 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 20 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] 2338540 / 17969886 = 0.1301 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 13:45:42: # Command line: callpeak -t SRX4085440.bam -f BAM -g ce -n SRX4085440.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085440.20 # format = BAM # ChIP-seq file = ['SRX4085440.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 13:45:42: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:42: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:42: # Command line: callpeak -t SRX4085440.bam -f BAM -g ce -n SRX4085440.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085440.05 # format = BAM # ChIP-seq file = ['SRX4085440.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 13:45:42: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:42: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:42: # Command line: callpeak -t SRX4085440.bam -f BAM -g ce -n SRX4085440.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085440.10 # format = BAM # ChIP-seq file = ['SRX4085440.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 13:45:42: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:42: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:48: 1000000 INFO @ Sun, 03 Jun 2018 13:45:48: 1000000 INFO @ Sun, 03 Jun 2018 13:45:48: 1000000 INFO @ Sun, 03 Jun 2018 13:45:54: 2000000 INFO @ Sun, 03 Jun 2018 13:45:54: 2000000 INFO @ Sun, 03 Jun 2018 13:45:54: 2000000 INFO @ Sun, 03 Jun 2018 13:46:00: 3000000 INFO @ Sun, 03 Jun 2018 13:46:00: 3000000 INFO @ Sun, 03 Jun 2018 13:46:00: 3000000 INFO @ Sun, 03 Jun 2018 13:46:05: 4000000 INFO @ Sun, 03 Jun 2018 13:46:05: 4000000 INFO @ Sun, 03 Jun 2018 13:46:06: 4000000 INFO @ Sun, 03 Jun 2018 13:46:11: 5000000 INFO @ Sun, 03 Jun 2018 13:46:11: 5000000 INFO @ Sun, 03 Jun 2018 13:46:11: 5000000 INFO @ Sun, 03 Jun 2018 13:46:17: 6000000 INFO @ Sun, 03 Jun 2018 13:46:17: 6000000 INFO @ Sun, 03 Jun 2018 13:46:17: 6000000 INFO @ Sun, 03 Jun 2018 13:46:23: 7000000 INFO @ Sun, 03 Jun 2018 13:46:23: 7000000 INFO @ Sun, 03 Jun 2018 13:46:23: 7000000 INFO @ Sun, 03 Jun 2018 13:46:29: 8000000 INFO @ Sun, 03 Jun 2018 13:46:29: 8000000 INFO @ Sun, 03 Jun 2018 13:46:30: 8000000 INFO @ Sun, 03 Jun 2018 13:46:36: 9000000 INFO @ Sun, 03 Jun 2018 13:46:36: 9000000 INFO @ Sun, 03 Jun 2018 13:46:36: 9000000 INFO @ Sun, 03 Jun 2018 13:46:42: 10000000 INFO @ Sun, 03 Jun 2018 13:46:43: 10000000 INFO @ Sun, 03 Jun 2018 13:46:43: 10000000 INFO @ Sun, 03 Jun 2018 13:46:49: 11000000 INFO @ Sun, 03 Jun 2018 13:46:49: 11000000 INFO @ Sun, 03 Jun 2018 13:46:49: 11000000 INFO @ Sun, 03 Jun 2018 13:46:56: 12000000 INFO @ Sun, 03 Jun 2018 13:46:56: 12000000 INFO @ Sun, 03 Jun 2018 13:46:56: 12000000 INFO @ Sun, 03 Jun 2018 13:47:02: 13000000 INFO @ Sun, 03 Jun 2018 13:47:02: 13000000 INFO @ Sun, 03 Jun 2018 13:47:03: 13000000 INFO @ Sun, 03 Jun 2018 13:47:09: 14000000 INFO @ Sun, 03 Jun 2018 13:47:09: 14000000 INFO @ Sun, 03 Jun 2018 13:47:09: 14000000 INFO @ Sun, 03 Jun 2018 13:47:15: 15000000 INFO @ Sun, 03 Jun 2018 13:47:16: 15000000 INFO @ Sun, 03 Jun 2018 13:47:16: 15000000 INFO @ Sun, 03 Jun 2018 13:47:22: 16000000 INFO @ Sun, 03 Jun 2018 13:47:23: 16000000 INFO @ Sun, 03 Jun 2018 13:47:23: 16000000 INFO @ Sun, 03 Jun 2018 13:47:29: 17000000 INFO @ Sun, 03 Jun 2018 13:47:30: 17000000 INFO @ Sun, 03 Jun 2018 13:47:30: 17000000 INFO @ Sun, 03 Jun 2018 13:47:35: 18000000 INFO @ Sun, 03 Jun 2018 13:47:36: 18000000 INFO @ Sun, 03 Jun 2018 13:47:36: 18000000 INFO @ Sun, 03 Jun 2018 13:47:42: 19000000 INFO @ Sun, 03 Jun 2018 13:47:43: 19000000 INFO @ Sun, 03 Jun 2018 13:47:43: 19000000 INFO @ Sun, 03 Jun 2018 13:47:48: 20000000 INFO @ Sun, 03 Jun 2018 13:47:50: 20000000 INFO @ Sun, 03 Jun 2018 13:47:50: 20000000 INFO @ Sun, 03 Jun 2018 13:47:55: 21000000 INFO @ Sun, 03 Jun 2018 13:47:56: 21000000 INFO @ Sun, 03 Jun 2018 13:47:57: 21000000 INFO @ Sun, 03 Jun 2018 13:48:02: 22000000 INFO @ Sun, 03 Jun 2018 13:48:03: 22000000 INFO @ Sun, 03 Jun 2018 13:48:04: 22000000 INFO @ Sun, 03 Jun 2018 13:48:08: 23000000 INFO @ Sun, 03 Jun 2018 13:48:09: 23000000 INFO @ Sun, 03 Jun 2018 13:48:11: 23000000 INFO @ Sun, 03 Jun 2018 13:48:15: 24000000 INFO @ Sun, 03 Jun 2018 13:48:16: 24000000 INFO @ Sun, 03 Jun 2018 13:48:18: 24000000 INFO @ Sun, 03 Jun 2018 13:48:21: 25000000 INFO @ Sun, 03 Jun 2018 13:48:23: 25000000 INFO @ Sun, 03 Jun 2018 13:48:25: 25000000 INFO @ Sun, 03 Jun 2018 13:48:28: 26000000 INFO @ Sun, 03 Jun 2018 13:48:29: 26000000 INFO @ Sun, 03 Jun 2018 13:48:31: 26000000 INFO @ Sun, 03 Jun 2018 13:48:34: 27000000 INFO @ Sun, 03 Jun 2018 13:48:36: 27000000 INFO @ Sun, 03 Jun 2018 13:48:38: 27000000 INFO @ Sun, 03 Jun 2018 13:48:41: 28000000 INFO @ Sun, 03 Jun 2018 13:48:43: 28000000 INFO @ Sun, 03 Jun 2018 13:48:45: 28000000 INFO @ Sun, 03 Jun 2018 13:48:48: 29000000 INFO @ Sun, 03 Jun 2018 13:48:49: 29000000 INFO @ Sun, 03 Jun 2018 13:48:51: 29000000 INFO @ Sun, 03 Jun 2018 13:48:54: 30000000 INFO @ Sun, 03 Jun 2018 13:48:56: 30000000 INFO @ Sun, 03 Jun 2018 13:48:57: 30000000 INFO @ Sun, 03 Jun 2018 13:49:01: 31000000 INFO @ Sun, 03 Jun 2018 13:49:03: 31000000 INFO @ Sun, 03 Jun 2018 13:49:03: 31000000 INFO @ Sun, 03 Jun 2018 13:49:07: 32000000 INFO @ Sun, 03 Jun 2018 13:49:08: 32000000 INFO @ Sun, 03 Jun 2018 13:49:09: 32000000 INFO @ Sun, 03 Jun 2018 13:49:13: 33000000 INFO @ Sun, 03 Jun 2018 13:49:14: 33000000 INFO @ Sun, 03 Jun 2018 13:49:15: 33000000 INFO @ Sun, 03 Jun 2018 13:49:18: 34000000 INFO @ Sun, 03 Jun 2018 13:49:19: 34000000 INFO @ Sun, 03 Jun 2018 13:49:20: 34000000 INFO @ Sun, 03 Jun 2018 13:49:23: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:49:23: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:49:23: #1 total tags in treatment: 15393971 INFO @ Sun, 03 Jun 2018 13:49:23: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:49:23: #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 13:49:23: #1 tags after filtering in treatment: 12520943 INFO @ Sun, 03 Jun 2018 13:49:23: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:49:23: #1 finished! INFO @ Sun, 03 Jun 2018 13:49:23: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:49:24: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:49:24: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:49:24: #1 total tags in treatment: 15393971 INFO @ Sun, 03 Jun 2018 13:49:24: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:49:24: #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 13:49:24: #1 tags after filtering in treatment: 12520943 INFO @ Sun, 03 Jun 2018 13:49:24: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:49:24: #1 finished! INFO @ Sun, 03 Jun 2018 13:49:24: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:49:24: #2 number of paired peaks: 263 WARNING @ Sun, 03 Jun 2018 13:49:24: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sun, 03 Jun 2018 13:49:24: start model_add_line... INFO @ Sun, 03 Jun 2018 13:49:24: start X-correlation... INFO @ Sun, 03 Jun 2018 13:49:24: end of X-cor INFO @ Sun, 03 Jun 2018 13:49:24: #2 finished! INFO @ Sun, 03 Jun 2018 13:49:24: #2 predicted fragment length is 89 bps INFO @ Sun, 03 Jun 2018 13:49:24: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sun, 03 Jun 2018 13:49:24: #2.2 Generate R script for model : SRX4085440.10_model.r WARNING @ Sun, 03 Jun 2018 13:49:24: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:49:24: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sun, 03 Jun 2018 13:49:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:49:24: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:49:25: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:49:25: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:49:25: #1 total tags in treatment: 15393971 INFO @ Sun, 03 Jun 2018 13:49:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:49:25: #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 13:49:25: #2 number of paired peaks: 263 WARNING @ Sun, 03 Jun 2018 13:49:25: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sun, 03 Jun 2018 13:49:25: start model_add_line... INFO @ Sun, 03 Jun 2018 13:49:25: start X-correlation... INFO @ Sun, 03 Jun 2018 13:49:25: end of X-cor INFO @ Sun, 03 Jun 2018 13:49:25: #2 finished! INFO @ Sun, 03 Jun 2018 13:49:25: #2 predicted fragment length is 89 bps INFO @ Sun, 03 Jun 2018 13:49:25: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sun, 03 Jun 2018 13:49:25: #2.2 Generate R script for model : SRX4085440.20_model.r WARNING @ Sun, 03 Jun 2018 13:49:25: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:49:25: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sun, 03 Jun 2018 13:49:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:49:25: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:49:25: #1 tags after filtering in treatment: 12520943 INFO @ Sun, 03 Jun 2018 13:49:25: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:49:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:49:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:49:26: #2 number of paired peaks: 263 WARNING @ Sun, 03 Jun 2018 13:49:26: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sun, 03 Jun 2018 13:49:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:49:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:49:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:49:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:49:26: #2 predicted fragment length is 89 bps INFO @ Sun, 03 Jun 2018 13:49:26: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sun, 03 Jun 2018 13:49:26: #2.2 Generate R script for model : SRX4085440.05_model.r WARNING @ Sun, 03 Jun 2018 13:49:26: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:49:26: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sun, 03 Jun 2018 13:49:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:49:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:49:50: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:49:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:49:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:50:03: #4 Write output xls file... SRX4085440.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:50:03: #4 Write peak in narrowPeak format file... SRX4085440.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:50:03: #4 Write summits bed file... SRX4085440.20_summits.bed INFO @ Sun, 03 Jun 2018 13:50:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (747 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:50:05: #4 Write output xls file... SRX4085440.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:50:05: #4 Write peak in narrowPeak format file... SRX4085440.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:50:05: #4 Write summits bed file... SRX4085440.10_summits.bed INFO @ Sun, 03 Jun 2018 13:50:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2359 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:50:09: #4 Write output xls file... SRX4085440.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:50:09: #4 Write peak in narrowPeak format file... SRX4085440.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:50:09: #4 Write summits bed file... SRX4085440.05_summits.bed INFO @ Sun, 03 Jun 2018 13:50:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4456 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。