Job ID = 10714454 sra ファイルのダウンロード中... Completed: 1431761K bytes transferred in 24 seconds (474918K 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 21514033 spots for /home/okishinya/chipatlas/results/ce10/SRX4085370/SRR7167399.sra Written 21514033 spots for /home/okishinya/chipatlas/results/ce10/SRX4085370/SRR7167399.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: 00:17:02 21514033 reads; of these: 21514033 (100.00%) were paired; of these: 7543932 (35.07%) aligned concordantly 0 times 12318537 (57.26%) aligned concordantly exactly 1 time 1651564 (7.68%) aligned concordantly >1 times ---- 7543932 pairs aligned concordantly 0 times; of these: 366193 (4.85%) aligned discordantly 1 time ---- 7177739 pairs aligned 0 times concordantly or discordantly; of these: 14355478 mates make up the pairs; of these: 11347548 (79.05%) aligned 0 times 2636069 (18.36%) aligned exactly 1 time 371861 (2.59%) aligned >1 times 73.63% overall alignment rate Time searching: 00:17:02 Overall time: 00:17:02 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] 967903 / 14222307 = 0.0681 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 13:07:45: # Command line: callpeak -t SRX4085370.bam -f BAM -g ce -n SRX4085370.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085370.10 # format = BAM # ChIP-seq file = ['SRX4085370.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 13:07:45: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:07:45: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:07:45: # Command line: callpeak -t SRX4085370.bam -f BAM -g ce -n SRX4085370.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085370.20 # format = BAM # ChIP-seq file = ['SRX4085370.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 13:07:45: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:07:45: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:07:45: # Command line: callpeak -t SRX4085370.bam -f BAM -g ce -n SRX4085370.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085370.05 # format = BAM # ChIP-seq file = ['SRX4085370.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 13:07:45: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:07:45: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:07:50: 1000000 INFO @ Sun, 03 Jun 2018 13:07:51: 1000000 INFO @ Sun, 03 Jun 2018 13:07:51: 1000000 INFO @ Sun, 03 Jun 2018 13:07:55: 2000000 INFO @ Sun, 03 Jun 2018 13:07:57: 2000000 INFO @ Sun, 03 Jun 2018 13:07:57: 2000000 INFO @ Sun, 03 Jun 2018 13:08:01: 3000000 INFO @ Sun, 03 Jun 2018 13:08:03: 3000000 INFO @ Sun, 03 Jun 2018 13:08:03: 3000000 INFO @ Sun, 03 Jun 2018 13:08:06: 4000000 INFO @ Sun, 03 Jun 2018 13:08:08: 4000000 INFO @ Sun, 03 Jun 2018 13:08:09: 4000000 INFO @ Sun, 03 Jun 2018 13:08:11: 5000000 INFO @ Sun, 03 Jun 2018 13:08:14: 5000000 INFO @ Sun, 03 Jun 2018 13:08:15: 5000000 INFO @ Sun, 03 Jun 2018 13:08:16: 6000000 INFO @ Sun, 03 Jun 2018 13:08:20: 6000000 INFO @ Sun, 03 Jun 2018 13:08:21: 6000000 INFO @ Sun, 03 Jun 2018 13:08:22: 7000000 INFO @ Sun, 03 Jun 2018 13:08:25: 7000000 INFO @ Sun, 03 Jun 2018 13:08:27: 7000000 INFO @ Sun, 03 Jun 2018 13:08:27: 8000000 INFO @ Sun, 03 Jun 2018 13:08:31: 8000000 INFO @ Sun, 03 Jun 2018 13:08:33: 8000000 INFO @ Sun, 03 Jun 2018 13:08:33: 9000000 INFO @ Sun, 03 Jun 2018 13:08:36: 9000000 INFO @ Sun, 03 Jun 2018 13:08:38: 9000000 INFO @ Sun, 03 Jun 2018 13:08:38: 10000000 INFO @ Sun, 03 Jun 2018 13:08:42: 10000000 INFO @ Sun, 03 Jun 2018 13:08:44: 11000000 INFO @ Sun, 03 Jun 2018 13:08:44: 10000000 INFO @ Sun, 03 Jun 2018 13:08:47: 11000000 INFO @ Sun, 03 Jun 2018 13:08:49: 12000000 INFO @ Sun, 03 Jun 2018 13:08:50: 11000000 INFO @ Sun, 03 Jun 2018 13:08:53: 12000000 INFO @ Sun, 03 Jun 2018 13:08:55: 13000000 INFO @ Sun, 03 Jun 2018 13:08:56: 12000000 INFO @ Sun, 03 Jun 2018 13:08:58: 13000000 INFO @ Sun, 03 Jun 2018 13:09:01: 14000000 INFO @ Sun, 03 Jun 2018 13:09:01: 13000000 INFO @ Sun, 03 Jun 2018 13:09:04: 14000000 INFO @ Sun, 03 Jun 2018 13:09:07: 15000000 INFO @ Sun, 03 Jun 2018 13:09:07: 14000000 INFO @ Sun, 03 Jun 2018 13:09:10: 15000000 INFO @ Sun, 03 Jun 2018 13:09:12: 16000000 INFO @ Sun, 03 Jun 2018 13:09:13: 15000000 INFO @ Sun, 03 Jun 2018 13:09:15: 16000000 INFO @ Sun, 03 Jun 2018 13:09:18: 17000000 INFO @ Sun, 03 Jun 2018 13:09:19: 16000000 INFO @ Sun, 03 Jun 2018 13:09:21: 17000000 INFO @ Sun, 03 Jun 2018 13:09:23: 18000000 INFO @ Sun, 03 Jun 2018 13:09:25: 17000000 INFO @ Sun, 03 Jun 2018 13:09:26: 18000000 INFO @ Sun, 03 Jun 2018 13:09:28: 19000000 INFO @ Sun, 03 Jun 2018 13:09:31: 18000000 INFO @ Sun, 03 Jun 2018 13:09:32: 19000000 INFO @ Sun, 03 Jun 2018 13:09:34: 20000000 INFO @ Sun, 03 Jun 2018 13:09:37: 19000000 INFO @ Sun, 03 Jun 2018 13:09:38: 20000000 INFO @ Sun, 03 Jun 2018 13:09:39: 21000000 INFO @ Sun, 03 Jun 2018 13:09:42: 20000000 INFO @ Sun, 03 Jun 2018 13:09:43: 21000000 INFO @ Sun, 03 Jun 2018 13:09:45: 22000000 INFO @ Sun, 03 Jun 2018 13:09:48: 21000000 INFO @ Sun, 03 Jun 2018 13:09:49: 22000000 INFO @ Sun, 03 Jun 2018 13:09:50: 23000000 INFO @ Sun, 03 Jun 2018 13:09:54: 22000000 INFO @ Sun, 03 Jun 2018 13:09:54: 23000000 INFO @ Sun, 03 Jun 2018 13:09:56: 24000000 INFO @ Sun, 03 Jun 2018 13:10:00: 23000000 INFO @ Sun, 03 Jun 2018 13:10:00: 24000000 INFO @ Sun, 03 Jun 2018 13:10:01: 25000000 INFO @ Sun, 03 Jun 2018 13:10:05: 25000000 INFO @ Sun, 03 Jun 2018 13:10:06: 24000000 INFO @ Sun, 03 Jun 2018 13:10:07: 26000000 INFO @ Sun, 03 Jun 2018 13:10:11: 26000000 INFO @ Sun, 03 Jun 2018 13:10:11: 25000000 INFO @ Sun, 03 Jun 2018 13:10:12: 27000000 INFO @ Sun, 03 Jun 2018 13:10:17: 27000000 INFO @ Sun, 03 Jun 2018 13:10:17: 26000000 INFO @ Sun, 03 Jun 2018 13:10:18: 28000000 INFO @ Sun, 03 Jun 2018 13:10:22: 28000000 INFO @ Sun, 03 Jun 2018 13:10:23: 29000000 INFO @ Sun, 03 Jun 2018 13:10:23: 27000000 INFO @ Sun, 03 Jun 2018 13:10:27: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:10:27: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:10:27: #1 total tags in treatment: 13018811 INFO @ Sun, 03 Jun 2018 13:10:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:10:27: #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 13:10:27: #1 tags after filtering in treatment: 11295931 INFO @ Sun, 03 Jun 2018 13:10:27: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:10:27: #1 finished! INFO @ Sun, 03 Jun 2018 13:10:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:10:28: #2 number of paired peaks: 185 WARNING @ Sun, 03 Jun 2018 13:10:28: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 03 Jun 2018 13:10:28: start model_add_line... INFO @ Sun, 03 Jun 2018 13:10:28: 29000000 INFO @ Sun, 03 Jun 2018 13:10:28: start X-correlation... INFO @ Sun, 03 Jun 2018 13:10:28: end of X-cor INFO @ Sun, 03 Jun 2018 13:10:28: #2 finished! INFO @ Sun, 03 Jun 2018 13:10:28: #2 predicted fragment length is 95 bps INFO @ Sun, 03 Jun 2018 13:10:28: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sun, 03 Jun 2018 13:10:28: #2.2 Generate R script for model : SRX4085370.10_model.r WARNING @ Sun, 03 Jun 2018 13:10:28: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:10:28: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Sun, 03 Jun 2018 13:10:28: #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 13:10:28: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:10:29: 28000000 INFO @ Sun, 03 Jun 2018 13:10:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:10:32: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:10:32: #1 total tags in treatment: 13018811 INFO @ Sun, 03 Jun 2018 13:10:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:10:32: #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 13:10:32: #1 tags after filtering in treatment: 11295931 INFO @ Sun, 03 Jun 2018 13:10:32: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:10:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:10:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:10:33: #2 number of paired peaks: 185 WARNING @ Sun, 03 Jun 2018 13:10:33: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 03 Jun 2018 13:10:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:10:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:10:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:10:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:10:33: #2 predicted fragment length is 95 bps INFO @ Sun, 03 Jun 2018 13:10:33: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sun, 03 Jun 2018 13:10:33: #2.2 Generate R script for model : SRX4085370.05_model.r WARNING @ Sun, 03 Jun 2018 13:10:33: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:10:33: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Sun, 03 Jun 2018 13:10:33: #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 13:10:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:10:35: 29000000 INFO @ Sun, 03 Jun 2018 13:10:39: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:10:39: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:10:39: #1 total tags in treatment: 13018811 INFO @ Sun, 03 Jun 2018 13:10:39: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:10:39: #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 13:10:39: #1 tags after filtering in treatment: 11295931 INFO @ Sun, 03 Jun 2018 13:10:39: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:10:39: #1 finished! INFO @ Sun, 03 Jun 2018 13:10:39: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:10:40: #2 number of paired peaks: 185 WARNING @ Sun, 03 Jun 2018 13:10:40: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sun, 03 Jun 2018 13:10:40: start model_add_line... INFO @ Sun, 03 Jun 2018 13:10:40: start X-correlation... INFO @ Sun, 03 Jun 2018 13:10:40: end of X-cor INFO @ Sun, 03 Jun 2018 13:10:40: #2 finished! INFO @ Sun, 03 Jun 2018 13:10:40: #2 predicted fragment length is 95 bps INFO @ Sun, 03 Jun 2018 13:10:40: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sun, 03 Jun 2018 13:10:40: #2.2 Generate R script for model : SRX4085370.20_model.r WARNING @ Sun, 03 Jun 2018 13:10:40: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:10:40: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Sun, 03 Jun 2018 13:10:40: #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 13:10:40: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:10:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:10:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:11:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:11:07: #4 Write output xls file... SRX4085370.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:11:07: #4 Write peak in narrowPeak format file... SRX4085370.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:11:07: #4 Write summits bed file... SRX4085370.10_summits.bed INFO @ Sun, 03 Jun 2018 13:11:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1858 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:11:10: #4 Write output xls file... SRX4085370.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:11:10: #4 Write peak in narrowPeak format file... SRX4085370.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:11:10: #4 Write summits bed file... SRX4085370.05_summits.bed INFO @ Sun, 03 Jun 2018 13:11:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4073 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:11:19: #4 Write output xls file... SRX4085370.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:11:19: #4 Write peak in narrowPeak format file... SRX4085370.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:11:19: #4 Write summits bed file... SRX4085370.20_summits.bed INFO @ Sun, 03 Jun 2018 13:11:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 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。