Job ID = 10714427 sra ファイルのダウンロード中... Completed: 1566775K bytes transferred in 39 seconds (321338K 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 22476535 spots for /home/okishinya/chipatlas/results/ce10/SRX4085343/SRR7167372.sra Written 22476535 spots for /home/okishinya/chipatlas/results/ce10/SRX4085343/SRR7167372.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: 00:22:28 22476535 reads; of these: 22476535 (100.00%) were paired; of these: 1464331 (6.51%) aligned concordantly 0 times 18442593 (82.05%) aligned concordantly exactly 1 time 2569611 (11.43%) aligned concordantly >1 times ---- 1464331 pairs aligned concordantly 0 times; of these: 164314 (11.22%) aligned discordantly 1 time ---- 1300017 pairs aligned 0 times concordantly or discordantly; of these: 2600034 mates make up the pairs; of these: 1426080 (54.85%) aligned 0 times 968856 (37.26%) aligned exactly 1 time 205098 (7.89%) aligned >1 times 96.83% overall alignment rate Time searching: 00:22:28 Overall time: 00:22:28 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] 2439805 / 21110895 = 0.1156 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 13:06:45: # Command line: callpeak -t SRX4085343.bam -f BAM -g ce -n SRX4085343.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085343.20 # format = BAM # ChIP-seq file = ['SRX4085343.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 13:06:45: # Command line: callpeak -t SRX4085343.bam -f BAM -g ce -n SRX4085343.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085343.05 # format = BAM # ChIP-seq file = ['SRX4085343.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 13:06:45: # Command line: callpeak -t SRX4085343.bam -f BAM -g ce -n SRX4085343.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085343.10 # format = BAM # ChIP-seq file = ['SRX4085343.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 13:06:45: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:06:45: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:06:45: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:06:45: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:06:45: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:06:45: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:06:51: 1000000 INFO @ Sun, 03 Jun 2018 13:06:51: 1000000 INFO @ Sun, 03 Jun 2018 13:06:51: 1000000 INFO @ Sun, 03 Jun 2018 13:06:57: 2000000 INFO @ Sun, 03 Jun 2018 13:06:57: 2000000 INFO @ Sun, 03 Jun 2018 13:06:57: 2000000 INFO @ Sun, 03 Jun 2018 13:07:03: 3000000 INFO @ Sun, 03 Jun 2018 13:07:03: 3000000 INFO @ Sun, 03 Jun 2018 13:07:03: 3000000 INFO @ Sun, 03 Jun 2018 13:07:08: 4000000 INFO @ Sun, 03 Jun 2018 13:07:09: 4000000 INFO @ Sun, 03 Jun 2018 13:07:09: 4000000 INFO @ Sun, 03 Jun 2018 13:07:14: 5000000 INFO @ Sun, 03 Jun 2018 13:07:14: 5000000 INFO @ Sun, 03 Jun 2018 13:07:15: 5000000 INFO @ Sun, 03 Jun 2018 13:07:20: 6000000 INFO @ Sun, 03 Jun 2018 13:07:20: 6000000 INFO @ Sun, 03 Jun 2018 13:07:21: 6000000 INFO @ Sun, 03 Jun 2018 13:07:26: 7000000 INFO @ Sun, 03 Jun 2018 13:07:26: 7000000 INFO @ Sun, 03 Jun 2018 13:07:27: 7000000 INFO @ Sun, 03 Jun 2018 13:07:31: 8000000 INFO @ Sun, 03 Jun 2018 13:07:32: 8000000 INFO @ Sun, 03 Jun 2018 13:07:33: 8000000 INFO @ Sun, 03 Jun 2018 13:07:37: 9000000 INFO @ Sun, 03 Jun 2018 13:07:38: 9000000 INFO @ Sun, 03 Jun 2018 13:07:39: 9000000 INFO @ Sun, 03 Jun 2018 13:07:43: 10000000 INFO @ Sun, 03 Jun 2018 13:07:44: 10000000 INFO @ Sun, 03 Jun 2018 13:07:45: 10000000 INFO @ Sun, 03 Jun 2018 13:07:48: 11000000 INFO @ Sun, 03 Jun 2018 13:07:50: 11000000 INFO @ Sun, 03 Jun 2018 13:07:52: 11000000 INFO @ Sun, 03 Jun 2018 13:07:54: 12000000 INFO @ Sun, 03 Jun 2018 13:07:56: 12000000 INFO @ Sun, 03 Jun 2018 13:07:58: 12000000 INFO @ Sun, 03 Jun 2018 13:08:00: 13000000 INFO @ Sun, 03 Jun 2018 13:08:02: 13000000 INFO @ Sun, 03 Jun 2018 13:08:04: 13000000 INFO @ Sun, 03 Jun 2018 13:08:06: 14000000 INFO @ Sun, 03 Jun 2018 13:08:08: 14000000 INFO @ Sun, 03 Jun 2018 13:08:10: 14000000 INFO @ Sun, 03 Jun 2018 13:08:11: 15000000 INFO @ Sun, 03 Jun 2018 13:08:14: 15000000 INFO @ Sun, 03 Jun 2018 13:08:16: 15000000 INFO @ Sun, 03 Jun 2018 13:08:17: 16000000 INFO @ Sun, 03 Jun 2018 13:08:20: 16000000 INFO @ Sun, 03 Jun 2018 13:08:22: 16000000 INFO @ Sun, 03 Jun 2018 13:08:23: 17000000 INFO @ Sun, 03 Jun 2018 13:08:26: 17000000 INFO @ Sun, 03 Jun 2018 13:08:28: 17000000 INFO @ Sun, 03 Jun 2018 13:08:28: 18000000 INFO @ Sun, 03 Jun 2018 13:08:32: 18000000 INFO @ Sun, 03 Jun 2018 13:08:34: 18000000 INFO @ Sun, 03 Jun 2018 13:08:34: 19000000 INFO @ Sun, 03 Jun 2018 13:08:38: 19000000 INFO @ Sun, 03 Jun 2018 13:08:40: 19000000 INFO @ Sun, 03 Jun 2018 13:08:40: 20000000 INFO @ Sun, 03 Jun 2018 13:08:44: 20000000 INFO @ Sun, 03 Jun 2018 13:08:46: 20000000 INFO @ Sun, 03 Jun 2018 13:08:46: 21000000 INFO @ Sun, 03 Jun 2018 13:08:50: 21000000 INFO @ Sun, 03 Jun 2018 13:08:52: 21000000 INFO @ Sun, 03 Jun 2018 13:08:52: 22000000 INFO @ Sun, 03 Jun 2018 13:08:56: 22000000 INFO @ Sun, 03 Jun 2018 13:08:57: 22000000 INFO @ Sun, 03 Jun 2018 13:08:58: 23000000 INFO @ Sun, 03 Jun 2018 13:09:02: 23000000 INFO @ Sun, 03 Jun 2018 13:09:03: 23000000 INFO @ Sun, 03 Jun 2018 13:09:05: 24000000 INFO @ Sun, 03 Jun 2018 13:09:08: 24000000 INFO @ Sun, 03 Jun 2018 13:09:09: 24000000 INFO @ Sun, 03 Jun 2018 13:09:10: 25000000 INFO @ Sun, 03 Jun 2018 13:09:14: 25000000 INFO @ Sun, 03 Jun 2018 13:09:15: 25000000 INFO @ Sun, 03 Jun 2018 13:09:16: 26000000 INFO @ Sun, 03 Jun 2018 13:09:20: 26000000 INFO @ Sun, 03 Jun 2018 13:09:22: 26000000 INFO @ Sun, 03 Jun 2018 13:09:22: 27000000 INFO @ Sun, 03 Jun 2018 13:09:26: 27000000 INFO @ Sun, 03 Jun 2018 13:09:27: 28000000 INFO @ Sun, 03 Jun 2018 13:09:28: 27000000 INFO @ Sun, 03 Jun 2018 13:09:32: 28000000 INFO @ Sun, 03 Jun 2018 13:09:33: 29000000 INFO @ Sun, 03 Jun 2018 13:09:34: 28000000 INFO @ Sun, 03 Jun 2018 13:09:38: 29000000 INFO @ Sun, 03 Jun 2018 13:09:39: 30000000 INFO @ Sun, 03 Jun 2018 13:09:40: 29000000 INFO @ Sun, 03 Jun 2018 13:09:44: 30000000 INFO @ Sun, 03 Jun 2018 13:09:44: 31000000 INFO @ Sun, 03 Jun 2018 13:09:46: 30000000 INFO @ Sun, 03 Jun 2018 13:09:50: 32000000 INFO @ Sun, 03 Jun 2018 13:09:50: 31000000 INFO @ Sun, 03 Jun 2018 13:09:52: 31000000 INFO @ Sun, 03 Jun 2018 13:09:56: 33000000 INFO @ Sun, 03 Jun 2018 13:09:56: 32000000 INFO @ Sun, 03 Jun 2018 13:09:58: 32000000 INFO @ Sun, 03 Jun 2018 13:10:02: 34000000 INFO @ Sun, 03 Jun 2018 13:10:02: 33000000 INFO @ Sun, 03 Jun 2018 13:10:04: 33000000 INFO @ Sun, 03 Jun 2018 13:10:08: 35000000 INFO @ Sun, 03 Jun 2018 13:10:08: 34000000 INFO @ Sun, 03 Jun 2018 13:10:10: 34000000 INFO @ Sun, 03 Jun 2018 13:10:14: 36000000 INFO @ Sun, 03 Jun 2018 13:10:15: 35000000 INFO @ Sun, 03 Jun 2018 13:10:16: 35000000 INFO @ Sun, 03 Jun 2018 13:10:20: 37000000 INFO @ Sun, 03 Jun 2018 13:10:20: 36000000 INFO @ Sun, 03 Jun 2018 13:10:22: 36000000 INFO @ Sun, 03 Jun 2018 13:10:26: 38000000 INFO @ Sun, 03 Jun 2018 13:10:26: 37000000 INFO @ Sun, 03 Jun 2018 13:10:28: 37000000 INFO @ Sun, 03 Jun 2018 13:10:29: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:10:29: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:10:29: #1 total tags in treatment: 18579045 INFO @ Sun, 03 Jun 2018 13:10:29: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:10:29: #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 13:10:30: #1 tags after filtering in treatment: 15899853 INFO @ Sun, 03 Jun 2018 13:10:30: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:10:30: #1 finished! INFO @ Sun, 03 Jun 2018 13:10:30: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:10:31: #2 number of paired peaks: 188 WARNING @ Sun, 03 Jun 2018 13:10:31: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 03 Jun 2018 13:10:31: start model_add_line... INFO @ Sun, 03 Jun 2018 13:10:31: start X-correlation... INFO @ Sun, 03 Jun 2018 13:10:31: end of X-cor INFO @ Sun, 03 Jun 2018 13:10:31: #2 finished! INFO @ Sun, 03 Jun 2018 13:10:31: #2 predicted fragment length is 95 bps INFO @ Sun, 03 Jun 2018 13:10:31: #2 alternative fragment length(s) may be 3,95,129,155 bps INFO @ Sun, 03 Jun 2018 13:10:31: #2.2 Generate R script for model : SRX4085343.05_model.r WARNING @ Sun, 03 Jun 2018 13:10:31: #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 13:10:31: #2 You may need to consider one of the other alternative d(s): 3,95,129,155 WARNING @ Sun, 03 Jun 2018 13:10:31: #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 13:10:31: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:10:32: 38000000 INFO @ Sun, 03 Jun 2018 13:10:34: 38000000 INFO @ Sun, 03 Jun 2018 13:10:36: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:10:36: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:10:36: #1 total tags in treatment: 18579045 INFO @ Sun, 03 Jun 2018 13:10:36: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:10:36: #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 13:10:37: #1 tags after filtering in treatment: 15899853 INFO @ Sun, 03 Jun 2018 13:10:37: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:10:37: #1 finished! INFO @ Sun, 03 Jun 2018 13:10:37: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:10:38: #2 number of paired peaks: 188 WARNING @ Sun, 03 Jun 2018 13:10:38: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 03 Jun 2018 13:10:38: start model_add_line... INFO @ Sun, 03 Jun 2018 13:10:38: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:10:38: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:10:38: #1 total tags in treatment: 18579045 INFO @ Sun, 03 Jun 2018 13:10:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:10:38: #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 13:10:38: start X-correlation... INFO @ Sun, 03 Jun 2018 13:10:38: end of X-cor INFO @ Sun, 03 Jun 2018 13:10:38: #2 finished! INFO @ Sun, 03 Jun 2018 13:10:38: #2 predicted fragment length is 95 bps INFO @ Sun, 03 Jun 2018 13:10:38: #2 alternative fragment length(s) may be 3,95,129,155 bps INFO @ Sun, 03 Jun 2018 13:10:38: #2.2 Generate R script for model : SRX4085343.10_model.r WARNING @ Sun, 03 Jun 2018 13:10:38: #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 13:10:38: #2 You may need to consider one of the other alternative d(s): 3,95,129,155 WARNING @ Sun, 03 Jun 2018 13:10:38: #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 13:10:38: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:10:38: #1 tags after filtering in treatment: 15899853 INFO @ Sun, 03 Jun 2018 13:10:38: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:10:38: #1 finished! INFO @ Sun, 03 Jun 2018 13:10:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:10:39: #2 number of paired peaks: 188 WARNING @ Sun, 03 Jun 2018 13:10:39: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 03 Jun 2018 13:10:39: start model_add_line... INFO @ Sun, 03 Jun 2018 13:10:39: start X-correlation... INFO @ Sun, 03 Jun 2018 13:10:39: end of X-cor INFO @ Sun, 03 Jun 2018 13:10:39: #2 finished! INFO @ Sun, 03 Jun 2018 13:10:39: #2 predicted fragment length is 95 bps INFO @ Sun, 03 Jun 2018 13:10:39: #2 alternative fragment length(s) may be 3,95,129,155 bps INFO @ Sun, 03 Jun 2018 13:10:39: #2.2 Generate R script for model : SRX4085343.20_model.r WARNING @ Sun, 03 Jun 2018 13:10:39: #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 13:10:39: #2 You may need to consider one of the other alternative d(s): 3,95,129,155 WARNING @ Sun, 03 Jun 2018 13:10:39: #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 13:10:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:11:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:11:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:11:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:11:18: #4 Write output xls file... SRX4085343.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:11:19: #4 Write peak in narrowPeak format file... SRX4085343.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:11:19: #4 Write summits bed file... SRX4085343.05_summits.bed INFO @ Sun, 03 Jun 2018 13:11:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4012 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:11:25: #4 Write output xls file... SRX4085343.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:11:25: #4 Write peak in narrowPeak format file... SRX4085343.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:11:25: #4 Write summits bed file... SRX4085343.10_summits.bed INFO @ Sun, 03 Jun 2018 13:11:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1585 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:11:31: #4 Write output xls file... SRX4085343.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:11:31: #4 Write peak in narrowPeak format file... SRX4085343.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:11:31: #4 Write summits bed file... SRX4085343.20_summits.bed INFO @ Sun, 03 Jun 2018 13:11:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。