Job ID = 10714431 sra ファイルのダウンロード中... Completed: 1708959K bytes transferred in 16 seconds (869815K 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 24577688 spots for /home/okishinya/chipatlas/results/ce10/SRX4085347/SRR7167376.sra Written 24577688 spots for /home/okishinya/chipatlas/results/ce10/SRX4085347/SRR7167376.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: 00:24:03 24577688 reads; of these: 24577688 (100.00%) were paired; of these: 1512851 (6.16%) aligned concordantly 0 times 20118231 (81.86%) aligned concordantly exactly 1 time 2946606 (11.99%) aligned concordantly >1 times ---- 1512851 pairs aligned concordantly 0 times; of these: 137989 (9.12%) aligned discordantly 1 time ---- 1374862 pairs aligned 0 times concordantly or discordantly; of these: 2749724 mates make up the pairs; of these: 2127563 (77.37%) aligned 0 times 486466 (17.69%) aligned exactly 1 time 135695 (4.93%) aligned >1 times 95.67% overall alignment rate Time searching: 00:24:04 Overall time: 00:24:04 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] 6082269 / 23177044 = 0.2624 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 13:08:08: # Command line: callpeak -t SRX4085347.bam -f BAM -g ce -n SRX4085347.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085347.20 # format = BAM # ChIP-seq file = ['SRX4085347.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 13:08:08: # Command line: callpeak -t SRX4085347.bam -f BAM -g ce -n SRX4085347.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085347.10 # format = BAM # ChIP-seq file = ['SRX4085347.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 13:08:08: # Command line: callpeak -t SRX4085347.bam -f BAM -g ce -n SRX4085347.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085347.05 # format = BAM # ChIP-seq file = ['SRX4085347.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 13:08:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:08:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:08:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:08:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:08:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:08:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:08:15: 1000000 INFO @ Sun, 03 Jun 2018 13:08:15: 1000000 INFO @ Sun, 03 Jun 2018 13:08:15: 1000000 INFO @ Sun, 03 Jun 2018 13:08:21: 2000000 INFO @ Sun, 03 Jun 2018 13:08:21: 2000000 INFO @ Sun, 03 Jun 2018 13:08:21: 2000000 INFO @ Sun, 03 Jun 2018 13:08:27: 3000000 INFO @ Sun, 03 Jun 2018 13:08:27: 3000000 INFO @ Sun, 03 Jun 2018 13:08:27: 3000000 INFO @ Sun, 03 Jun 2018 13:08:33: 4000000 INFO @ Sun, 03 Jun 2018 13:08:34: 4000000 INFO @ Sun, 03 Jun 2018 13:08:34: 4000000 INFO @ Sun, 03 Jun 2018 13:08:40: 5000000 INFO @ Sun, 03 Jun 2018 13:08:40: 5000000 INFO @ Sun, 03 Jun 2018 13:08:40: 5000000 INFO @ Sun, 03 Jun 2018 13:08:46: 6000000 INFO @ Sun, 03 Jun 2018 13:08:46: 6000000 INFO @ Sun, 03 Jun 2018 13:08:46: 6000000 INFO @ Sun, 03 Jun 2018 13:08:52: 7000000 INFO @ Sun, 03 Jun 2018 13:08:53: 7000000 INFO @ Sun, 03 Jun 2018 13:08:53: 7000000 INFO @ Sun, 03 Jun 2018 13:08:58: 8000000 INFO @ Sun, 03 Jun 2018 13:08:59: 8000000 INFO @ Sun, 03 Jun 2018 13:08:59: 8000000 INFO @ Sun, 03 Jun 2018 13:09:04: 9000000 INFO @ Sun, 03 Jun 2018 13:09:05: 9000000 INFO @ Sun, 03 Jun 2018 13:09:05: 9000000 INFO @ Sun, 03 Jun 2018 13:09:10: 10000000 INFO @ Sun, 03 Jun 2018 13:09:12: 10000000 INFO @ Sun, 03 Jun 2018 13:09:12: 10000000 INFO @ Sun, 03 Jun 2018 13:09:16: 11000000 INFO @ Sun, 03 Jun 2018 13:09:18: 11000000 INFO @ Sun, 03 Jun 2018 13:09:18: 11000000 INFO @ Sun, 03 Jun 2018 13:09:22: 12000000 INFO @ Sun, 03 Jun 2018 13:09:25: 12000000 INFO @ Sun, 03 Jun 2018 13:09:25: 12000000 INFO @ Sun, 03 Jun 2018 13:09:28: 13000000 INFO @ Sun, 03 Jun 2018 13:09:31: 13000000 INFO @ Sun, 03 Jun 2018 13:09:31: 13000000 INFO @ Sun, 03 Jun 2018 13:09:34: 14000000 INFO @ Sun, 03 Jun 2018 13:09:37: 14000000 INFO @ Sun, 03 Jun 2018 13:09:37: 14000000 INFO @ Sun, 03 Jun 2018 13:09:40: 15000000 INFO @ Sun, 03 Jun 2018 13:09:44: 15000000 INFO @ Sun, 03 Jun 2018 13:09:44: 15000000 INFO @ Sun, 03 Jun 2018 13:09:46: 16000000 INFO @ Sun, 03 Jun 2018 13:09:50: 16000000 INFO @ Sun, 03 Jun 2018 13:09:50: 16000000 INFO @ Sun, 03 Jun 2018 13:09:52: 17000000 INFO @ Sun, 03 Jun 2018 13:09:56: 17000000 INFO @ Sun, 03 Jun 2018 13:09:56: 17000000 INFO @ Sun, 03 Jun 2018 13:09:58: 18000000 INFO @ Sun, 03 Jun 2018 13:10:03: 18000000 INFO @ Sun, 03 Jun 2018 13:10:03: 18000000 INFO @ Sun, 03 Jun 2018 13:10:04: 19000000 INFO @ Sun, 03 Jun 2018 13:10:09: 19000000 INFO @ Sun, 03 Jun 2018 13:10:09: 19000000 INFO @ Sun, 03 Jun 2018 13:10:10: 20000000 INFO @ Sun, 03 Jun 2018 13:10:15: 20000000 INFO @ Sun, 03 Jun 2018 13:10:15: 20000000 INFO @ Sun, 03 Jun 2018 13:10:16: 21000000 INFO @ Sun, 03 Jun 2018 13:10:21: 21000000 INFO @ Sun, 03 Jun 2018 13:10:22: 21000000 INFO @ Sun, 03 Jun 2018 13:10:22: 22000000 INFO @ Sun, 03 Jun 2018 13:10:27: 22000000 INFO @ Sun, 03 Jun 2018 13:10:28: 22000000 INFO @ Sun, 03 Jun 2018 13:10:29: 23000000 INFO @ Sun, 03 Jun 2018 13:10:33: 23000000 INFO @ Sun, 03 Jun 2018 13:10:34: 23000000 INFO @ Sun, 03 Jun 2018 13:10:35: 24000000 INFO @ Sun, 03 Jun 2018 13:10:40: 24000000 INFO @ Sun, 03 Jun 2018 13:10:40: 24000000 INFO @ Sun, 03 Jun 2018 13:10:41: 25000000 INFO @ Sun, 03 Jun 2018 13:10:46: 25000000 INFO @ Sun, 03 Jun 2018 13:10:47: 25000000 INFO @ Sun, 03 Jun 2018 13:10:48: 26000000 INFO @ Sun, 03 Jun 2018 13:10:52: 26000000 INFO @ Sun, 03 Jun 2018 13:10:53: 26000000 INFO @ Sun, 03 Jun 2018 13:10:54: 27000000 INFO @ Sun, 03 Jun 2018 13:10:58: 27000000 INFO @ Sun, 03 Jun 2018 13:11:00: 27000000 INFO @ Sun, 03 Jun 2018 13:11:00: 28000000 INFO @ Sun, 03 Jun 2018 13:11:04: 28000000 INFO @ Sun, 03 Jun 2018 13:11:06: 28000000 INFO @ Sun, 03 Jun 2018 13:11:07: 29000000 INFO @ Sun, 03 Jun 2018 13:11:10: 29000000 INFO @ Sun, 03 Jun 2018 13:11:13: 29000000 INFO @ Sun, 03 Jun 2018 13:11:13: 30000000 INFO @ Sun, 03 Jun 2018 13:11:16: 30000000 INFO @ Sun, 03 Jun 2018 13:11:19: 30000000 INFO @ Sun, 03 Jun 2018 13:11:20: 31000000 INFO @ Sun, 03 Jun 2018 13:11:23: 31000000 INFO @ Sun, 03 Jun 2018 13:11:26: 31000000 INFO @ Sun, 03 Jun 2018 13:11:26: 32000000 INFO @ Sun, 03 Jun 2018 13:11:29: 32000000 INFO @ Sun, 03 Jun 2018 13:11:32: 32000000 INFO @ Sun, 03 Jun 2018 13:11:33: 33000000 INFO @ Sun, 03 Jun 2018 13:11:35: 33000000 INFO @ Sun, 03 Jun 2018 13:11:38: 34000000 INFO @ Sun, 03 Jun 2018 13:11:39: 33000000 INFO @ Sun, 03 Jun 2018 13:11:41: 34000000 INFO @ Sun, 03 Jun 2018 13:11:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:11:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:11:43: #1 total tags in treatment: 16999680 INFO @ Sun, 03 Jun 2018 13:11:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:11:43: #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 13:11:44: #1 tags after filtering in treatment: 14300441 INFO @ Sun, 03 Jun 2018 13:11:44: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:11:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:11:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:11:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:11:45: #2 number of paired peaks: 213 WARNING @ Sun, 03 Jun 2018 13:11:45: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sun, 03 Jun 2018 13:11:45: start model_add_line... INFO @ Sun, 03 Jun 2018 13:11:45: start X-correlation... INFO @ Sun, 03 Jun 2018 13:11:45: end of X-cor INFO @ Sun, 03 Jun 2018 13:11:45: #2 finished! INFO @ Sun, 03 Jun 2018 13:11:45: #2 predicted fragment length is 92 bps INFO @ Sun, 03 Jun 2018 13:11:45: #2 alternative fragment length(s) may be 3,64,92 bps INFO @ Sun, 03 Jun 2018 13:11:45: #2.2 Generate R script for model : SRX4085347.20_model.r WARNING @ Sun, 03 Jun 2018 13:11:45: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:11:45: #2 You may need to consider one of the other alternative d(s): 3,64,92 WARNING @ Sun, 03 Jun 2018 13:11:45: #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 13:11:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:11:45: 34000000 INFO @ Sun, 03 Jun 2018 13:11:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:11:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:11:47: #1 total tags in treatment: 16999680 INFO @ Sun, 03 Jun 2018 13:11:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:11:47: #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 13:11:47: #1 tags after filtering in treatment: 14300441 INFO @ Sun, 03 Jun 2018 13:11:47: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:11:47: #1 finished! INFO @ Sun, 03 Jun 2018 13:11:47: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:11:48: #2 number of paired peaks: 213 WARNING @ Sun, 03 Jun 2018 13:11:48: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sun, 03 Jun 2018 13:11:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:11:48: start X-correlation... INFO @ Sun, 03 Jun 2018 13:11:48: end of X-cor INFO @ Sun, 03 Jun 2018 13:11:48: #2 finished! INFO @ Sun, 03 Jun 2018 13:11:48: #2 predicted fragment length is 92 bps INFO @ Sun, 03 Jun 2018 13:11:48: #2 alternative fragment length(s) may be 3,64,92 bps INFO @ Sun, 03 Jun 2018 13:11:48: #2.2 Generate R script for model : SRX4085347.05_model.r WARNING @ Sun, 03 Jun 2018 13:11:48: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:11:48: #2 You may need to consider one of the other alternative d(s): 3,64,92 WARNING @ Sun, 03 Jun 2018 13:11:48: #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 13:11:48: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:11:50: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:11:50: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:11:50: #1 total tags in treatment: 16999680 INFO @ Sun, 03 Jun 2018 13:11:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:11:50: #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 13:11:51: #1 tags after filtering in treatment: 14300441 INFO @ Sun, 03 Jun 2018 13:11:51: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:11:51: #1 finished! INFO @ Sun, 03 Jun 2018 13:11:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:11:52: #2 number of paired peaks: 213 WARNING @ Sun, 03 Jun 2018 13:11:52: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sun, 03 Jun 2018 13:11:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:11:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:11:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:11:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:11:52: #2 predicted fragment length is 92 bps INFO @ Sun, 03 Jun 2018 13:11:52: #2 alternative fragment length(s) may be 3,64,92 bps INFO @ Sun, 03 Jun 2018 13:11:52: #2.2 Generate R script for model : SRX4085347.10_model.r WARNING @ Sun, 03 Jun 2018 13:11:52: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:11:52: #2 You may need to consider one of the other alternative d(s): 3,64,92 WARNING @ Sun, 03 Jun 2018 13:11:52: #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 13:11:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:11:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:13: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:28: #4 Write output xls file... SRX4085347.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:12:28: #4 Write peak in narrowPeak format file... SRX4085347.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:28: #4 Write summits bed file... SRX4085347.20_summits.bed INFO @ Sun, 03 Jun 2018 13:12:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:12:33: #4 Write output xls file... SRX4085347.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:12:33: #4 Write peak in narrowPeak format file... SRX4085347.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:33: #4 Write summits bed file... SRX4085347.05_summits.bed INFO @ Sun, 03 Jun 2018 13:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:12:36: #4 Write output xls file... SRX4085347.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:12:36: #4 Write peak in narrowPeak format file... SRX4085347.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:36: #4 Write summits bed file... SRX4085347.10_summits.bed INFO @ Sun, 03 Jun 2018 13:12:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。