Job ID = 10714428 sra ファイルのダウンロード中... Completed: 1087444K bytes transferred in 30 seconds (293226K 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 15586363 spots for /home/okishinya/chipatlas/results/ce10/SRX4085344/SRR7167373.sra Written 15586363 spots for /home/okishinya/chipatlas/results/ce10/SRX4085344/SRR7167373.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: 00:14:52 15586363 reads; of these: 15586363 (100.00%) were paired; of these: 729539 (4.68%) aligned concordantly 0 times 13232780 (84.90%) aligned concordantly exactly 1 time 1624044 (10.42%) aligned concordantly >1 times ---- 729539 pairs aligned concordantly 0 times; of these: 144296 (19.78%) aligned discordantly 1 time ---- 585243 pairs aligned 0 times concordantly or discordantly; of these: 1170486 mates make up the pairs; of these: 627377 (53.60%) aligned 0 times 433608 (37.05%) aligned exactly 1 time 109501 (9.36%) aligned >1 times 97.99% overall alignment rate Time searching: 00:14:52 Overall time: 00:14:52 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] 1247330 / 14935003 = 0.0835 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 12:54:38: # Command line: callpeak -t SRX4085344.bam -f BAM -g ce -n SRX4085344.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085344.05 # format = BAM # ChIP-seq file = ['SRX4085344.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 12:54:38: # Command line: callpeak -t SRX4085344.bam -f BAM -g ce -n SRX4085344.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085344.20 # format = BAM # ChIP-seq file = ['SRX4085344.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 12:54:38: # Command line: callpeak -t SRX4085344.bam -f BAM -g ce -n SRX4085344.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085344.10 # format = BAM # ChIP-seq file = ['SRX4085344.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 12:54:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:45: 1000000 INFO @ Sun, 03 Jun 2018 12:54:45: 1000000 INFO @ Sun, 03 Jun 2018 12:54:45: 1000000 INFO @ Sun, 03 Jun 2018 12:54:51: 2000000 INFO @ Sun, 03 Jun 2018 12:54:51: 2000000 INFO @ Sun, 03 Jun 2018 12:54:51: 2000000 INFO @ Sun, 03 Jun 2018 12:54:57: 3000000 INFO @ Sun, 03 Jun 2018 12:54:58: 3000000 INFO @ Sun, 03 Jun 2018 12:54:58: 3000000 INFO @ Sun, 03 Jun 2018 12:55:04: 4000000 INFO @ Sun, 03 Jun 2018 12:55:04: 4000000 INFO @ Sun, 03 Jun 2018 12:55:04: 4000000 INFO @ Sun, 03 Jun 2018 12:55:10: 5000000 INFO @ Sun, 03 Jun 2018 12:55:10: 5000000 INFO @ Sun, 03 Jun 2018 12:55:10: 5000000 INFO @ Sun, 03 Jun 2018 12:55:16: 6000000 INFO @ Sun, 03 Jun 2018 12:55:17: 6000000 INFO @ Sun, 03 Jun 2018 12:55:17: 6000000 INFO @ Sun, 03 Jun 2018 12:55:22: 7000000 INFO @ Sun, 03 Jun 2018 12:55:23: 7000000 INFO @ Sun, 03 Jun 2018 12:55:23: 7000000 INFO @ Sun, 03 Jun 2018 12:55:28: 8000000 INFO @ Sun, 03 Jun 2018 12:55:29: 8000000 INFO @ Sun, 03 Jun 2018 12:55:29: 8000000 INFO @ Sun, 03 Jun 2018 12:55:35: 9000000 INFO @ Sun, 03 Jun 2018 12:55:35: 9000000 INFO @ Sun, 03 Jun 2018 12:55:35: 9000000 INFO @ Sun, 03 Jun 2018 12:55:41: 10000000 INFO @ Sun, 03 Jun 2018 12:55:42: 10000000 INFO @ Sun, 03 Jun 2018 12:55:42: 10000000 INFO @ Sun, 03 Jun 2018 12:55:47: 11000000 INFO @ Sun, 03 Jun 2018 12:55:48: 11000000 INFO @ Sun, 03 Jun 2018 12:55:48: 11000000 INFO @ Sun, 03 Jun 2018 12:55:53: 12000000 INFO @ Sun, 03 Jun 2018 12:55:54: 12000000 INFO @ Sun, 03 Jun 2018 12:55:54: 12000000 INFO @ Sun, 03 Jun 2018 12:55:59: 13000000 INFO @ Sun, 03 Jun 2018 12:56:00: 13000000 INFO @ Sun, 03 Jun 2018 12:56:00: 13000000 INFO @ Sun, 03 Jun 2018 12:56:06: 14000000 INFO @ Sun, 03 Jun 2018 12:56:07: 14000000 INFO @ Sun, 03 Jun 2018 12:56:07: 14000000 INFO @ Sun, 03 Jun 2018 12:56:13: 15000000 INFO @ Sun, 03 Jun 2018 12:56:13: 15000000 INFO @ Sun, 03 Jun 2018 12:56:13: 15000000 INFO @ Sun, 03 Jun 2018 12:56:19: 16000000 INFO @ Sun, 03 Jun 2018 12:56:19: 16000000 INFO @ Sun, 03 Jun 2018 12:56:19: 16000000 INFO @ Sun, 03 Jun 2018 12:56:25: 17000000 INFO @ Sun, 03 Jun 2018 12:56:26: 17000000 INFO @ Sun, 03 Jun 2018 12:56:26: 17000000 INFO @ Sun, 03 Jun 2018 12:56:31: 18000000 INFO @ Sun, 03 Jun 2018 12:56:32: 18000000 INFO @ Sun, 03 Jun 2018 12:56:32: 18000000 INFO @ Sun, 03 Jun 2018 12:56:37: 19000000 INFO @ Sun, 03 Jun 2018 12:56:38: 19000000 INFO @ Sun, 03 Jun 2018 12:56:38: 19000000 INFO @ Sun, 03 Jun 2018 12:56:43: 20000000 INFO @ Sun, 03 Jun 2018 12:56:44: 20000000 INFO @ Sun, 03 Jun 2018 12:56:44: 20000000 INFO @ Sun, 03 Jun 2018 12:56:49: 21000000 INFO @ Sun, 03 Jun 2018 12:56:50: 21000000 INFO @ Sun, 03 Jun 2018 12:56:51: 21000000 INFO @ Sun, 03 Jun 2018 12:56:55: 22000000 INFO @ Sun, 03 Jun 2018 12:56:57: 22000000 INFO @ Sun, 03 Jun 2018 12:56:57: 22000000 INFO @ Sun, 03 Jun 2018 12:57:01: 23000000 INFO @ Sun, 03 Jun 2018 12:57:03: 23000000 INFO @ Sun, 03 Jun 2018 12:57:04: 23000000 INFO @ Sun, 03 Jun 2018 12:57:07: 24000000 INFO @ Sun, 03 Jun 2018 12:57:10: 24000000 INFO @ Sun, 03 Jun 2018 12:57:11: 24000000 INFO @ Sun, 03 Jun 2018 12:57:14: 25000000 INFO @ Sun, 03 Jun 2018 12:57:16: 25000000 INFO @ Sun, 03 Jun 2018 12:57:17: 25000000 INFO @ Sun, 03 Jun 2018 12:57:20: 26000000 INFO @ Sun, 03 Jun 2018 12:57:22: 26000000 INFO @ Sun, 03 Jun 2018 12:57:23: 26000000 INFO @ Sun, 03 Jun 2018 12:57:26: 27000000 INFO @ Sun, 03 Jun 2018 12:57:29: 27000000 INFO @ Sun, 03 Jun 2018 12:57:29: 27000000 INFO @ Sun, 03 Jun 2018 12:57:33: 28000000 INFO @ Sun, 03 Jun 2018 12:57:33: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:33: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:33: #1 total tags in treatment: 13613218 INFO @ Sun, 03 Jun 2018 12:57:33: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:33: #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 12:57:33: #1 tags after filtering in treatment: 12071562 INFO @ Sun, 03 Jun 2018 12:57:33: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 12:57:33: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:33: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:34: #2 number of paired peaks: 148 WARNING @ Sun, 03 Jun 2018 12:57:34: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:34: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:34: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:34: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:34: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:34: #2 predicted fragment length is 97 bps INFO @ Sun, 03 Jun 2018 12:57:34: #2 alternative fragment length(s) may be 3,97,122,199,226 bps INFO @ Sun, 03 Jun 2018 12:57:34: #2.2 Generate R script for model : SRX4085344.10_model.r WARNING @ Sun, 03 Jun 2018 12:57:34: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:57:34: #2 You may need to consider one of the other alternative d(s): 3,97,122,199,226 WARNING @ Sun, 03 Jun 2018 12:57:34: #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 12:57:34: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:35: 28000000 INFO @ Sun, 03 Jun 2018 12:57:35: 28000000 INFO @ Sun, 03 Jun 2018 12:57:35: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:35: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:35: #1 total tags in treatment: 13613218 INFO @ Sun, 03 Jun 2018 12:57:35: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:35: #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 12:57:36: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:36: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:36: #1 total tags in treatment: 13613218 INFO @ Sun, 03 Jun 2018 12:57:36: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:36: #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 12:57:36: #1 tags after filtering in treatment: 12071562 INFO @ Sun, 03 Jun 2018 12:57:36: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 12:57:36: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:36: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:36: #1 tags after filtering in treatment: 12071562 INFO @ Sun, 03 Jun 2018 12:57:36: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 12:57:36: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:36: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:37: #2 number of paired peaks: 148 WARNING @ Sun, 03 Jun 2018 12:57:37: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:37: #2 number of paired peaks: 148 WARNING @ Sun, 03 Jun 2018 12:57:37: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:37: #2 predicted fragment length is 97 bps INFO @ Sun, 03 Jun 2018 12:57:37: #2 alternative fragment length(s) may be 3,97,122,199,226 bps INFO @ Sun, 03 Jun 2018 12:57:37: #2.2 Generate R script for model : SRX4085344.05_model.r WARNING @ Sun, 03 Jun 2018 12:57:37: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:57:37: #2 You may need to consider one of the other alternative d(s): 3,97,122,199,226 WARNING @ Sun, 03 Jun 2018 12:57:37: #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 12:57:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:37: #2 predicted fragment length is 97 bps INFO @ Sun, 03 Jun 2018 12:57:37: #2 alternative fragment length(s) may be 3,97,122,199,226 bps INFO @ Sun, 03 Jun 2018 12:57:37: #2.2 Generate R script for model : SRX4085344.20_model.r WARNING @ Sun, 03 Jun 2018 12:57:37: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:57:37: #2 You may need to consider one of the other alternative d(s): 3,97,122,199,226 WARNING @ Sun, 03 Jun 2018 12:57:37: #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 12:57:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:59: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:13: #4 Write output xls file... SRX4085344.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:13: #4 Write peak in narrowPeak format file... SRX4085344.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:13: #4 Write summits bed file... SRX4085344.10_summits.bed INFO @ Sun, 03 Jun 2018 12:58:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:15: #4 Write output xls file... SRX4085344.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:15: #4 Write peak in narrowPeak format file... SRX4085344.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:15: #4 Write summits bed file... SRX4085344.05_summits.bed INFO @ Sun, 03 Jun 2018 12:58:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2029 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:16: #4 Write output xls file... SRX4085344.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:16: #4 Write peak in narrowPeak format file... SRX4085344.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:16: #4 Write summits bed file... SRX4085344.20_summits.bed INFO @ Sun, 03 Jun 2018 12:58:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (107 records, 4 fields): 75 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。