Job ID = 10714479 sra ファイルのダウンロード中... Completed: 3009147K bytes transferred in 45 seconds (537156K 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 44130800 spots for /home/okishinya/chipatlas/results/ce10/SRX4085395/SRR7167424.sra Written 44130800 spots for /home/okishinya/chipatlas/results/ce10/SRX4085395/SRR7167424.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: 00:41:24 44130800 reads; of these: 44130800 (100.00%) were paired; of these: 3016633 (6.84%) aligned concordantly 0 times 36843633 (83.49%) aligned concordantly exactly 1 time 4270534 (9.68%) aligned concordantly >1 times ---- 3016633 pairs aligned concordantly 0 times; of these: 207677 (6.88%) aligned discordantly 1 time ---- 2808956 pairs aligned 0 times concordantly or discordantly; of these: 5617912 mates make up the pairs; of these: 4772653 (84.95%) aligned 0 times 671048 (11.94%) aligned exactly 1 time 174211 (3.10%) aligned >1 times 94.59% overall alignment rate Time searching: 00:41:24 Overall time: 00:41:24 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 36 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] 29465298 / 41239687 = 0.7145 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 13:46:19: # Command line: callpeak -t SRX4085395.bam -f BAM -g ce -n SRX4085395.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085395.10 # format = BAM # ChIP-seq file = ['SRX4085395.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 13:46:19: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:46:19: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:46:19: # Command line: callpeak -t SRX4085395.bam -f BAM -g ce -n SRX4085395.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085395.05 # format = BAM # ChIP-seq file = ['SRX4085395.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 13:46:19: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:46:19: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:46:19: # Command line: callpeak -t SRX4085395.bam -f BAM -g ce -n SRX4085395.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085395.20 # format = BAM # ChIP-seq file = ['SRX4085395.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 13:46:19: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:46:19: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:46:25: 1000000 INFO @ Sun, 03 Jun 2018 13:46:25: 1000000 INFO @ Sun, 03 Jun 2018 13:46:26: 1000000 INFO @ Sun, 03 Jun 2018 13:46:31: 2000000 INFO @ Sun, 03 Jun 2018 13:46:31: 2000000 INFO @ Sun, 03 Jun 2018 13:46:33: 2000000 INFO @ Sun, 03 Jun 2018 13:46:37: 3000000 INFO @ Sun, 03 Jun 2018 13:46:37: 3000000 INFO @ Sun, 03 Jun 2018 13:46:39: 3000000 INFO @ Sun, 03 Jun 2018 13:46:42: 4000000 INFO @ Sun, 03 Jun 2018 13:46:43: 4000000 INFO @ Sun, 03 Jun 2018 13:46:46: 4000000 INFO @ Sun, 03 Jun 2018 13:46:48: 5000000 INFO @ Sun, 03 Jun 2018 13:46:48: 5000000 INFO @ Sun, 03 Jun 2018 13:46:53: 5000000 INFO @ Sun, 03 Jun 2018 13:46:54: 6000000 INFO @ Sun, 03 Jun 2018 13:46:54: 6000000 INFO @ Sun, 03 Jun 2018 13:47:00: 6000000 INFO @ Sun, 03 Jun 2018 13:47:00: 7000000 INFO @ Sun, 03 Jun 2018 13:47:00: 7000000 INFO @ Sun, 03 Jun 2018 13:47:06: 8000000 INFO @ Sun, 03 Jun 2018 13:47:06: 8000000 INFO @ Sun, 03 Jun 2018 13:47:07: 7000000 INFO @ Sun, 03 Jun 2018 13:47:12: 9000000 INFO @ Sun, 03 Jun 2018 13:47:12: 9000000 INFO @ Sun, 03 Jun 2018 13:47:14: 8000000 INFO @ Sun, 03 Jun 2018 13:47:18: 10000000 INFO @ Sun, 03 Jun 2018 13:47:19: 10000000 INFO @ Sun, 03 Jun 2018 13:47:20: 9000000 INFO @ Sun, 03 Jun 2018 13:47:24: 11000000 INFO @ Sun, 03 Jun 2018 13:47:25: 11000000 INFO @ Sun, 03 Jun 2018 13:47:27: 10000000 INFO @ Sun, 03 Jun 2018 13:47:31: 12000000 INFO @ Sun, 03 Jun 2018 13:47:31: 12000000 INFO @ Sun, 03 Jun 2018 13:47:34: 11000000 INFO @ Sun, 03 Jun 2018 13:47:37: 13000000 INFO @ Sun, 03 Jun 2018 13:47:38: 13000000 INFO @ Sun, 03 Jun 2018 13:47:41: 12000000 INFO @ Sun, 03 Jun 2018 13:47:43: 14000000 INFO @ Sun, 03 Jun 2018 13:47:44: 14000000 INFO @ Sun, 03 Jun 2018 13:47:48: 13000000 INFO @ Sun, 03 Jun 2018 13:47:49: 15000000 INFO @ Sun, 03 Jun 2018 13:47:50: 15000000 INFO @ Sun, 03 Jun 2018 13:47:55: 14000000 INFO @ Sun, 03 Jun 2018 13:47:55: 16000000 INFO @ Sun, 03 Jun 2018 13:47:57: 16000000 INFO @ Sun, 03 Jun 2018 13:48:02: 15000000 INFO @ Sun, 03 Jun 2018 13:48:02: 17000000 INFO @ Sun, 03 Jun 2018 13:48:03: 17000000 INFO @ Sun, 03 Jun 2018 13:48:08: 18000000 INFO @ Sun, 03 Jun 2018 13:48:08: 16000000 INFO @ Sun, 03 Jun 2018 13:48:09: 18000000 INFO @ Sun, 03 Jun 2018 13:48:14: 19000000 INFO @ Sun, 03 Jun 2018 13:48:15: 17000000 INFO @ Sun, 03 Jun 2018 13:48:15: 19000000 INFO @ Sun, 03 Jun 2018 13:48:20: 20000000 INFO @ Sun, 03 Jun 2018 13:48:22: 20000000 INFO @ Sun, 03 Jun 2018 13:48:22: 18000000 INFO @ Sun, 03 Jun 2018 13:48:26: 21000000 INFO @ Sun, 03 Jun 2018 13:48:28: 21000000 INFO @ Sun, 03 Jun 2018 13:48:29: 19000000 INFO @ Sun, 03 Jun 2018 13:48:33: 22000000 INFO @ Sun, 03 Jun 2018 13:48:34: 22000000 INFO @ Sun, 03 Jun 2018 13:48:36: 20000000 INFO @ Sun, 03 Jun 2018 13:48:38: 23000000 INFO @ Sun, 03 Jun 2018 13:48:40: 23000000 INFO @ Sun, 03 Jun 2018 13:48:43: 21000000 INFO @ Sun, 03 Jun 2018 13:48:44: 24000000 INFO @ Sun, 03 Jun 2018 13:48:46: 24000000 INFO @ Sun, 03 Jun 2018 13:48:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:48:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:48:47: #1 total tags in treatment: 11730988 INFO @ Sun, 03 Jun 2018 13:48:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:48:47: #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 13:48:48: #1 tags after filtering in treatment: 9395063 INFO @ Sun, 03 Jun 2018 13:48:48: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:48:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:48:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:48:48: #2 number of paired peaks: 580 WARNING @ Sun, 03 Jun 2018 13:48:48: Fewer paired peaks (580) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 580 pairs to build model! INFO @ Sun, 03 Jun 2018 13:48:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:48:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:48:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:48:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:48:49: #2 predicted fragment length is 122 bps INFO @ Sun, 03 Jun 2018 13:48:49: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 03 Jun 2018 13:48:49: #2.2 Generate R script for model : SRX4085395.05_model.r INFO @ Sun, 03 Jun 2018 13:48:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:48:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:48:49: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:48:49: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:48:49: #1 total tags in treatment: 11730988 INFO @ Sun, 03 Jun 2018 13:48:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:48:49: #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 13:48:50: 22000000 INFO @ Sun, 03 Jun 2018 13:48:50: #1 tags after filtering in treatment: 9395063 INFO @ Sun, 03 Jun 2018 13:48:50: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:48:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:48:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:48:50: #2 number of paired peaks: 580 WARNING @ Sun, 03 Jun 2018 13:48:50: Fewer paired peaks (580) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 580 pairs to build model! INFO @ Sun, 03 Jun 2018 13:48:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:48:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:48:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:48:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:48:50: #2 predicted fragment length is 122 bps INFO @ Sun, 03 Jun 2018 13:48:50: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 03 Jun 2018 13:48:50: #2.2 Generate R script for model : SRX4085395.10_model.r INFO @ Sun, 03 Jun 2018 13:48:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:48:56: 23000000 INFO @ Sun, 03 Jun 2018 13:49:02: 24000000 INFO @ Sun, 03 Jun 2018 13:49:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:49:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:49:06: #1 total tags in treatment: 11730988 INFO @ Sun, 03 Jun 2018 13:49:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:49:06: #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 13:49:06: #1 tags after filtering in treatment: 9395063 INFO @ Sun, 03 Jun 2018 13:49:06: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:49:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:49:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:49:07: #2 number of paired peaks: 580 WARNING @ Sun, 03 Jun 2018 13:49:07: Fewer paired peaks (580) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 580 pairs to build model! INFO @ Sun, 03 Jun 2018 13:49:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:49:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:49:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:49:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:49:07: #2 predicted fragment length is 122 bps INFO @ Sun, 03 Jun 2018 13:49:07: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 03 Jun 2018 13:49:07: #2.2 Generate R script for model : SRX4085395.20_model.r INFO @ Sun, 03 Jun 2018 13:49:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:49:10: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:49:13: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:49:21: #4 Write output xls file... SRX4085395.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:49:21: #4 Write peak in narrowPeak format file... SRX4085395.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:49:21: #4 Write summits bed file... SRX4085395.05_summits.bed INFO @ Sun, 03 Jun 2018 13:49:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3001 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:49:24: #4 Write output xls file... SRX4085395.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:49:24: #4 Write peak in narrowPeak format file... SRX4085395.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:49:24: #4 Write summits bed file... SRX4085395.10_summits.bed INFO @ Sun, 03 Jun 2018 13:49:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1871 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:49:30: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:49:41: #4 Write output xls file... SRX4085395.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:49:41: #4 Write peak in narrowPeak format file... SRX4085395.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:49:41: #4 Write summits bed file... SRX4085395.20_summits.bed INFO @ Sun, 03 Jun 2018 13:49:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (984 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。