Job ID = 10714481 sra ファイルのダウンロード中... Completed: 2572842K bytes transferred in 44 seconds (472394K 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 37938920 spots for /home/okishinya/chipatlas/results/ce10/SRX4085397/SRR7167426.sra Written 37938920 spots for /home/okishinya/chipatlas/results/ce10/SRX4085397/SRR7167426.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: 00:38:29 37938920 reads; of these: 37938920 (100.00%) were paired; of these: 3083802 (8.13%) aligned concordantly 0 times 30970010 (81.63%) aligned concordantly exactly 1 time 3885108 (10.24%) aligned concordantly >1 times ---- 3083802 pairs aligned concordantly 0 times; of these: 1182141 (38.33%) aligned discordantly 1 time ---- 1901661 pairs aligned 0 times concordantly or discordantly; of these: 3803322 mates make up the pairs; of these: 2326713 (61.18%) aligned 0 times 950854 (25.00%) aligned exactly 1 time 525755 (13.82%) aligned >1 times 96.93% overall alignment rate Time searching: 00:38:29 Overall time: 00:38:29 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 32 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] 25772175 / 35098036 = 0.7343 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 13:42:50: # Command line: callpeak -t SRX4085397.bam -f BAM -g ce -n SRX4085397.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085397.20 # format = BAM # ChIP-seq file = ['SRX4085397.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 13:42:50: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:50: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:50: # Command line: callpeak -t SRX4085397.bam -f BAM -g ce -n SRX4085397.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085397.10 # format = BAM # ChIP-seq file = ['SRX4085397.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 13:42:50: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:50: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:50: # Command line: callpeak -t SRX4085397.bam -f BAM -g ce -n SRX4085397.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085397.05 # format = BAM # ChIP-seq file = ['SRX4085397.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 13:42:50: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:50: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:56: 1000000 INFO @ Sun, 03 Jun 2018 13:42:56: 1000000 INFO @ Sun, 03 Jun 2018 13:42:57: 1000000 INFO @ Sun, 03 Jun 2018 13:43:03: 2000000 INFO @ Sun, 03 Jun 2018 13:43:03: 2000000 INFO @ Sun, 03 Jun 2018 13:43:05: 2000000 INFO @ Sun, 03 Jun 2018 13:43:10: 3000000 INFO @ Sun, 03 Jun 2018 13:43:10: 3000000 INFO @ Sun, 03 Jun 2018 13:43:12: 3000000 INFO @ Sun, 03 Jun 2018 13:43:16: 4000000 INFO @ Sun, 03 Jun 2018 13:43:16: 4000000 INFO @ Sun, 03 Jun 2018 13:43:20: 4000000 INFO @ Sun, 03 Jun 2018 13:43:23: 5000000 INFO @ Sun, 03 Jun 2018 13:43:23: 5000000 INFO @ Sun, 03 Jun 2018 13:43:28: 5000000 INFO @ Sun, 03 Jun 2018 13:43:30: 6000000 INFO @ Sun, 03 Jun 2018 13:43:30: 6000000 INFO @ Sun, 03 Jun 2018 13:43:35: 6000000 INFO @ Sun, 03 Jun 2018 13:43:37: 7000000 INFO @ Sun, 03 Jun 2018 13:43:37: 7000000 INFO @ Sun, 03 Jun 2018 13:43:43: 7000000 INFO @ Sun, 03 Jun 2018 13:43:44: 8000000 INFO @ Sun, 03 Jun 2018 13:43:44: 8000000 INFO @ Sun, 03 Jun 2018 13:43:50: 8000000 INFO @ Sun, 03 Jun 2018 13:43:51: 9000000 INFO @ Sun, 03 Jun 2018 13:43:51: 9000000 INFO @ Sun, 03 Jun 2018 13:43:57: 10000000 INFO @ Sun, 03 Jun 2018 13:43:57: 10000000 INFO @ Sun, 03 Jun 2018 13:43:58: 9000000 INFO @ Sun, 03 Jun 2018 13:44:03: 11000000 INFO @ Sun, 03 Jun 2018 13:44:03: 11000000 INFO @ Sun, 03 Jun 2018 13:44:04: 10000000 INFO @ Sun, 03 Jun 2018 13:44:09: 12000000 INFO @ Sun, 03 Jun 2018 13:44:09: 12000000 INFO @ Sun, 03 Jun 2018 13:44:10: 11000000 INFO @ Sun, 03 Jun 2018 13:44:15: 13000000 INFO @ Sun, 03 Jun 2018 13:44:15: 13000000 INFO @ Sun, 03 Jun 2018 13:44:16: 12000000 INFO @ Sun, 03 Jun 2018 13:44:20: 14000000 INFO @ Sun, 03 Jun 2018 13:44:20: 14000000 INFO @ Sun, 03 Jun 2018 13:44:22: 13000000 INFO @ Sun, 03 Jun 2018 13:44:26: 15000000 INFO @ Sun, 03 Jun 2018 13:44:26: 15000000 INFO @ Sun, 03 Jun 2018 13:44:28: 14000000 INFO @ Sun, 03 Jun 2018 13:44:32: 16000000 INFO @ Sun, 03 Jun 2018 13:44:32: 16000000 INFO @ Sun, 03 Jun 2018 13:44:35: 15000000 INFO @ Sun, 03 Jun 2018 13:44:38: 17000000 INFO @ Sun, 03 Jun 2018 13:44:38: 17000000 INFO @ Sun, 03 Jun 2018 13:44:40: 16000000 INFO @ Sun, 03 Jun 2018 13:44:44: 18000000 INFO @ Sun, 03 Jun 2018 13:44:44: 18000000 INFO @ Sun, 03 Jun 2018 13:44:46: 17000000 INFO @ Sun, 03 Jun 2018 13:44:49: 19000000 INFO @ Sun, 03 Jun 2018 13:44:49: 19000000 INFO @ Sun, 03 Jun 2018 13:44:52: 18000000 INFO @ Sun, 03 Jun 2018 13:44:55: 20000000 INFO @ Sun, 03 Jun 2018 13:44:55: 20000000 INFO @ Sun, 03 Jun 2018 13:44:58: 19000000 INFO @ Sun, 03 Jun 2018 13:45:01: 21000000 INFO @ Sun, 03 Jun 2018 13:45:01: 21000000 INFO @ Sun, 03 Jun 2018 13:45:04: 20000000 INFO @ Sun, 03 Jun 2018 13:45:06: 22000000 INFO @ Sun, 03 Jun 2018 13:45:06: 22000000 INFO @ Sun, 03 Jun 2018 13:45:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:45:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:45:06: #1 total tags in treatment: 9261578 INFO @ Sun, 03 Jun 2018 13:45:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:45:06: #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 13:45:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:45:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:45:06: #1 total tags in treatment: 9261578 INFO @ Sun, 03 Jun 2018 13:45:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:45:06: #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 13:45:06: #1 tags after filtering in treatment: 7552856 INFO @ Sun, 03 Jun 2018 13:45:06: #1 tags after filtering in treatment: 7552856 INFO @ Sun, 03 Jun 2018 13:45:06: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 13:45:06: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 13:45:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:45:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:45:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:45:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:45:07: #2 number of paired peaks: 726 WARNING @ Sun, 03 Jun 2018 13:45:07: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sun, 03 Jun 2018 13:45:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:45:07: #2 number of paired peaks: 726 WARNING @ Sun, 03 Jun 2018 13:45:07: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sun, 03 Jun 2018 13:45:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:45:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:45:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:45:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:45:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:45:07: #2 predicted fragment length is 121 bps INFO @ Sun, 03 Jun 2018 13:45:07: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 03 Jun 2018 13:45:07: #2.2 Generate R script for model : SRX4085397.10_model.r INFO @ Sun, 03 Jun 2018 13:45:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:45:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:45:07: #2 predicted fragment length is 121 bps INFO @ Sun, 03 Jun 2018 13:45:07: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 03 Jun 2018 13:45:07: #2.2 Generate R script for model : SRX4085397.20_model.r INFO @ Sun, 03 Jun 2018 13:45:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:45:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:45:09: 21000000 INFO @ Sun, 03 Jun 2018 13:45:15: 22000000 INFO @ Sun, 03 Jun 2018 13:45:15: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:45:15: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:45:15: #1 total tags in treatment: 9261578 INFO @ Sun, 03 Jun 2018 13:45:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:45:15: #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 13:45:15: #1 tags after filtering in treatment: 7552856 INFO @ Sun, 03 Jun 2018 13:45:15: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 03 Jun 2018 13:45:15: #1 finished! INFO @ Sun, 03 Jun 2018 13:45:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:45:16: #2 number of paired peaks: 726 WARNING @ Sun, 03 Jun 2018 13:45:16: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sun, 03 Jun 2018 13:45:16: start model_add_line... INFO @ Sun, 03 Jun 2018 13:45:16: start X-correlation... INFO @ Sun, 03 Jun 2018 13:45:16: end of X-cor INFO @ Sun, 03 Jun 2018 13:45:16: #2 finished! INFO @ Sun, 03 Jun 2018 13:45:16: #2 predicted fragment length is 121 bps INFO @ Sun, 03 Jun 2018 13:45:16: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 03 Jun 2018 13:45:16: #2.2 Generate R script for model : SRX4085397.05_model.r INFO @ Sun, 03 Jun 2018 13:45:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:45:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:45:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:45:33: #4 Write output xls file... SRX4085397.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:45:33: #4 Write peak in narrowPeak format file... SRX4085397.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:45:33: #4 Write summits bed file... SRX4085397.20_summits.bed INFO @ Sun, 03 Jun 2018 13:45:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1111 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:45:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:45:35: #4 Write output xls file... SRX4085397.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:45:35: #4 Write peak in narrowPeak format file... SRX4085397.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:45:35: #4 Write summits bed file... SRX4085397.10_summits.bed INFO @ Sun, 03 Jun 2018 13:45:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2223 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:45:44: #4 Write output xls file... SRX4085397.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:45:44: #4 Write peak in narrowPeak format file... SRX4085397.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:45:44: #4 Write summits bed file... SRX4085397.05_summits.bed INFO @ Sun, 03 Jun 2018 13:45:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3783 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。