Job ID = 10714475 sra ファイルのダウンロード中... Completed: 680987K bytes transferred in 12 seconds (445615K 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 11256736 spots for /home/okishinya/chipatlas/results/ce10/SRX4085391/SRR7167420.sra Written 11256736 spots for /home/okishinya/chipatlas/results/ce10/SRX4085391/SRR7167420.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: 00:08:35 11256736 reads; of these: 11256736 (100.00%) were paired; of these: 6916100 (61.44%) aligned concordantly 0 times 3692982 (32.81%) aligned concordantly exactly 1 time 647654 (5.75%) aligned concordantly >1 times ---- 6916100 pairs aligned concordantly 0 times; of these: 328055 (4.74%) aligned discordantly 1 time ---- 6588045 pairs aligned 0 times concordantly or discordantly; of these: 13176090 mates make up the pairs; of these: 9684720 (73.50%) aligned 0 times 2979978 (22.62%) aligned exactly 1 time 511392 (3.88%) aligned >1 times 56.98% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:36 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 8 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] 319512 / 4507346 = 0.0709 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 12:55:05: # Command line: callpeak -t SRX4085391.bam -f BAM -g ce -n SRX4085391.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085391.10 # format = BAM # ChIP-seq file = ['SRX4085391.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 12:55:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:55:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:55:05: # Command line: callpeak -t SRX4085391.bam -f BAM -g ce -n SRX4085391.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085391.05 # format = BAM # ChIP-seq file = ['SRX4085391.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 12:55:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:55:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:55:05: # Command line: callpeak -t SRX4085391.bam -f BAM -g ce -n SRX4085391.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085391.20 # format = BAM # ChIP-seq file = ['SRX4085391.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 12:55:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:55:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:55:12: 1000000 INFO @ Sun, 03 Jun 2018 12:55:13: 1000000 INFO @ Sun, 03 Jun 2018 12:55:13: 1000000 INFO @ Sun, 03 Jun 2018 12:55:18: 2000000 INFO @ Sun, 03 Jun 2018 12:55:20: 2000000 INFO @ Sun, 03 Jun 2018 12:55:20: 2000000 INFO @ Sun, 03 Jun 2018 12:55:25: 3000000 INFO @ Sun, 03 Jun 2018 12:55:28: 3000000 INFO @ Sun, 03 Jun 2018 12:55:28: 3000000 INFO @ Sun, 03 Jun 2018 12:55:31: 4000000 INFO @ Sun, 03 Jun 2018 12:55:36: 4000000 INFO @ Sun, 03 Jun 2018 12:55:36: 4000000 INFO @ Sun, 03 Jun 2018 12:55:38: 5000000 INFO @ Sun, 03 Jun 2018 12:55:43: 5000000 INFO @ Sun, 03 Jun 2018 12:55:43: 5000000 INFO @ Sun, 03 Jun 2018 12:55:44: 6000000 INFO @ Sun, 03 Jun 2018 12:55:50: 7000000 INFO @ Sun, 03 Jun 2018 12:55:51: 6000000 INFO @ Sun, 03 Jun 2018 12:55:51: 6000000 INFO @ Sun, 03 Jun 2018 12:55:57: 8000000 INFO @ Sun, 03 Jun 2018 12:55:58: 7000000 INFO @ Sun, 03 Jun 2018 12:55:58: 7000000 INFO @ Sun, 03 Jun 2018 12:56:04: 9000000 INFO @ Sun, 03 Jun 2018 12:56:06: 8000000 INFO @ Sun, 03 Jun 2018 12:56:06: 8000000 INFO @ Sun, 03 Jun 2018 12:56:10: 10000000 INFO @ Sun, 03 Jun 2018 12:56:14: 9000000 INFO @ Sun, 03 Jun 2018 12:56:14: 9000000 INFO @ Sun, 03 Jun 2018 12:56:17: 11000000 INFO @ Sun, 03 Jun 2018 12:56:22: 10000000 INFO @ Sun, 03 Jun 2018 12:56:22: 10000000 INFO @ Sun, 03 Jun 2018 12:56:24: 12000000 INFO @ Sun, 03 Jun 2018 12:56:25: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:56:25: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:56:25: #1 total tags in treatment: 4033866 INFO @ Sun, 03 Jun 2018 12:56:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:56:25: #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 12:56:25: #1 tags after filtering in treatment: 3822755 INFO @ Sun, 03 Jun 2018 12:56:25: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Jun 2018 12:56:25: #1 finished! INFO @ Sun, 03 Jun 2018 12:56:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:56:26: #2 number of paired peaks: 337 WARNING @ Sun, 03 Jun 2018 12:56:26: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Sun, 03 Jun 2018 12:56:26: start model_add_line... INFO @ Sun, 03 Jun 2018 12:56:26: start X-correlation... INFO @ Sun, 03 Jun 2018 12:56:26: end of X-cor INFO @ Sun, 03 Jun 2018 12:56:26: #2 finished! INFO @ Sun, 03 Jun 2018 12:56:26: #2 predicted fragment length is 138 bps INFO @ Sun, 03 Jun 2018 12:56:26: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 03 Jun 2018 12:56:26: #2.2 Generate R script for model : SRX4085391.10_model.r INFO @ Sun, 03 Jun 2018 12:56:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:31: 11000000 INFO @ Sun, 03 Jun 2018 12:56:31: 11000000 INFO @ Sun, 03 Jun 2018 12:56:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:39: #4 Write output xls file... SRX4085391.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:39: #4 Write peak in narrowPeak format file... SRX4085391.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:39: #4 Write summits bed file... SRX4085391.10_summits.bed INFO @ Sun, 03 Jun 2018 12:56:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:56:41: 12000000 INFO @ Sun, 03 Jun 2018 12:56:41: 12000000 INFO @ Sun, 03 Jun 2018 12:56:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:56:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:56:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:56:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:56:43: #1 total tags in treatment: 4033866 INFO @ Sun, 03 Jun 2018 12:56:43: #1 total tags in treatment: 4033866 INFO @ Sun, 03 Jun 2018 12:56:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:56:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:56:43: #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 12:56:43: #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 12:56:43: #1 tags after filtering in treatment: 3822755 INFO @ Sun, 03 Jun 2018 12:56:43: #1 tags after filtering in treatment: 3822755 INFO @ Sun, 03 Jun 2018 12:56:43: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Jun 2018 12:56:43: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Jun 2018 12:56:43: #1 finished! INFO @ Sun, 03 Jun 2018 12:56:43: #1 finished! INFO @ Sun, 03 Jun 2018 12:56:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:56:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:56:43: #2 number of paired peaks: 337 WARNING @ Sun, 03 Jun 2018 12:56:43: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Sun, 03 Jun 2018 12:56:43: start model_add_line... INFO @ Sun, 03 Jun 2018 12:56:43: #2 number of paired peaks: 337 INFO @ Sun, 03 Jun 2018 12:56:43: start X-correlation... WARNING @ Sun, 03 Jun 2018 12:56:43: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Sun, 03 Jun 2018 12:56:43: start model_add_line... INFO @ Sun, 03 Jun 2018 12:56:43: end of X-cor INFO @ Sun, 03 Jun 2018 12:56:43: #2 finished! INFO @ Sun, 03 Jun 2018 12:56:43: #2 predicted fragment length is 138 bps INFO @ Sun, 03 Jun 2018 12:56:43: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 03 Jun 2018 12:56:43: #2.2 Generate R script for model : SRX4085391.20_model.r INFO @ Sun, 03 Jun 2018 12:56:43: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:43: start X-correlation... INFO @ Sun, 03 Jun 2018 12:56:43: end of X-cor INFO @ Sun, 03 Jun 2018 12:56:43: #2 finished! INFO @ Sun, 03 Jun 2018 12:56:43: #2 predicted fragment length is 138 bps INFO @ Sun, 03 Jun 2018 12:56:43: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 03 Jun 2018 12:56:43: #2.2 Generate R script for model : SRX4085391.05_model.r INFO @ Sun, 03 Jun 2018 12:56:43: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:57: #4 Write output xls file... SRX4085391.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:57: #4 Write peak in narrowPeak format file... SRX4085391.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:57: #4 Write summits bed file... SRX4085391.20_summits.bed INFO @ Sun, 03 Jun 2018 12:56:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:56:57: #4 Write output xls file... SRX4085391.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:57: #4 Write peak in narrowPeak format file... SRX4085391.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:57: #4 Write summits bed file... SRX4085391.05_summits.bed INFO @ Sun, 03 Jun 2018 12:56:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。