Job ID = 10201977 sra ファイルのダウンロード中... Completed: 432185K bytes transferred in 12 seconds (277851K 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: SINGLE fastq に変換中... Written 18222104 spots for /home/okishinya/chipatlas/results/ce10/SRX2576646/SRR5272603.sra Written 18222104 spots total 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: 00:03:24 18222104 reads; of these: 18222104 (100.00%) were unpaired; of these: 1069467 (5.87%) aligned 0 times 14159138 (77.70%) aligned exactly 1 time 2993499 (16.43%) aligned >1 times 94.13% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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 8 files... [bam_rmdupse_core] 2940717 / 17152637 = 0.1714 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 @ Mon, 13 Nov 2017 13:16:20: # Command line: callpeak -t SRX2576646.bam -f BAM -g ce -n SRX2576646.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576646.05 # format = BAM # ChIP-seq file = ['SRX2576646.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 @ Mon, 13 Nov 2017 13:16:20: # Command line: callpeak -t SRX2576646.bam -f BAM -g ce -n SRX2576646.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576646.10 # format = BAM # ChIP-seq file = ['SRX2576646.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 @ Mon, 13 Nov 2017 13:16:20: # Command line: callpeak -t SRX2576646.bam -f BAM -g ce -n SRX2576646.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576646.20 # format = BAM # ChIP-seq file = ['SRX2576646.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 @ Mon, 13 Nov 2017 13:16:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:27: 1000000 INFO @ Mon, 13 Nov 2017 13:16:27: 1000000 INFO @ Mon, 13 Nov 2017 13:16:27: 1000000 INFO @ Mon, 13 Nov 2017 13:16:34: 2000000 INFO @ Mon, 13 Nov 2017 13:16:34: 2000000 INFO @ Mon, 13 Nov 2017 13:16:34: 2000000 INFO @ Mon, 13 Nov 2017 13:16:40: 3000000 INFO @ Mon, 13 Nov 2017 13:16:41: 3000000 INFO @ Mon, 13 Nov 2017 13:16:41: 3000000 INFO @ Mon, 13 Nov 2017 13:16:47: 4000000 INFO @ Mon, 13 Nov 2017 13:16:48: 4000000 INFO @ Mon, 13 Nov 2017 13:16:49: 4000000 INFO @ Mon, 13 Nov 2017 13:16:54: 5000000 INFO @ Mon, 13 Nov 2017 13:16:55: 5000000 INFO @ Mon, 13 Nov 2017 13:16:56: 5000000 INFO @ Mon, 13 Nov 2017 13:17:01: 6000000 INFO @ Mon, 13 Nov 2017 13:17:02: 6000000 INFO @ Mon, 13 Nov 2017 13:17:03: 6000000 INFO @ Mon, 13 Nov 2017 13:17:08: 7000000 INFO @ Mon, 13 Nov 2017 13:17:09: 7000000 INFO @ Mon, 13 Nov 2017 13:17:10: 7000000 INFO @ Mon, 13 Nov 2017 13:17:15: 8000000 INFO @ Mon, 13 Nov 2017 13:17:16: 8000000 INFO @ Mon, 13 Nov 2017 13:17:17: 8000000 INFO @ Mon, 13 Nov 2017 13:17:22: 9000000 INFO @ Mon, 13 Nov 2017 13:17:23: 9000000 INFO @ Mon, 13 Nov 2017 13:17:24: 9000000 INFO @ Mon, 13 Nov 2017 13:17:29: 10000000 INFO @ Mon, 13 Nov 2017 13:17:30: 10000000 INFO @ Mon, 13 Nov 2017 13:17:32: 10000000 INFO @ Mon, 13 Nov 2017 13:17:36: 11000000 INFO @ Mon, 13 Nov 2017 13:17:37: 11000000 INFO @ Mon, 13 Nov 2017 13:17:39: 11000000 INFO @ Mon, 13 Nov 2017 13:17:43: 12000000 INFO @ Mon, 13 Nov 2017 13:17:44: 12000000 INFO @ Mon, 13 Nov 2017 13:17:46: 12000000 INFO @ Mon, 13 Nov 2017 13:17:50: 13000000 INFO @ Mon, 13 Nov 2017 13:17:51: 13000000 INFO @ Mon, 13 Nov 2017 13:17:53: 13000000 INFO @ Mon, 13 Nov 2017 13:17:57: 14000000 INFO @ Mon, 13 Nov 2017 13:17:58: 14000000 INFO @ Mon, 13 Nov 2017 13:17:58: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:58: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:58: #1 total tags in treatment: 14211920 INFO @ Mon, 13 Nov 2017 13:17:58: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:59: #1 tags after filtering in treatment: 14211920 INFO @ Mon, 13 Nov 2017 13:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:59: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:59: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:59: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:59: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:59: #1 total tags in treatment: 14211920 INFO @ Mon, 13 Nov 2017 13:17:59: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:00: #1 tags after filtering in treatment: 14211920 INFO @ Mon, 13 Nov 2017 13:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:00: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:00: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:00: #2 number of paired peaks: 550 WARNING @ Mon, 13 Nov 2017 13:18:00: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:00: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:00: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:00: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:00: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:00: #2 predicted fragment length is 120 bps INFO @ Mon, 13 Nov 2017 13:18:00: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 13 Nov 2017 13:18:00: #2.2 Generate R script for model : SRX2576646.10_model.r INFO @ Mon, 13 Nov 2017 13:18:00: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:00: 14000000 INFO @ Mon, 13 Nov 2017 13:18:01: #2 number of paired peaks: 550 WARNING @ Mon, 13 Nov 2017 13:18:01: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:01: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:01: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:01: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:01: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:01: #2 predicted fragment length is 120 bps INFO @ Mon, 13 Nov 2017 13:18:01: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 13 Nov 2017 13:18:01: #2.2 Generate R script for model : SRX2576646.05_model.r INFO @ Mon, 13 Nov 2017 13:18:01: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:02: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:18:02: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:18:02: #1 total tags in treatment: 14211920 INFO @ Mon, 13 Nov 2017 13:18:02: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:18:02: #1 tags after filtering in treatment: 14211920 INFO @ Mon, 13 Nov 2017 13:18:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:02: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:02: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:03: #2 number of paired peaks: 550 WARNING @ Mon, 13 Nov 2017 13:18:03: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:03: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:03: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:03: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:03: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:03: #2 predicted fragment length is 120 bps INFO @ Mon, 13 Nov 2017 13:18:03: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 13 Nov 2017 13:18:03: #2.2 Generate R script for model : SRX2576646.20_model.r INFO @ Mon, 13 Nov 2017 13:18:03: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:29: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:31: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:34: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:47: #4 Write output xls file... SRX2576646.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:47: #4 Write peak in narrowPeak format file... SRX2576646.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:47: #4 Write summits bed file... SRX2576646.10_summits.bed INFO @ Mon, 13 Nov 2017 13:18:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1975 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:49: #4 Write output xls file... SRX2576646.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:49: #4 Write peak in narrowPeak format file... SRX2576646.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:49: #4 Write summits bed file... SRX2576646.05_summits.bed INFO @ Mon, 13 Nov 2017 13:18:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2777 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:53: #4 Write output xls file... SRX2576646.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:53: #4 Write peak in narrowPeak format file... SRX2576646.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:53: #4 Write summits bed file... SRX2576646.20_summits.bed INFO @ Mon, 13 Nov 2017 13:18:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1327 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。