Job ID = 10201964 sra ファイルのダウンロード中... Completed: 457143K bytes transferred in 13 seconds (269869K 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 17967710 spots for /home/okishinya/chipatlas/results/ce10/SRX2576633/SRR5272590.sra Written 17967710 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: 00:03:15 17967710 reads; of these: 17967710 (100.00%) were unpaired; of these: 1838026 (10.23%) aligned 0 times 13419516 (74.69%) aligned exactly 1 time 2710168 (15.08%) aligned >1 times 89.77% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 3453250 / 16129684 = 0.2141 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 13:15:41: # Command line: callpeak -t SRX2576633.bam -f BAM -g ce -n SRX2576633.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576633.05 # format = BAM # ChIP-seq file = ['SRX2576633.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 13:15:41: # Command line: callpeak -t SRX2576633.bam -f BAM -g ce -n SRX2576633.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576633.20 # format = BAM # ChIP-seq file = ['SRX2576633.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 13:15:41: # Command line: callpeak -t SRX2576633.bam -f BAM -g ce -n SRX2576633.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576633.10 # format = BAM # ChIP-seq file = ['SRX2576633.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 13:15:41: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:41: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:41: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:41: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:41: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:41: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:48: 1000000 INFO @ Mon, 13 Nov 2017 13:15:48: 1000000 INFO @ Mon, 13 Nov 2017 13:15:48: 1000000 INFO @ Mon, 13 Nov 2017 13:15:54: 2000000 INFO @ Mon, 13 Nov 2017 13:15:55: 2000000 INFO @ Mon, 13 Nov 2017 13:15:55: 2000000 INFO @ Mon, 13 Nov 2017 13:16:00: 3000000 INFO @ Mon, 13 Nov 2017 13:16:01: 3000000 INFO @ Mon, 13 Nov 2017 13:16:01: 3000000 INFO @ Mon, 13 Nov 2017 13:16:06: 4000000 INFO @ Mon, 13 Nov 2017 13:16:08: 4000000 INFO @ Mon, 13 Nov 2017 13:16:08: 4000000 INFO @ Mon, 13 Nov 2017 13:16:13: 5000000 INFO @ Mon, 13 Nov 2017 13:16:14: 5000000 INFO @ Mon, 13 Nov 2017 13:16:14: 5000000 INFO @ Mon, 13 Nov 2017 13:16:19: 6000000 INFO @ Mon, 13 Nov 2017 13:16:21: 6000000 INFO @ Mon, 13 Nov 2017 13:16:21: 6000000 INFO @ Mon, 13 Nov 2017 13:16:25: 7000000 INFO @ Mon, 13 Nov 2017 13:16:28: 7000000 INFO @ Mon, 13 Nov 2017 13:16:28: 7000000 INFO @ Mon, 13 Nov 2017 13:16:32: 8000000 INFO @ Mon, 13 Nov 2017 13:16:35: 8000000 INFO @ Mon, 13 Nov 2017 13:16:35: 8000000 INFO @ Mon, 13 Nov 2017 13:16:38: 9000000 INFO @ Mon, 13 Nov 2017 13:16:41: 9000000 INFO @ Mon, 13 Nov 2017 13:16:41: 9000000 INFO @ Mon, 13 Nov 2017 13:16:45: 10000000 INFO @ Mon, 13 Nov 2017 13:16:49: 10000000 INFO @ Mon, 13 Nov 2017 13:16:49: 10000000 INFO @ Mon, 13 Nov 2017 13:16:53: 11000000 INFO @ Mon, 13 Nov 2017 13:16:57: 11000000 INFO @ Mon, 13 Nov 2017 13:16:57: 11000000 INFO @ Mon, 13 Nov 2017 13:17:01: 12000000 INFO @ Mon, 13 Nov 2017 13:17:04: 12000000 INFO @ Mon, 13 Nov 2017 13:17:04: 12000000 INFO @ Mon, 13 Nov 2017 13:17:06: #1 tag size is determined as 36 bps INFO @ Mon, 13 Nov 2017 13:17:06: #1 tag size = 36 INFO @ Mon, 13 Nov 2017 13:17:06: #1 total tags in treatment: 12676434 INFO @ Mon, 13 Nov 2017 13:17:06: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:06: #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 13:17:07: #1 tags after filtering in treatment: 12676434 INFO @ Mon, 13 Nov 2017 13:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:07: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:07: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:07: #2 number of paired peaks: 602 WARNING @ Mon, 13 Nov 2017 13:17:07: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:07: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:08: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:08: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:08: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:08: #2 predicted fragment length is 119 bps INFO @ Mon, 13 Nov 2017 13:17:08: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 13 Nov 2017 13:17:08: #2.2 Generate R script for model : SRX2576633.20_model.r INFO @ Mon, 13 Nov 2017 13:17:08: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:10: #1 tag size is determined as 36 bps INFO @ Mon, 13 Nov 2017 13:17:10: #1 tag size = 36 INFO @ Mon, 13 Nov 2017 13:17:10: #1 total tags in treatment: 12676434 INFO @ Mon, 13 Nov 2017 13:17:10: #1 tag size is determined as 36 bps INFO @ Mon, 13 Nov 2017 13:17:10: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:10: #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 13:17:10: #1 tag size = 36 INFO @ Mon, 13 Nov 2017 13:17:10: #1 total tags in treatment: 12676434 INFO @ Mon, 13 Nov 2017 13:17:10: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:10: #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 13:17:10: #1 tags after filtering in treatment: 12676434 INFO @ Mon, 13 Nov 2017 13:17:10: #1 tags after filtering in treatment: 12676434 INFO @ Mon, 13 Nov 2017 13:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:10: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:10: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:10: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:10: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:11: #2 number of paired peaks: 602 WARNING @ Mon, 13 Nov 2017 13:17:11: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:11: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:11: #2 number of paired peaks: 602 WARNING @ Mon, 13 Nov 2017 13:17:11: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:11: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:11: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:11: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:11: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:11: #2 predicted fragment length is 119 bps INFO @ Mon, 13 Nov 2017 13:17:11: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 13 Nov 2017 13:17:11: #2.2 Generate R script for model : SRX2576633.10_model.r INFO @ Mon, 13 Nov 2017 13:17:11: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:11: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:11: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:11: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:11: #2 predicted fragment length is 119 bps INFO @ Mon, 13 Nov 2017 13:17:11: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 13 Nov 2017 13:17:11: #2.2 Generate R script for model : SRX2576633.05_model.r INFO @ Mon, 13 Nov 2017 13:17:11: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:40: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:41: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:54: #4 Write output xls file... SRX2576633.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:54: #4 Write peak in narrowPeak format file... SRX2576633.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:54: #4 Write summits bed file... SRX2576633.20_summits.bed INFO @ Mon, 13 Nov 2017 13:17:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2056 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:17:58: #4 Write output xls file... SRX2576633.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:58: #4 Write peak in narrowPeak format file... SRX2576633.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:58: #4 Write summits bed file... SRX2576633.10_summits.bed INFO @ Mon, 13 Nov 2017 13:17:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3348 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:17:59: #4 Write output xls file... SRX2576633.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:59: #4 Write peak in narrowPeak format file... SRX2576633.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:59: #4 Write summits bed file... SRX2576633.05_summits.bed INFO @ Mon, 13 Nov 2017 13:17:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6766 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。