Job ID = 10480743 sra ファイルのダウンロード中... Completed: 390595K bytes transferred in 27 seconds (117190K 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 12218820 spots for /home/okishinya/chipatlas/results/dm3/SRX3380802/SRR6278165.sra Written 12218820 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: 00:05:26 12218820 reads; of these: 12218820 (100.00%) were unpaired; of these: 326035 (2.67%) aligned 0 times 7896189 (64.62%) aligned exactly 1 time 3996596 (32.71%) aligned >1 times 97.33% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2113814 / 11892785 = 0.1777 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 @ Fri, 16 Mar 2018 07:56:01: # Command line: callpeak -t SRX3380802.bam -f BAM -g dm -n SRX3380802.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380802.20 # format = BAM # ChIP-seq file = ['SRX3380802.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:56:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:01: # Command line: callpeak -t SRX3380802.bam -f BAM -g dm -n SRX3380802.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380802.05 # format = BAM # ChIP-seq file = ['SRX3380802.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:56:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:01: # Command line: callpeak -t SRX3380802.bam -f BAM -g dm -n SRX3380802.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380802.10 # format = BAM # ChIP-seq file = ['SRX3380802.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:56:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:07: 1000000 INFO @ Fri, 16 Mar 2018 07:56:07: 1000000 INFO @ Fri, 16 Mar 2018 07:56:07: 1000000 INFO @ Fri, 16 Mar 2018 07:56:13: 2000000 INFO @ Fri, 16 Mar 2018 07:56:13: 2000000 INFO @ Fri, 16 Mar 2018 07:56:14: 2000000 INFO @ Fri, 16 Mar 2018 07:56:19: 3000000 INFO @ Fri, 16 Mar 2018 07:56:19: 3000000 INFO @ Fri, 16 Mar 2018 07:56:20: 3000000 INFO @ Fri, 16 Mar 2018 07:56:25: 4000000 INFO @ Fri, 16 Mar 2018 07:56:25: 4000000 INFO @ Fri, 16 Mar 2018 07:56:26: 4000000 INFO @ Fri, 16 Mar 2018 07:56:32: 5000000 INFO @ Fri, 16 Mar 2018 07:56:32: 5000000 INFO @ Fri, 16 Mar 2018 07:56:33: 5000000 INFO @ Fri, 16 Mar 2018 07:56:38: 6000000 INFO @ Fri, 16 Mar 2018 07:56:38: 6000000 INFO @ Fri, 16 Mar 2018 07:56:39: 6000000 INFO @ Fri, 16 Mar 2018 07:56:44: 7000000 INFO @ Fri, 16 Mar 2018 07:56:44: 7000000 INFO @ Fri, 16 Mar 2018 07:56:46: 7000000 INFO @ Fri, 16 Mar 2018 07:56:50: 8000000 INFO @ Fri, 16 Mar 2018 07:56:50: 8000000 INFO @ Fri, 16 Mar 2018 07:56:52: 8000000 INFO @ Fri, 16 Mar 2018 07:56:56: 9000000 INFO @ Fri, 16 Mar 2018 07:56:56: 9000000 INFO @ Fri, 16 Mar 2018 07:56:58: 9000000 INFO @ Fri, 16 Mar 2018 07:57:01: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:57:01: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:57:01: #1 total tags in treatment: 9778971 INFO @ Fri, 16 Mar 2018 07:57:01: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:01: #1 tags after filtering in treatment: 9778971 INFO @ Fri, 16 Mar 2018 07:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:01: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:01: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:01: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:57:01: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:57:01: #1 total tags in treatment: 9778971 INFO @ Fri, 16 Mar 2018 07:57:01: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:01: #1 tags after filtering in treatment: 9778971 INFO @ Fri, 16 Mar 2018 07:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:01: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:01: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:02: #2 number of paired peaks: 1089 INFO @ Fri, 16 Mar 2018 07:57:02: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:02: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:02: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:02: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:02: #2 predicted fragment length is 118 bps INFO @ Fri, 16 Mar 2018 07:57:02: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 16 Mar 2018 07:57:02: #2.2 Generate R script for model : SRX3380802.10_model.r INFO @ Fri, 16 Mar 2018 07:57:02: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:02: #2 number of paired peaks: 1089 INFO @ Fri, 16 Mar 2018 07:57:02: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:02: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:02: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:02: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:02: #2 predicted fragment length is 118 bps INFO @ Fri, 16 Mar 2018 07:57:02: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 16 Mar 2018 07:57:02: #2.2 Generate R script for model : SRX3380802.20_model.r INFO @ Fri, 16 Mar 2018 07:57:02: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:03: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:57:03: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:57:03: #1 total tags in treatment: 9778971 INFO @ Fri, 16 Mar 2018 07:57:03: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:04: #1 tags after filtering in treatment: 9778971 INFO @ Fri, 16 Mar 2018 07:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:04: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:04: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:04: #2 number of paired peaks: 1089 INFO @ Fri, 16 Mar 2018 07:57:04: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:05: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:05: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:05: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:05: #2 predicted fragment length is 118 bps INFO @ Fri, 16 Mar 2018 07:57:05: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 16 Mar 2018 07:57:05: #2.2 Generate R script for model : SRX3380802.05_model.r INFO @ Fri, 16 Mar 2018 07:57:05: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:24: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:57:26: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:57:28: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:57:37: #4 Write output xls file... SRX3380802.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:57:37: #4 Write peak in narrowPeak format file... SRX3380802.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:57:37: #4 Write summits bed file... SRX3380802.10_summits.bed INFO @ Fri, 16 Mar 2018 07:57:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3508 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:57:40: #4 Write output xls file... SRX3380802.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:57:40: #4 Write peak in narrowPeak format file... SRX3380802.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:57:40: #4 Write summits bed file... SRX3380802.05_summits.bed INFO @ Fri, 16 Mar 2018 07:57:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8199 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:57:41: #4 Write output xls file... SRX3380802.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:57:41: #4 Write peak in narrowPeak format file... SRX3380802.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:57:41: #4 Write summits bed file... SRX3380802.20_summits.bed INFO @ Fri, 16 Mar 2018 07:57:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1432 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。