Job ID = 10714510 sra ファイルのダウンロード中... Completed: 841695K bytes transferred in 12 seconds (549739K 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 13417697 spots for /home/okishinya/chipatlas/results/ce10/SRX4085426/SRR7167455.sra Written 13417697 spots for /home/okishinya/chipatlas/results/ce10/SRX4085426/SRR7167455.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: 00:08:22 13417697 reads; of these: 13417697 (100.00%) were paired; of these: 11199521 (83.47%) aligned concordantly 0 times 1916873 (14.29%) aligned concordantly exactly 1 time 301303 (2.25%) aligned concordantly >1 times ---- 11199521 pairs aligned concordantly 0 times; of these: 241902 (2.16%) aligned discordantly 1 time ---- 10957619 pairs aligned 0 times concordantly or discordantly; of these: 21915238 mates make up the pairs; of these: 15600776 (71.19%) aligned 0 times 5479112 (25.00%) aligned exactly 1 time 835350 (3.81%) aligned >1 times 41.86% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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] 114722 / 2311299 = 0.0496 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 13:15:34: # Command line: callpeak -t SRX4085426.bam -f BAM -g ce -n SRX4085426.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085426.20 # format = BAM # ChIP-seq file = ['SRX4085426.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 13:15:34: # Command line: callpeak -t SRX4085426.bam -f BAM -g ce -n SRX4085426.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085426.10 # format = BAM # ChIP-seq file = ['SRX4085426.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 13:15:34: # Command line: callpeak -t SRX4085426.bam -f BAM -g ce -n SRX4085426.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085426.05 # format = BAM # ChIP-seq file = ['SRX4085426.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 13:15:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:15:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:15:40: 1000000 INFO @ Sun, 03 Jun 2018 13:15:40: 1000000 INFO @ Sun, 03 Jun 2018 13:15:40: 1000000 INFO @ Sun, 03 Jun 2018 13:15:46: 2000000 INFO @ Sun, 03 Jun 2018 13:15:46: 2000000 INFO @ Sun, 03 Jun 2018 13:15:46: 2000000 INFO @ Sun, 03 Jun 2018 13:15:52: 3000000 INFO @ Sun, 03 Jun 2018 13:15:52: 3000000 INFO @ Sun, 03 Jun 2018 13:15:52: 3000000 INFO @ Sun, 03 Jun 2018 13:15:58: 4000000 INFO @ Sun, 03 Jun 2018 13:15:58: 4000000 INFO @ Sun, 03 Jun 2018 13:15:58: 4000000 INFO @ Sun, 03 Jun 2018 13:16:04: 5000000 INFO @ Sun, 03 Jun 2018 13:16:04: 5000000 INFO @ Sun, 03 Jun 2018 13:16:05: 5000000 INFO @ Sun, 03 Jun 2018 13:16:09: 6000000 INFO @ Sun, 03 Jun 2018 13:16:10: 6000000 INFO @ Sun, 03 Jun 2018 13:16:11: 6000000 INFO @ Sun, 03 Jun 2018 13:16:15: 7000000 INFO @ Sun, 03 Jun 2018 13:16:17: 7000000 INFO @ Sun, 03 Jun 2018 13:16:17: 7000000 INFO @ Sun, 03 Jun 2018 13:16:23: 8000000 INFO @ Sun, 03 Jun 2018 13:16:24: 8000000 INFO @ Sun, 03 Jun 2018 13:16:24: 8000000 INFO @ Sun, 03 Jun 2018 13:16:30: 9000000 INFO @ Sun, 03 Jun 2018 13:16:30: 9000000 INFO @ Sun, 03 Jun 2018 13:16:31: 9000000 INFO @ Sun, 03 Jun 2018 13:16:37: 10000000 INFO @ Sun, 03 Jun 2018 13:16:38: 10000000 INFO @ Sun, 03 Jun 2018 13:16:38: 10000000 INFO @ Sun, 03 Jun 2018 13:16:44: 11000000 INFO @ Sun, 03 Jun 2018 13:16:44: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:16:44: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:16:44: #1 total tags in treatment: 2105052 INFO @ Sun, 03 Jun 2018 13:16:44: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:16:44: #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 13:16:44: #1 tags after filtering in treatment: 2028432 INFO @ Sun, 03 Jun 2018 13:16:44: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 03 Jun 2018 13:16:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:16:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:16:44: #2 number of paired peaks: 320 WARNING @ Sun, 03 Jun 2018 13:16:44: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sun, 03 Jun 2018 13:16:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:16:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:16:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:16:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:16:44: #2 predicted fragment length is 193 bps INFO @ Sun, 03 Jun 2018 13:16:44: #2 alternative fragment length(s) may be 89,193 bps INFO @ Sun, 03 Jun 2018 13:16:44: #2.2 Generate R script for model : SRX4085426.10_model.r INFO @ Sun, 03 Jun 2018 13:16:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:16:45: 11000000 INFO @ Sun, 03 Jun 2018 13:16:45: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:16:45: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:16:45: #1 total tags in treatment: 2105052 INFO @ Sun, 03 Jun 2018 13:16:45: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:16:45: #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 13:16:45: #1 tags after filtering in treatment: 2028432 INFO @ Sun, 03 Jun 2018 13:16:45: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 03 Jun 2018 13:16:45: #1 finished! INFO @ Sun, 03 Jun 2018 13:16:45: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:16:45: #2 number of paired peaks: 320 WARNING @ Sun, 03 Jun 2018 13:16:45: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sun, 03 Jun 2018 13:16:45: start model_add_line... INFO @ Sun, 03 Jun 2018 13:16:45: start X-correlation... INFO @ Sun, 03 Jun 2018 13:16:45: end of X-cor INFO @ Sun, 03 Jun 2018 13:16:45: #2 finished! INFO @ Sun, 03 Jun 2018 13:16:45: #2 predicted fragment length is 193 bps INFO @ Sun, 03 Jun 2018 13:16:45: #2 alternative fragment length(s) may be 89,193 bps INFO @ Sun, 03 Jun 2018 13:16:45: #2.2 Generate R script for model : SRX4085426.05_model.r INFO @ Sun, 03 Jun 2018 13:16:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:16:45: 11000000 INFO @ Sun, 03 Jun 2018 13:16:46: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:16:46: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:16:46: #1 total tags in treatment: 2105052 INFO @ Sun, 03 Jun 2018 13:16:46: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:16:46: #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 13:16:46: #1 tags after filtering in treatment: 2028432 INFO @ Sun, 03 Jun 2018 13:16:46: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 03 Jun 2018 13:16:46: #1 finished! INFO @ Sun, 03 Jun 2018 13:16:46: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:16:46: #2 number of paired peaks: 320 WARNING @ Sun, 03 Jun 2018 13:16:46: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sun, 03 Jun 2018 13:16:46: start model_add_line... INFO @ Sun, 03 Jun 2018 13:16:46: start X-correlation... INFO @ Sun, 03 Jun 2018 13:16:46: end of X-cor INFO @ Sun, 03 Jun 2018 13:16:46: #2 finished! INFO @ Sun, 03 Jun 2018 13:16:46: #2 predicted fragment length is 193 bps INFO @ Sun, 03 Jun 2018 13:16:46: #2 alternative fragment length(s) may be 89,193 bps INFO @ Sun, 03 Jun 2018 13:16:46: #2.2 Generate R script for model : SRX4085426.20_model.r INFO @ Sun, 03 Jun 2018 13:16:46: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:16:49: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:16:50: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:16:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:16:52: #4 Write output xls file... SRX4085426.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:16:52: #4 Write peak in narrowPeak format file... SRX4085426.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:16:52: #4 Write summits bed file... SRX4085426.10_summits.bed INFO @ Sun, 03 Jun 2018 13:16:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:16:53: #4 Write output xls file... SRX4085426.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:16:53: #4 Write peak in narrowPeak format file... SRX4085426.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:16:53: #4 Write summits bed file... SRX4085426.05_summits.bed INFO @ Sun, 03 Jun 2018 13:16:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:16:54: #4 Write output xls file... SRX4085426.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:16:54: #4 Write peak in narrowPeak format file... SRX4085426.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:16:54: #4 Write summits bed file... SRX4085426.20_summits.bed INFO @ Sun, 03 Jun 2018 13:16:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (53 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。