Job ID = 10714518 sra ファイルのダウンロード中... Completed: 558905K bytes transferred in 13 seconds (334454K 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 8102108 spots for /home/okishinya/chipatlas/results/ce10/SRX4085432/SRR7167461.sra Written 8102108 spots for /home/okishinya/chipatlas/results/ce10/SRX4085432/SRR7167461.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: 00:08:32 8102108 reads; of these: 8102108 (100.00%) were paired; of these: 835456 (10.31%) aligned concordantly 0 times 6384653 (78.80%) aligned concordantly exactly 1 time 881999 (10.89%) aligned concordantly >1 times ---- 835456 pairs aligned concordantly 0 times; of these: 413927 (49.55%) aligned discordantly 1 time ---- 421529 pairs aligned 0 times concordantly or discordantly; of these: 843058 mates make up the pairs; of these: 329747 (39.11%) aligned 0 times 318466 (37.78%) aligned exactly 1 time 194845 (23.11%) aligned >1 times 97.97% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 1544326 / 7361838 = 0.2098 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 13:17:44: # Command line: callpeak -t SRX4085432.bam -f BAM -g ce -n SRX4085432.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085432.05 # format = BAM # ChIP-seq file = ['SRX4085432.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 13:17:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:17:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:17:44: # Command line: callpeak -t SRX4085432.bam -f BAM -g ce -n SRX4085432.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085432.10 # format = BAM # ChIP-seq file = ['SRX4085432.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 13:17:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:17:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:17:44: # Command line: callpeak -t SRX4085432.bam -f BAM -g ce -n SRX4085432.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085432.20 # format = BAM # ChIP-seq file = ['SRX4085432.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 13:17:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:17:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:17:50: 1000000 INFO @ Sun, 03 Jun 2018 13:17:51: 1000000 INFO @ Sun, 03 Jun 2018 13:17:51: 1000000 INFO @ Sun, 03 Jun 2018 13:17:56: 2000000 INFO @ Sun, 03 Jun 2018 13:17:57: 2000000 INFO @ Sun, 03 Jun 2018 13:17:57: 2000000 INFO @ Sun, 03 Jun 2018 13:18:02: 3000000 INFO @ Sun, 03 Jun 2018 13:18:03: 3000000 INFO @ Sun, 03 Jun 2018 13:18:03: 3000000 INFO @ Sun, 03 Jun 2018 13:18:08: 4000000 INFO @ Sun, 03 Jun 2018 13:18:10: 4000000 INFO @ Sun, 03 Jun 2018 13:18:10: 4000000 INFO @ Sun, 03 Jun 2018 13:18:14: 5000000 INFO @ Sun, 03 Jun 2018 13:18:16: 5000000 INFO @ Sun, 03 Jun 2018 13:18:16: 5000000 INFO @ Sun, 03 Jun 2018 13:18:20: 6000000 INFO @ Sun, 03 Jun 2018 13:18:23: 6000000 INFO @ Sun, 03 Jun 2018 13:18:23: 6000000 INFO @ Sun, 03 Jun 2018 13:18:26: 7000000 INFO @ Sun, 03 Jun 2018 13:18:29: 7000000 INFO @ Sun, 03 Jun 2018 13:18:29: 7000000 INFO @ Sun, 03 Jun 2018 13:18:31: 8000000 INFO @ Sun, 03 Jun 2018 13:18:35: 8000000 INFO @ Sun, 03 Jun 2018 13:18:35: 8000000 INFO @ Sun, 03 Jun 2018 13:18:37: 9000000 INFO @ Sun, 03 Jun 2018 13:18:41: 9000000 INFO @ Sun, 03 Jun 2018 13:18:42: 9000000 INFO @ Sun, 03 Jun 2018 13:18:43: 10000000 INFO @ Sun, 03 Jun 2018 13:18:47: 10000000 INFO @ Sun, 03 Jun 2018 13:18:48: 10000000 INFO @ Sun, 03 Jun 2018 13:18:50: 11000000 INFO @ Sun, 03 Jun 2018 13:18:53: 11000000 INFO @ Sun, 03 Jun 2018 13:18:55: 11000000 INFO @ Sun, 03 Jun 2018 13:18:56: 12000000 INFO @ Sun, 03 Jun 2018 13:18:59: 12000000 INFO @ Sun, 03 Jun 2018 13:19:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:01: #1 total tags in treatment: 5741428 INFO @ Sun, 03 Jun 2018 13:19:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:01: #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 13:19:01: #1 tags after filtering in treatment: 5367196 INFO @ Sun, 03 Jun 2018 13:19:01: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 13:19:01: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:01: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:01: #2 number of paired peaks: 309 WARNING @ Sun, 03 Jun 2018 13:19:01: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:01: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:01: #2 predicted fragment length is 155 bps INFO @ Sun, 03 Jun 2018 13:19:01: #2 alternative fragment length(s) may be 4,128,155 bps INFO @ Sun, 03 Jun 2018 13:19:01: #2.2 Generate R script for model : SRX4085432.20_model.r INFO @ Sun, 03 Jun 2018 13:19:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:02: 12000000 INFO @ Sun, 03 Jun 2018 13:19:03: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:03: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:03: #1 total tags in treatment: 5741428 INFO @ Sun, 03 Jun 2018 13:19:03: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:03: #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 13:19:03: #1 tags after filtering in treatment: 5367196 INFO @ Sun, 03 Jun 2018 13:19:03: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 13:19:03: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:03: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:04: #2 number of paired peaks: 309 WARNING @ Sun, 03 Jun 2018 13:19:04: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:04: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:04: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:04: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:04: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:04: #2 predicted fragment length is 155 bps INFO @ Sun, 03 Jun 2018 13:19:04: #2 alternative fragment length(s) may be 4,128,155 bps INFO @ Sun, 03 Jun 2018 13:19:04: #2.2 Generate R script for model : SRX4085432.05_model.r INFO @ Sun, 03 Jun 2018 13:19:04: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:19:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:19:06: #1 total tags in treatment: 5741428 INFO @ Sun, 03 Jun 2018 13:19:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:19:06: #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 13:19:06: #1 tags after filtering in treatment: 5367196 INFO @ Sun, 03 Jun 2018 13:19:06: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 13:19:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:19:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:19:07: #2 number of paired peaks: 309 WARNING @ Sun, 03 Jun 2018 13:19:07: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 03 Jun 2018 13:19:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:19:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:19:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:19:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:19:07: #2 predicted fragment length is 155 bps INFO @ Sun, 03 Jun 2018 13:19:07: #2 alternative fragment length(s) may be 4,128,155 bps INFO @ Sun, 03 Jun 2018 13:19:07: #2.2 Generate R script for model : SRX4085432.10_model.r INFO @ Sun, 03 Jun 2018 13:19:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:19:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:16: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:19:20: #4 Write output xls file... SRX4085432.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:20: #4 Write peak in narrowPeak format file... SRX4085432.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:20: #4 Write summits bed file... SRX4085432.20_summits.bed INFO @ Sun, 03 Jun 2018 13:19:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (103 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:23: #4 Write output xls file... SRX4085432.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:23: #4 Write peak in narrowPeak format file... SRX4085432.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:23: #4 Write summits bed file... SRX4085432.05_summits.bed INFO @ Sun, 03 Jun 2018 13:19:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:19:27: #4 Write output xls file... SRX4085432.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:19:27: #4 Write peak in narrowPeak format file... SRX4085432.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:19:27: #4 Write summits bed file... SRX4085432.10_summits.bed INFO @ Sun, 03 Jun 2018 13:19:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。