Job ID = 10714478 sra ファイルのダウンロード中... Completed: 2553081K bytes transferred in 52 seconds (395782K 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 37931177 spots for /home/okishinya/chipatlas/results/ce10/SRX4085394/SRR7167423.sra Written 37931177 spots for /home/okishinya/chipatlas/results/ce10/SRX4085394/SRR7167423.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: 00:34:08 37931177 reads; of these: 37931177 (100.00%) were paired; of these: 2502254 (6.60%) aligned concordantly 0 times 32420657 (85.47%) aligned concordantly exactly 1 time 3008266 (7.93%) aligned concordantly >1 times ---- 2502254 pairs aligned concordantly 0 times; of these: 185529 (7.41%) aligned discordantly 1 time ---- 2316725 pairs aligned 0 times concordantly or discordantly; of these: 4633450 mates make up the pairs; of these: 3695170 (79.75%) aligned 0 times 753937 (16.27%) aligned exactly 1 time 184343 (3.98%) aligned >1 times 95.13% overall alignment rate Time searching: 00:34:08 Overall time: 00:34:08 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 32 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] 22223337 / 35538853 = 0.6253 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 13:36:36: # Command line: callpeak -t SRX4085394.bam -f BAM -g ce -n SRX4085394.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085394.10 # format = BAM # ChIP-seq file = ['SRX4085394.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 13:36:36: # Command line: callpeak -t SRX4085394.bam -f BAM -g ce -n SRX4085394.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085394.05 # format = BAM # ChIP-seq file = ['SRX4085394.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 13:36:36: # Command line: callpeak -t SRX4085394.bam -f BAM -g ce -n SRX4085394.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085394.20 # format = BAM # ChIP-seq file = ['SRX4085394.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 13:36:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:44: 1000000 INFO @ Sun, 03 Jun 2018 13:36:44: 1000000 INFO @ Sun, 03 Jun 2018 13:36:44: 1000000 INFO @ Sun, 03 Jun 2018 13:36:52: 2000000 INFO @ Sun, 03 Jun 2018 13:36:52: 2000000 INFO @ Sun, 03 Jun 2018 13:36:52: 2000000 INFO @ Sun, 03 Jun 2018 13:37:00: 3000000 INFO @ Sun, 03 Jun 2018 13:37:00: 3000000 INFO @ Sun, 03 Jun 2018 13:37:00: 3000000 INFO @ Sun, 03 Jun 2018 13:37:08: 4000000 INFO @ Sun, 03 Jun 2018 13:37:08: 4000000 INFO @ Sun, 03 Jun 2018 13:37:08: 4000000 INFO @ Sun, 03 Jun 2018 13:37:16: 5000000 INFO @ Sun, 03 Jun 2018 13:37:16: 5000000 INFO @ Sun, 03 Jun 2018 13:37:16: 5000000 INFO @ Sun, 03 Jun 2018 13:37:24: 6000000 INFO @ Sun, 03 Jun 2018 13:37:24: 6000000 INFO @ Sun, 03 Jun 2018 13:37:24: 6000000 INFO @ Sun, 03 Jun 2018 13:37:31: 7000000 INFO @ Sun, 03 Jun 2018 13:37:31: 7000000 INFO @ Sun, 03 Jun 2018 13:37:31: 7000000 INFO @ Sun, 03 Jun 2018 13:37:39: 8000000 INFO @ Sun, 03 Jun 2018 13:37:39: 8000000 INFO @ Sun, 03 Jun 2018 13:37:39: 8000000 INFO @ Sun, 03 Jun 2018 13:37:47: 9000000 INFO @ Sun, 03 Jun 2018 13:37:47: 9000000 INFO @ Sun, 03 Jun 2018 13:37:47: 9000000 INFO @ Sun, 03 Jun 2018 13:37:54: 10000000 INFO @ Sun, 03 Jun 2018 13:37:54: 10000000 INFO @ Sun, 03 Jun 2018 13:37:54: 10000000 INFO @ Sun, 03 Jun 2018 13:38:02: 11000000 INFO @ Sun, 03 Jun 2018 13:38:02: 11000000 INFO @ Sun, 03 Jun 2018 13:38:02: 11000000 INFO @ Sun, 03 Jun 2018 13:38:10: 12000000 INFO @ Sun, 03 Jun 2018 13:38:10: 12000000 INFO @ Sun, 03 Jun 2018 13:38:10: 12000000 INFO @ Sun, 03 Jun 2018 13:38:18: 13000000 INFO @ Sun, 03 Jun 2018 13:38:18: 13000000 INFO @ Sun, 03 Jun 2018 13:38:18: 13000000 INFO @ Sun, 03 Jun 2018 13:38:26: 14000000 INFO @ Sun, 03 Jun 2018 13:38:26: 14000000 INFO @ Sun, 03 Jun 2018 13:38:26: 14000000 INFO @ Sun, 03 Jun 2018 13:38:34: 15000000 INFO @ Sun, 03 Jun 2018 13:38:34: 15000000 INFO @ Sun, 03 Jun 2018 13:38:34: 15000000 INFO @ Sun, 03 Jun 2018 13:38:42: 16000000 INFO @ Sun, 03 Jun 2018 13:38:42: 16000000 INFO @ Sun, 03 Jun 2018 13:38:42: 16000000 INFO @ Sun, 03 Jun 2018 13:38:50: 17000000 INFO @ Sun, 03 Jun 2018 13:38:50: 17000000 INFO @ Sun, 03 Jun 2018 13:38:50: 17000000 INFO @ Sun, 03 Jun 2018 13:38:58: 18000000 INFO @ Sun, 03 Jun 2018 13:38:58: 18000000 INFO @ Sun, 03 Jun 2018 13:38:58: 18000000 INFO @ Sun, 03 Jun 2018 13:39:06: 19000000 INFO @ Sun, 03 Jun 2018 13:39:06: 19000000 INFO @ Sun, 03 Jun 2018 13:39:06: 19000000 INFO @ Sun, 03 Jun 2018 13:39:14: 20000000 INFO @ Sun, 03 Jun 2018 13:39:14: 20000000 INFO @ Sun, 03 Jun 2018 13:39:14: 20000000 INFO @ Sun, 03 Jun 2018 13:39:22: 21000000 INFO @ Sun, 03 Jun 2018 13:39:22: 21000000 INFO @ Sun, 03 Jun 2018 13:39:22: 21000000 INFO @ Sun, 03 Jun 2018 13:39:30: 22000000 INFO @ Sun, 03 Jun 2018 13:39:30: 22000000 INFO @ Sun, 03 Jun 2018 13:39:30: 22000000 INFO @ Sun, 03 Jun 2018 13:39:38: 23000000 INFO @ Sun, 03 Jun 2018 13:39:38: 23000000 INFO @ Sun, 03 Jun 2018 13:39:38: 23000000 INFO @ Sun, 03 Jun 2018 13:39:46: 24000000 INFO @ Sun, 03 Jun 2018 13:39:46: 24000000 INFO @ Sun, 03 Jun 2018 13:39:46: 24000000 INFO @ Sun, 03 Jun 2018 13:39:54: 25000000 INFO @ Sun, 03 Jun 2018 13:39:54: 25000000 INFO @ Sun, 03 Jun 2018 13:39:54: 25000000 INFO @ Sun, 03 Jun 2018 13:40:01: 26000000 INFO @ Sun, 03 Jun 2018 13:40:01: 26000000 INFO @ Sun, 03 Jun 2018 13:40:01: 26000000 INFO @ Sun, 03 Jun 2018 13:40:08: 27000000 INFO @ Sun, 03 Jun 2018 13:40:08: 27000000 INFO @ Sun, 03 Jun 2018 13:40:08: 27000000 INFO @ Sun, 03 Jun 2018 13:40:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:40:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:40:13: #1 total tags in treatment: 13271155 INFO @ Sun, 03 Jun 2018 13:40:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:40:13: #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 13:40:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:40:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:40:13: #1 total tags in treatment: 13271155 INFO @ Sun, 03 Jun 2018 13:40:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:40:13: #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 13:40:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:40:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:40:13: #1 total tags in treatment: 13271155 INFO @ Sun, 03 Jun 2018 13:40:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:40:13: #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 13:40:14: #1 tags after filtering in treatment: 11057227 INFO @ Sun, 03 Jun 2018 13:40:14: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:40:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:40:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:40:14: #1 tags after filtering in treatment: 11057227 INFO @ Sun, 03 Jun 2018 13:40:14: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:40:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:40:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:40:14: #1 tags after filtering in treatment: 11057227 INFO @ Sun, 03 Jun 2018 13:40:14: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:40:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:40:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:40:14: #2 number of paired peaks: 395 WARNING @ Sun, 03 Jun 2018 13:40:14: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 03 Jun 2018 13:40:14: start model_add_line... INFO @ Sun, 03 Jun 2018 13:40:14: #2 number of paired peaks: 395 WARNING @ Sun, 03 Jun 2018 13:40:14: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 03 Jun 2018 13:40:14: start model_add_line... INFO @ Sun, 03 Jun 2018 13:40:14: #2 number of paired peaks: 395 WARNING @ Sun, 03 Jun 2018 13:40:14: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 03 Jun 2018 13:40:14: start model_add_line... INFO @ Sun, 03 Jun 2018 13:40:14: start X-correlation... INFO @ Sun, 03 Jun 2018 13:40:14: start X-correlation... INFO @ Sun, 03 Jun 2018 13:40:14: start X-correlation... INFO @ Sun, 03 Jun 2018 13:40:15: end of X-cor INFO @ Sun, 03 Jun 2018 13:40:15: end of X-cor INFO @ Sun, 03 Jun 2018 13:40:15: end of X-cor INFO @ Sun, 03 Jun 2018 13:40:15: #2 finished! INFO @ Sun, 03 Jun 2018 13:40:15: #2 finished! INFO @ Sun, 03 Jun 2018 13:40:15: #2 finished! INFO @ Sun, 03 Jun 2018 13:40:15: #2 predicted fragment length is 143 bps INFO @ Sun, 03 Jun 2018 13:40:15: #2 predicted fragment length is 143 bps INFO @ Sun, 03 Jun 2018 13:40:15: #2 predicted fragment length is 143 bps INFO @ Sun, 03 Jun 2018 13:40:15: #2 alternative fragment length(s) may be 4,119,143 bps INFO @ Sun, 03 Jun 2018 13:40:15: #2 alternative fragment length(s) may be 4,119,143 bps INFO @ Sun, 03 Jun 2018 13:40:15: #2 alternative fragment length(s) may be 4,119,143 bps INFO @ Sun, 03 Jun 2018 13:40:15: #2.2 Generate R script for model : SRX4085394.10_model.r INFO @ Sun, 03 Jun 2018 13:40:15: #2.2 Generate R script for model : SRX4085394.05_model.r INFO @ Sun, 03 Jun 2018 13:40:15: #2.2 Generate R script for model : SRX4085394.20_model.r INFO @ Sun, 03 Jun 2018 13:40:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:40:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:40:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:38: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:40: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:40: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:50: #4 Write output xls file... SRX4085394.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:50: #4 Write peak in narrowPeak format file... SRX4085394.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:50: #4 Write summits bed file... SRX4085394.10_summits.bed INFO @ Sun, 03 Jun 2018 13:40:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:52: #4 Write output xls file... SRX4085394.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:52: #4 Write peak in narrowPeak format file... SRX4085394.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:52: #4 Write summits bed file... SRX4085394.20_summits.bed INFO @ Sun, 03 Jun 2018 13:40:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:52: #4 Write output xls file... SRX4085394.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:52: #4 Write peak in narrowPeak format file... SRX4085394.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:52: #4 Write summits bed file... SRX4085394.05_summits.bed INFO @ Sun, 03 Jun 2018 13:40:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1145 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。