Job ID = 10714513 sra ファイルのダウンロード中... Completed: 1793158K bytes transferred in 26 seconds (545414K 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 25946572 spots for /home/okishinya/chipatlas/results/ce10/SRX4085429/SRR7167458.sra Written 25946572 spots for /home/okishinya/chipatlas/results/ce10/SRX4085429/SRR7167458.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: 00:27:21 25946572 reads; of these: 25946572 (100.00%) were paired; of these: 2223834 (8.57%) aligned concordantly 0 times 20560661 (79.24%) aligned concordantly exactly 1 time 3162077 (12.19%) aligned concordantly >1 times ---- 2223834 pairs aligned concordantly 0 times; of these: 205828 (9.26%) aligned discordantly 1 time ---- 2018006 pairs aligned 0 times concordantly or discordantly; of these: 4036012 mates make up the pairs; of these: 2829562 (70.11%) aligned 0 times 936175 (23.20%) aligned exactly 1 time 270275 (6.70%) aligned >1 times 94.55% overall alignment rate Time searching: 00:27:21 Overall time: 00:27:21 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 20 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] 13866520 / 23848685 = 0.5814 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 13:45:39: # Command line: callpeak -t SRX4085429.bam -f BAM -g ce -n SRX4085429.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085429.10 # format = BAM # ChIP-seq file = ['SRX4085429.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 13:45:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:39: # Command line: callpeak -t SRX4085429.bam -f BAM -g ce -n SRX4085429.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085429.20 # format = BAM # ChIP-seq file = ['SRX4085429.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 13:45:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:39: # Command line: callpeak -t SRX4085429.bam -f BAM -g ce -n SRX4085429.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085429.05 # format = BAM # ChIP-seq file = ['SRX4085429.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 13:45:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:45: 1000000 INFO @ Sun, 03 Jun 2018 13:45:45: 1000000 INFO @ Sun, 03 Jun 2018 13:45:45: 1000000 INFO @ Sun, 03 Jun 2018 13:45:51: 2000000 INFO @ Sun, 03 Jun 2018 13:45:51: 2000000 INFO @ Sun, 03 Jun 2018 13:45:51: 2000000 INFO @ Sun, 03 Jun 2018 13:45:56: 3000000 INFO @ Sun, 03 Jun 2018 13:45:57: 3000000 INFO @ Sun, 03 Jun 2018 13:45:57: 3000000 INFO @ Sun, 03 Jun 2018 13:46:02: 4000000 INFO @ Sun, 03 Jun 2018 13:46:02: 4000000 INFO @ Sun, 03 Jun 2018 13:46:02: 4000000 INFO @ Sun, 03 Jun 2018 13:46:07: 5000000 INFO @ Sun, 03 Jun 2018 13:46:08: 5000000 INFO @ Sun, 03 Jun 2018 13:46:08: 5000000 INFO @ Sun, 03 Jun 2018 13:46:13: 6000000 INFO @ Sun, 03 Jun 2018 13:46:14: 6000000 INFO @ Sun, 03 Jun 2018 13:46:14: 6000000 INFO @ Sun, 03 Jun 2018 13:46:19: 7000000 INFO @ Sun, 03 Jun 2018 13:46:19: 7000000 INFO @ Sun, 03 Jun 2018 13:46:19: 7000000 INFO @ Sun, 03 Jun 2018 13:46:25: 8000000 INFO @ Sun, 03 Jun 2018 13:46:25: 8000000 INFO @ Sun, 03 Jun 2018 13:46:25: 8000000 INFO @ Sun, 03 Jun 2018 13:46:30: 9000000 INFO @ Sun, 03 Jun 2018 13:46:31: 9000000 INFO @ Sun, 03 Jun 2018 13:46:31: 9000000 INFO @ Sun, 03 Jun 2018 13:46:36: 10000000 INFO @ Sun, 03 Jun 2018 13:46:36: 10000000 INFO @ Sun, 03 Jun 2018 13:46:37: 10000000 INFO @ Sun, 03 Jun 2018 13:46:42: 11000000 INFO @ Sun, 03 Jun 2018 13:46:42: 11000000 INFO @ Sun, 03 Jun 2018 13:46:43: 11000000 INFO @ Sun, 03 Jun 2018 13:46:48: 12000000 INFO @ Sun, 03 Jun 2018 13:46:48: 12000000 INFO @ Sun, 03 Jun 2018 13:46:48: 12000000 INFO @ Sun, 03 Jun 2018 13:46:54: 13000000 INFO @ Sun, 03 Jun 2018 13:46:54: 13000000 INFO @ Sun, 03 Jun 2018 13:46:54: 13000000 INFO @ Sun, 03 Jun 2018 13:47:00: 14000000 INFO @ Sun, 03 Jun 2018 13:47:00: 14000000 INFO @ Sun, 03 Jun 2018 13:47:01: 14000000 INFO @ Sun, 03 Jun 2018 13:47:06: 15000000 INFO @ Sun, 03 Jun 2018 13:47:07: 15000000 INFO @ Sun, 03 Jun 2018 13:47:07: 15000000 INFO @ Sun, 03 Jun 2018 13:47:12: 16000000 INFO @ Sun, 03 Jun 2018 13:47:13: 16000000 INFO @ Sun, 03 Jun 2018 13:47:14: 16000000 INFO @ Sun, 03 Jun 2018 13:47:18: 17000000 INFO @ Sun, 03 Jun 2018 13:47:19: 17000000 INFO @ Sun, 03 Jun 2018 13:47:20: 17000000 INFO @ Sun, 03 Jun 2018 13:47:23: 18000000 INFO @ Sun, 03 Jun 2018 13:47:26: 18000000 INFO @ Sun, 03 Jun 2018 13:47:27: 18000000 INFO @ Sun, 03 Jun 2018 13:47:30: 19000000 INFO @ Sun, 03 Jun 2018 13:47:32: 19000000 INFO @ Sun, 03 Jun 2018 13:47:33: 19000000 INFO @ Sun, 03 Jun 2018 13:47:35: 20000000 INFO @ Sun, 03 Jun 2018 13:47:38: 20000000 INFO @ Sun, 03 Jun 2018 13:47:39: 20000000 INFO @ Sun, 03 Jun 2018 13:47:41: 21000000 INFO @ Sun, 03 Jun 2018 13:47:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:47:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:47:43: #1 total tags in treatment: 9912937 INFO @ Sun, 03 Jun 2018 13:47:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:47:43: #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 13:47:43: #1 tags after filtering in treatment: 8308197 INFO @ Sun, 03 Jun 2018 13:47:43: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:47:43: #1 finished! INFO @ Sun, 03 Jun 2018 13:47:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:47:44: #2 number of paired peaks: 372 WARNING @ Sun, 03 Jun 2018 13:47:44: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 03 Jun 2018 13:47:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:47:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:47:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:47:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:47:44: #2 predicted fragment length is 120 bps INFO @ Sun, 03 Jun 2018 13:47:44: #2 alternative fragment length(s) may be 4,120,141 bps INFO @ Sun, 03 Jun 2018 13:47:44: #2.2 Generate R script for model : SRX4085429.05_model.r INFO @ Sun, 03 Jun 2018 13:47:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:47:44: 21000000 INFO @ Sun, 03 Jun 2018 13:47:45: 21000000 INFO @ Sun, 03 Jun 2018 13:47:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:47:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:47:47: #1 total tags in treatment: 9912937 INFO @ Sun, 03 Jun 2018 13:47:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:47:47: #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 13:47:47: #1 tags after filtering in treatment: 8308197 INFO @ Sun, 03 Jun 2018 13:47:47: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:47:47: #1 finished! INFO @ Sun, 03 Jun 2018 13:47:47: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:47:48: #2 number of paired peaks: 372 WARNING @ Sun, 03 Jun 2018 13:47:48: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 03 Jun 2018 13:47:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:47:48: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:47:48: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:47:48: #1 total tags in treatment: 9912937 INFO @ Sun, 03 Jun 2018 13:47:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:47:48: #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 13:47:48: start X-correlation... INFO @ Sun, 03 Jun 2018 13:47:48: end of X-cor INFO @ Sun, 03 Jun 2018 13:47:48: #2 finished! INFO @ Sun, 03 Jun 2018 13:47:48: #2 predicted fragment length is 120 bps INFO @ Sun, 03 Jun 2018 13:47:48: #2 alternative fragment length(s) may be 4,120,141 bps INFO @ Sun, 03 Jun 2018 13:47:48: #2.2 Generate R script for model : SRX4085429.10_model.r INFO @ Sun, 03 Jun 2018 13:47:48: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:47:48: #1 tags after filtering in treatment: 8308197 INFO @ Sun, 03 Jun 2018 13:47:48: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:47:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:47:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:47:48: #2 number of paired peaks: 372 WARNING @ Sun, 03 Jun 2018 13:47:48: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 03 Jun 2018 13:47:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:47:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:47:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:47:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:47:49: #2 predicted fragment length is 120 bps INFO @ Sun, 03 Jun 2018 13:47:49: #2 alternative fragment length(s) may be 4,120,141 bps INFO @ Sun, 03 Jun 2018 13:47:49: #2.2 Generate R script for model : SRX4085429.20_model.r INFO @ Sun, 03 Jun 2018 13:47:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:47:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:48:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:48:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:48:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:48:13: #4 Write output xls file... SRX4085429.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:48:13: #4 Write peak in narrowPeak format file... SRX4085429.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:48:13: #4 Write summits bed file... SRX4085429.05_summits.bed INFO @ Sun, 03 Jun 2018 13:48:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1603 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:48:19: #4 Write output xls file... SRX4085429.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:48:19: #4 Write peak in narrowPeak format file... SRX4085429.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:48:19: #4 Write summits bed file... SRX4085429.10_summits.bed INFO @ Sun, 03 Jun 2018 13:48:19: Done! INFO @ Sun, 03 Jun 2018 13:48:19: #4 Write output xls file... SRX4085429.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:48:19: #4 Write peak in narrowPeak format file... SRX4085429.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:48:19: #4 Write summits bed file... SRX4085429.20_summits.bed INFO @ Sun, 03 Jun 2018 13:48:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (200 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。