Job ID = 10714486 sra ファイルのダウンロード中... Completed: 701410K bytes transferred in 9 seconds (619204K 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 9862121 spots for /home/okishinya/chipatlas/results/ce10/SRX4085402/SRR7167431.sra Written 9862121 spots for /home/okishinya/chipatlas/results/ce10/SRX4085402/SRR7167431.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: 00:08:00 9862121 reads; of these: 9862121 (100.00%) were paired; of these: 1381534 (14.01%) aligned concordantly 0 times 7803716 (79.13%) aligned concordantly exactly 1 time 676871 (6.86%) aligned concordantly >1 times ---- 1381534 pairs aligned concordantly 0 times; of these: 36880 (2.67%) aligned discordantly 1 time ---- 1344654 pairs aligned 0 times concordantly or discordantly; of these: 2689308 mates make up the pairs; of these: 2368328 (88.06%) aligned 0 times 274996 (10.23%) aligned exactly 1 time 45984 (1.71%) aligned >1 times 87.99% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 4134917 / 8507411 = 0.4860 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 12:58:33: # Command line: callpeak -t SRX4085402.bam -f BAM -g ce -n SRX4085402.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085402.20 # format = BAM # ChIP-seq file = ['SRX4085402.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 12:58:33: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:58:33: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:58:33: # Command line: callpeak -t SRX4085402.bam -f BAM -g ce -n SRX4085402.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085402.05 # format = BAM # ChIP-seq file = ['SRX4085402.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 12:58:33: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:58:33: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:58:33: # Command line: callpeak -t SRX4085402.bam -f BAM -g ce -n SRX4085402.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085402.10 # format = BAM # ChIP-seq file = ['SRX4085402.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 12:58:33: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:58:33: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:58:40: 1000000 INFO @ Sun, 03 Jun 2018 12:58:41: 1000000 INFO @ Sun, 03 Jun 2018 12:58:41: 1000000 INFO @ Sun, 03 Jun 2018 12:58:47: 2000000 INFO @ Sun, 03 Jun 2018 12:58:48: 2000000 INFO @ Sun, 03 Jun 2018 12:58:48: 2000000 INFO @ Sun, 03 Jun 2018 12:58:54: 3000000 INFO @ Sun, 03 Jun 2018 12:58:56: 3000000 INFO @ Sun, 03 Jun 2018 12:58:56: 3000000 INFO @ Sun, 03 Jun 2018 12:59:01: 4000000 INFO @ Sun, 03 Jun 2018 12:59:04: 4000000 INFO @ Sun, 03 Jun 2018 12:59:04: 4000000 INFO @ Sun, 03 Jun 2018 12:59:09: 5000000 INFO @ Sun, 03 Jun 2018 12:59:12: 5000000 INFO @ Sun, 03 Jun 2018 12:59:12: 5000000 INFO @ Sun, 03 Jun 2018 12:59:16: 6000000 INFO @ Sun, 03 Jun 2018 12:59:20: 6000000 INFO @ Sun, 03 Jun 2018 12:59:20: 6000000 INFO @ Sun, 03 Jun 2018 12:59:23: 7000000 INFO @ Sun, 03 Jun 2018 12:59:28: 7000000 INFO @ Sun, 03 Jun 2018 12:59:28: 7000000 INFO @ Sun, 03 Jun 2018 12:59:30: 8000000 INFO @ Sun, 03 Jun 2018 12:59:35: 8000000 INFO @ Sun, 03 Jun 2018 12:59:35: 8000000 INFO @ Sun, 03 Jun 2018 12:59:36: 9000000 INFO @ Sun, 03 Jun 2018 12:59:37: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:59:37: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:59:37: #1 total tags in treatment: 4359110 INFO @ Sun, 03 Jun 2018 12:59:37: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:59:37: #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 12:59:37: #1 tags after filtering in treatment: 3505096 INFO @ Sun, 03 Jun 2018 12:59:37: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 12:59:37: #1 finished! INFO @ Sun, 03 Jun 2018 12:59:37: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:59:37: #2 number of paired peaks: 468 WARNING @ Sun, 03 Jun 2018 12:59:37: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 03 Jun 2018 12:59:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:59:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:59:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:59:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:59:37: #2 predicted fragment length is 141 bps INFO @ Sun, 03 Jun 2018 12:59:37: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 03 Jun 2018 12:59:37: #2.2 Generate R script for model : SRX4085402.10_model.r INFO @ Sun, 03 Jun 2018 12:59:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:59:43: 9000000 INFO @ Sun, 03 Jun 2018 12:59:43: 9000000 INFO @ Sun, 03 Jun 2018 12:59:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:59:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:59:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:59:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:59:43: #1 total tags in treatment: 4359110 INFO @ Sun, 03 Jun 2018 12:59:43: #1 total tags in treatment: 4359110 INFO @ Sun, 03 Jun 2018 12:59:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:59:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:59:43: #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 12:59:43: #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 12:59:43: #1 tags after filtering in treatment: 3505096 INFO @ Sun, 03 Jun 2018 12:59:43: #1 tags after filtering in treatment: 3505096 INFO @ Sun, 03 Jun 2018 12:59:43: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 12:59:43: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 12:59:43: #1 finished! INFO @ Sun, 03 Jun 2018 12:59:43: #1 finished! INFO @ Sun, 03 Jun 2018 12:59:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:59:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:59:44: #2 number of paired peaks: 468 WARNING @ Sun, 03 Jun 2018 12:59:44: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 03 Jun 2018 12:59:44: start model_add_line... INFO @ Sun, 03 Jun 2018 12:59:44: #2 number of paired peaks: 468 WARNING @ Sun, 03 Jun 2018 12:59:44: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 03 Jun 2018 12:59:44: start model_add_line... INFO @ Sun, 03 Jun 2018 12:59:44: start X-correlation... INFO @ Sun, 03 Jun 2018 12:59:44: end of X-cor INFO @ Sun, 03 Jun 2018 12:59:44: #2 finished! INFO @ Sun, 03 Jun 2018 12:59:44: #2 predicted fragment length is 141 bps INFO @ Sun, 03 Jun 2018 12:59:44: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 03 Jun 2018 12:59:44: #2.2 Generate R script for model : SRX4085402.05_model.r INFO @ Sun, 03 Jun 2018 12:59:44: start X-correlation... INFO @ Sun, 03 Jun 2018 12:59:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:59:44: end of X-cor INFO @ Sun, 03 Jun 2018 12:59:44: #2 finished! INFO @ Sun, 03 Jun 2018 12:59:44: #2 predicted fragment length is 141 bps INFO @ Sun, 03 Jun 2018 12:59:44: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 03 Jun 2018 12:59:44: #2.2 Generate R script for model : SRX4085402.20_model.r INFO @ Sun, 03 Jun 2018 12:59:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:59:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:59:50: #4 Write output xls file... SRX4085402.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:59:50: #4 Write peak in narrowPeak format file... SRX4085402.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:59:50: #4 Write summits bed file... SRX4085402.10_summits.bed INFO @ Sun, 03 Jun 2018 12:59:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (460 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:59:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:59:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:59:57: #4 Write output xls file... SRX4085402.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:59:57: #4 Write peak in narrowPeak format file... SRX4085402.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:59:57: #4 Write summits bed file... SRX4085402.05_summits.bed INFO @ Sun, 03 Jun 2018 12:59:57: #4 Write output xls file... SRX4085402.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:59:57: #4 Write peak in narrowPeak format file... SRX4085402.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:59:57: Done! INFO @ Sun, 03 Jun 2018 12:59:57: #4 Write summits bed file... SRX4085402.20_summits.bed INFO @ Sun, 03 Jun 2018 12:59:57: Done! pass1 - making usageList (7 chroms): 1 millis pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (755 records, 4 fields): 2 millis pass2 - checking and writing primary data (241 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。