Job ID = 10714468 sra ファイルのダウンロード中... Completed: 1094655K bytes transferred in 17 seconds (501871K 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 17580922 spots for /home/okishinya/chipatlas/results/ce10/SRX4085384/SRR7167413.sra Written 17580922 spots for /home/okishinya/chipatlas/results/ce10/SRX4085384/SRR7167413.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: 00:13:29 17580922 reads; of these: 17580922 (100.00%) were paired; of these: 9574557 (54.46%) aligned concordantly 0 times 6821936 (38.80%) aligned concordantly exactly 1 time 1184429 (6.74%) aligned concordantly >1 times ---- 9574557 pairs aligned concordantly 0 times; of these: 265201 (2.77%) aligned discordantly 1 time ---- 9309356 pairs aligned 0 times concordantly or discordantly; of these: 18618712 mates make up the pairs; of these: 13631120 (73.21%) aligned 0 times 4357637 (23.40%) aligned exactly 1 time 629955 (3.38%) aligned >1 times 61.23% overall alignment rate Time searching: 00:13:29 Overall time: 00:13:29 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 12 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] 1891997 / 8149498 = 0.2322 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 13:01:32: # Command line: callpeak -t SRX4085384.bam -f BAM -g ce -n SRX4085384.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085384.10 # format = BAM # ChIP-seq file = ['SRX4085384.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 13:01:32: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:01:32: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:01:32: # Command line: callpeak -t SRX4085384.bam -f BAM -g ce -n SRX4085384.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085384.20 # format = BAM # ChIP-seq file = ['SRX4085384.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 13:01:32: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:01:32: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:01:32: # Command line: callpeak -t SRX4085384.bam -f BAM -g ce -n SRX4085384.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085384.05 # format = BAM # ChIP-seq file = ['SRX4085384.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 13:01:32: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:01:32: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:01:39: 1000000 INFO @ Sun, 03 Jun 2018 13:01:39: 1000000 INFO @ Sun, 03 Jun 2018 13:01:40: 1000000 INFO @ Sun, 03 Jun 2018 13:01:46: 2000000 INFO @ Sun, 03 Jun 2018 13:01:46: 2000000 INFO @ Sun, 03 Jun 2018 13:01:47: 2000000 INFO @ Sun, 03 Jun 2018 13:01:53: 3000000 INFO @ Sun, 03 Jun 2018 13:01:53: 3000000 INFO @ Sun, 03 Jun 2018 13:01:55: 3000000 INFO @ Sun, 03 Jun 2018 13:02:01: 4000000 INFO @ Sun, 03 Jun 2018 13:02:01: 4000000 INFO @ Sun, 03 Jun 2018 13:02:03: 4000000 INFO @ Sun, 03 Jun 2018 13:02:08: 5000000 INFO @ Sun, 03 Jun 2018 13:02:08: 5000000 INFO @ Sun, 03 Jun 2018 13:02:11: 5000000 INFO @ Sun, 03 Jun 2018 13:02:15: 6000000 INFO @ Sun, 03 Jun 2018 13:02:15: 6000000 INFO @ Sun, 03 Jun 2018 13:02:18: 6000000 INFO @ Sun, 03 Jun 2018 13:02:22: 7000000 INFO @ Sun, 03 Jun 2018 13:02:22: 7000000 INFO @ Sun, 03 Jun 2018 13:02:26: 7000000 INFO @ Sun, 03 Jun 2018 13:02:29: 8000000 INFO @ Sun, 03 Jun 2018 13:02:29: 8000000 INFO @ Sun, 03 Jun 2018 13:02:34: 8000000 INFO @ Sun, 03 Jun 2018 13:02:37: 9000000 INFO @ Sun, 03 Jun 2018 13:02:37: 9000000 INFO @ Sun, 03 Jun 2018 13:02:42: 9000000 INFO @ Sun, 03 Jun 2018 13:02:44: 10000000 INFO @ Sun, 03 Jun 2018 13:02:44: 10000000 INFO @ Sun, 03 Jun 2018 13:02:49: 10000000 INFO @ Sun, 03 Jun 2018 13:02:51: 11000000 INFO @ Sun, 03 Jun 2018 13:02:51: 11000000 INFO @ Sun, 03 Jun 2018 13:02:57: 11000000 INFO @ Sun, 03 Jun 2018 13:02:58: 12000000 INFO @ Sun, 03 Jun 2018 13:02:59: 12000000 INFO @ Sun, 03 Jun 2018 13:03:05: 12000000 INFO @ Sun, 03 Jun 2018 13:03:05: 13000000 INFO @ Sun, 03 Jun 2018 13:03:07: 13000000 INFO @ Sun, 03 Jun 2018 13:03:12: 14000000 INFO @ Sun, 03 Jun 2018 13:03:13: 13000000 INFO @ Sun, 03 Jun 2018 13:03:15: 14000000 INFO @ Sun, 03 Jun 2018 13:03:20: 15000000 INFO @ Sun, 03 Jun 2018 13:03:20: 14000000 INFO @ Sun, 03 Jun 2018 13:03:23: 15000000 INFO @ Sun, 03 Jun 2018 13:03:27: 15000000 INFO @ Sun, 03 Jun 2018 13:03:27: 16000000 INFO @ Sun, 03 Jun 2018 13:03:30: 16000000 INFO @ Sun, 03 Jun 2018 13:03:33: 16000000 INFO @ Sun, 03 Jun 2018 13:03:34: 17000000 INFO @ Sun, 03 Jun 2018 13:03:37: 17000000 INFO @ Sun, 03 Jun 2018 13:03:38: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:03:38: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:03:38: #1 total tags in treatment: 6145428 INFO @ Sun, 03 Jun 2018 13:03:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:03:38: #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 13:03:38: #1 tags after filtering in treatment: 5530072 INFO @ Sun, 03 Jun 2018 13:03:38: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 03 Jun 2018 13:03:38: #1 finished! INFO @ Sun, 03 Jun 2018 13:03:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:03:39: #2 number of paired peaks: 394 WARNING @ Sun, 03 Jun 2018 13:03:39: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sun, 03 Jun 2018 13:03:39: start model_add_line... INFO @ Sun, 03 Jun 2018 13:03:39: start X-correlation... INFO @ Sun, 03 Jun 2018 13:03:39: end of X-cor INFO @ Sun, 03 Jun 2018 13:03:39: #2 finished! INFO @ Sun, 03 Jun 2018 13:03:39: #2 predicted fragment length is 105 bps INFO @ Sun, 03 Jun 2018 13:03:39: #2 alternative fragment length(s) may be 4,105,124 bps INFO @ Sun, 03 Jun 2018 13:03:39: #2.2 Generate R script for model : SRX4085384.20_model.r INFO @ Sun, 03 Jun 2018 13:03:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:03:39: 17000000 INFO @ Sun, 03 Jun 2018 13:03:41: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:03:41: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:03:41: #1 total tags in treatment: 6145428 INFO @ Sun, 03 Jun 2018 13:03:41: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:03:41: #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 13:03:41: #1 tags after filtering in treatment: 5530072 INFO @ Sun, 03 Jun 2018 13:03:41: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 03 Jun 2018 13:03:41: #1 finished! INFO @ Sun, 03 Jun 2018 13:03:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:03:41: #2 number of paired peaks: 394 WARNING @ Sun, 03 Jun 2018 13:03:41: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sun, 03 Jun 2018 13:03:41: start model_add_line... INFO @ Sun, 03 Jun 2018 13:03:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:03:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:03:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:03:42: #2 predicted fragment length is 105 bps INFO @ Sun, 03 Jun 2018 13:03:42: #2 alternative fragment length(s) may be 4,105,124 bps INFO @ Sun, 03 Jun 2018 13:03:42: #2.2 Generate R script for model : SRX4085384.10_model.r INFO @ Sun, 03 Jun 2018 13:03:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:03:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:03:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:03:43: #1 total tags in treatment: 6145428 INFO @ Sun, 03 Jun 2018 13:03:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:03:43: #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 13:03:43: #1 tags after filtering in treatment: 5530072 INFO @ Sun, 03 Jun 2018 13:03:43: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 03 Jun 2018 13:03:43: #1 finished! INFO @ Sun, 03 Jun 2018 13:03:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:03:44: #2 number of paired peaks: 394 WARNING @ Sun, 03 Jun 2018 13:03:44: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sun, 03 Jun 2018 13:03:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:03:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:03:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:03:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:03:44: #2 predicted fragment length is 105 bps INFO @ Sun, 03 Jun 2018 13:03:44: #2 alternative fragment length(s) may be 4,105,124 bps INFO @ Sun, 03 Jun 2018 13:03:44: #2.2 Generate R script for model : SRX4085384.05_model.r INFO @ Sun, 03 Jun 2018 13:03:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:03:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:03:55: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:03:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:03:59: #4 Write output xls file... SRX4085384.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:03:59: #4 Write peak in narrowPeak format file... SRX4085384.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:03:59: #4 Write summits bed file... SRX4085384.20_summits.bed INFO @ Sun, 03 Jun 2018 13:03:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:04:02: #4 Write output xls file... SRX4085384.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:04:02: #4 Write peak in narrowPeak format file... SRX4085384.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:04:02: #4 Write summits bed file... SRX4085384.10_summits.bed INFO @ Sun, 03 Jun 2018 13:04:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:04:04: #4 Write output xls file... SRX4085384.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:04:04: #4 Write peak in narrowPeak format file... SRX4085384.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:04:04: #4 Write summits bed file... SRX4085384.05_summits.bed INFO @ Sun, 03 Jun 2018 13:04:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (980 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。