Job ID = 11158460 sra ファイルのダウンロード中... Completed: 2985864K bytes transferred in 341 seconds (71719K 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 36173858 spots for /home/okishinya/chipatlas/results/ce10/SRX4012474/SRR7082715.sra Written 36173858 spots for /home/okishinya/chipatlas/results/ce10/SRX4012474/SRR7082715.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: 01:45:15 36173858 reads; of these: 36173858 (100.00%) were paired; of these: 26055158 (72.03%) aligned concordantly 0 times 2686386 (7.43%) aligned concordantly exactly 1 time 7432314 (20.55%) aligned concordantly >1 times ---- 26055158 pairs aligned concordantly 0 times; of these: 4088089 (15.69%) aligned discordantly 1 time ---- 21967069 pairs aligned 0 times concordantly or discordantly; of these: 43934138 mates make up the pairs; of these: 30254166 (68.86%) aligned 0 times 5151727 (11.73%) aligned exactly 1 time 8528245 (19.41%) aligned >1 times 58.18% overall alignment rate Time searching: 01:45:15 Overall time: 01:45:15 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] 3433702 / 10888993 = 0.3153 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 @ Tue, 04 Sep 2018 10:32:46: # Command line: callpeak -t SRX4012474.bam -f BAM -g ce -n SRX4012474.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4012474.05 # format = BAM # ChIP-seq file = ['SRX4012474.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 @ Tue, 04 Sep 2018 10:32:46: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:32:46: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:32:46: # Command line: callpeak -t SRX4012474.bam -f BAM -g ce -n SRX4012474.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4012474.10 # format = BAM # ChIP-seq file = ['SRX4012474.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 @ Tue, 04 Sep 2018 10:32:46: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:32:46: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:32:46: # Command line: callpeak -t SRX4012474.bam -f BAM -g ce -n SRX4012474.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4012474.20 # format = BAM # ChIP-seq file = ['SRX4012474.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 @ Tue, 04 Sep 2018 10:32:46: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:32:46: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:32:51: 1000000 INFO @ Tue, 04 Sep 2018 10:32:52: 1000000 INFO @ Tue, 04 Sep 2018 10:32:52: 1000000 INFO @ Tue, 04 Sep 2018 10:32:57: 2000000 INFO @ Tue, 04 Sep 2018 10:32:58: 2000000 INFO @ Tue, 04 Sep 2018 10:32:59: 2000000 INFO @ Tue, 04 Sep 2018 10:33:03: 3000000 INFO @ Tue, 04 Sep 2018 10:33:04: 3000000 INFO @ Tue, 04 Sep 2018 10:33:06: 3000000 INFO @ Tue, 04 Sep 2018 10:33:08: 4000000 INFO @ Tue, 04 Sep 2018 10:33:10: 4000000 INFO @ Tue, 04 Sep 2018 10:33:13: 4000000 INFO @ Tue, 04 Sep 2018 10:33:14: 5000000 INFO @ Tue, 04 Sep 2018 10:33:17: 5000000 INFO @ Tue, 04 Sep 2018 10:33:20: 6000000 INFO @ Tue, 04 Sep 2018 10:33:20: 5000000 INFO @ Tue, 04 Sep 2018 10:33:23: 6000000 INFO @ Tue, 04 Sep 2018 10:33:25: 7000000 INFO @ Tue, 04 Sep 2018 10:33:27: 6000000 INFO @ Tue, 04 Sep 2018 10:33:29: 7000000 INFO @ Tue, 04 Sep 2018 10:33:31: 8000000 INFO @ Tue, 04 Sep 2018 10:33:34: 7000000 INFO @ Tue, 04 Sep 2018 10:33:35: 8000000 INFO @ Tue, 04 Sep 2018 10:33:36: 9000000 INFO @ Tue, 04 Sep 2018 10:33:41: 8000000 INFO @ Tue, 04 Sep 2018 10:33:41: 9000000 INFO @ Tue, 04 Sep 2018 10:33:42: 10000000 INFO @ Tue, 04 Sep 2018 10:33:47: 10000000 INFO @ Tue, 04 Sep 2018 10:33:48: 9000000 INFO @ Tue, 04 Sep 2018 10:33:48: 11000000 INFO @ Tue, 04 Sep 2018 10:33:53: 11000000 INFO @ Tue, 04 Sep 2018 10:33:54: 12000000 INFO @ Tue, 04 Sep 2018 10:33:55: 10000000 INFO @ Tue, 04 Sep 2018 10:33:59: 13000000 INFO @ Tue, 04 Sep 2018 10:33:59: 12000000 INFO @ Tue, 04 Sep 2018 10:34:02: 11000000 INFO @ Tue, 04 Sep 2018 10:34:05: 14000000 INFO @ Tue, 04 Sep 2018 10:34:06: 13000000 INFO @ Tue, 04 Sep 2018 10:34:08: 12000000 INFO @ Tue, 04 Sep 2018 10:34:11: 15000000 INFO @ Tue, 04 Sep 2018 10:34:12: 14000000 INFO @ Tue, 04 Sep 2018 10:34:15: 13000000 INFO @ Tue, 04 Sep 2018 10:34:16: 16000000 INFO @ Tue, 04 Sep 2018 10:34:18: 15000000 INFO @ Tue, 04 Sep 2018 10:34:22: 17000000 INFO @ Tue, 04 Sep 2018 10:34:22: 14000000 INFO @ Tue, 04 Sep 2018 10:34:24: 16000000 INFO @ Tue, 04 Sep 2018 10:34:28: 18000000 INFO @ Tue, 04 Sep 2018 10:34:29: 15000000 INFO @ Tue, 04 Sep 2018 10:34:30: 17000000 INFO @ Tue, 04 Sep 2018 10:34:33: 19000000 INFO @ Tue, 04 Sep 2018 10:34:35: 16000000 INFO @ Tue, 04 Sep 2018 10:34:36: 18000000 INFO @ Tue, 04 Sep 2018 10:34:39: 20000000 INFO @ Tue, 04 Sep 2018 10:34:42: 17000000 INFO @ Tue, 04 Sep 2018 10:34:42: 19000000 INFO @ Tue, 04 Sep 2018 10:34:45: 21000000 INFO @ Tue, 04 Sep 2018 10:34:48: 20000000 INFO @ Tue, 04 Sep 2018 10:34:49: 18000000 INFO @ Tue, 04 Sep 2018 10:34:50: 22000000 INFO @ Tue, 04 Sep 2018 10:34:54: 21000000 INFO @ Tue, 04 Sep 2018 10:34:55: 19000000 INFO @ Tue, 04 Sep 2018 10:34:56: 23000000 INFO @ Tue, 04 Sep 2018 10:35:00: 22000000 INFO @ Tue, 04 Sep 2018 10:35:01: 24000000 INFO @ Tue, 04 Sep 2018 10:35:02: 20000000 INFO @ Tue, 04 Sep 2018 10:35:07: 23000000 INFO @ Tue, 04 Sep 2018 10:35:07: 25000000 INFO @ Tue, 04 Sep 2018 10:35:09: 21000000 INFO @ Tue, 04 Sep 2018 10:35:12: 26000000 INFO @ Tue, 04 Sep 2018 10:35:13: 24000000 INFO @ Tue, 04 Sep 2018 10:35:15: 22000000 INFO @ Tue, 04 Sep 2018 10:35:18: 27000000 INFO @ Tue, 04 Sep 2018 10:35:19: 25000000 INFO @ Tue, 04 Sep 2018 10:35:22: 23000000 INFO @ Tue, 04 Sep 2018 10:35:24: 28000000 INFO @ Tue, 04 Sep 2018 10:35:25: 26000000 INFO @ Tue, 04 Sep 2018 10:35:28: 24000000 INFO @ Tue, 04 Sep 2018 10:35:29: 29000000 INFO @ Tue, 04 Sep 2018 10:35:31: 27000000 INFO @ Tue, 04 Sep 2018 10:35:35: 25000000 INFO @ Tue, 04 Sep 2018 10:35:35: 30000000 INFO @ Tue, 04 Sep 2018 10:35:37: 28000000 INFO @ Tue, 04 Sep 2018 10:35:41: 31000000 INFO @ Tue, 04 Sep 2018 10:35:41: 26000000 INFO @ Tue, 04 Sep 2018 10:35:43: 29000000 INFO @ Tue, 04 Sep 2018 10:35:46: 32000000 INFO @ Tue, 04 Sep 2018 10:35:48: 27000000 INFO @ Tue, 04 Sep 2018 10:35:49: 30000000 INFO @ Tue, 04 Sep 2018 10:35:52: 33000000 INFO @ Tue, 04 Sep 2018 10:35:55: 28000000 INFO @ Tue, 04 Sep 2018 10:35:55: 31000000 INFO @ Tue, 04 Sep 2018 10:35:57: 34000000 INFO @ Tue, 04 Sep 2018 10:36:01: 32000000 INFO @ Tue, 04 Sep 2018 10:36:02: 29000000 INFO @ Tue, 04 Sep 2018 10:36:03: 35000000 INFO @ Tue, 04 Sep 2018 10:36:04: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:36:04: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:36:04: #1 total tags in treatment: 6881890 INFO @ Tue, 04 Sep 2018 10:36:04: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:36:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:36:05: #1 tags after filtering in treatment: 2832883 INFO @ Tue, 04 Sep 2018 10:36:05: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 04 Sep 2018 10:36:05: #1 finished! INFO @ Tue, 04 Sep 2018 10:36:05: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:36:05: #2 number of paired peaks: 2499 INFO @ Tue, 04 Sep 2018 10:36:05: start model_add_line... INFO @ Tue, 04 Sep 2018 10:36:05: start X-correlation... INFO @ Tue, 04 Sep 2018 10:36:05: end of X-cor INFO @ Tue, 04 Sep 2018 10:36:05: #2 finished! INFO @ Tue, 04 Sep 2018 10:36:05: #2 predicted fragment length is 243 bps INFO @ Tue, 04 Sep 2018 10:36:05: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 04 Sep 2018 10:36:05: #2.2 Generate R script for model : SRX4012474.05_model.r INFO @ Tue, 04 Sep 2018 10:36:05: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:36:07: 33000000 INFO @ Tue, 04 Sep 2018 10:36:08: 30000000 INFO @ Tue, 04 Sep 2018 10:36:13: 34000000 INFO @ Tue, 04 Sep 2018 10:36:15: 31000000 INFO @ Tue, 04 Sep 2018 10:36:18: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:36:19: 35000000 INFO @ Tue, 04 Sep 2018 10:36:21: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:36:21: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:36:21: #1 total tags in treatment: 6881890 INFO @ Tue, 04 Sep 2018 10:36:21: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:36:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:36:21: #1 tags after filtering in treatment: 2832883 INFO @ Tue, 04 Sep 2018 10:36:21: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 04 Sep 2018 10:36:21: #1 finished! INFO @ Tue, 04 Sep 2018 10:36:21: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:36:21: #2 number of paired peaks: 2499 INFO @ Tue, 04 Sep 2018 10:36:21: start model_add_line... INFO @ Tue, 04 Sep 2018 10:36:21: start X-correlation... INFO @ Tue, 04 Sep 2018 10:36:21: end of X-cor INFO @ Tue, 04 Sep 2018 10:36:21: #2 finished! INFO @ Tue, 04 Sep 2018 10:36:21: #2 predicted fragment length is 243 bps INFO @ Tue, 04 Sep 2018 10:36:21: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 04 Sep 2018 10:36:21: #2.2 Generate R script for model : SRX4012474.10_model.r INFO @ Tue, 04 Sep 2018 10:36:21: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:36:22: 32000000 INFO @ Tue, 04 Sep 2018 10:36:23: #4 Write output xls file... SRX4012474.05_peaks.xls INFO @ Tue, 04 Sep 2018 10:36:23: #4 Write peak in narrowPeak format file... SRX4012474.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:36:23: #4 Write summits bed file... SRX4012474.05_summits.bed INFO @ Tue, 04 Sep 2018 10:36:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3800 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:36:28: 33000000 INFO @ Tue, 04 Sep 2018 10:36:34: 34000000 INFO @ Tue, 04 Sep 2018 10:36:35: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:36:38: #4 Write output xls file... SRX4012474.10_peaks.xls INFO @ Tue, 04 Sep 2018 10:36:39: #4 Write peak in narrowPeak format file... SRX4012474.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:36:39: #4 Write summits bed file... SRX4012474.10_summits.bed INFO @ Tue, 04 Sep 2018 10:36:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2379 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:36:40: 35000000 INFO @ Tue, 04 Sep 2018 10:36:42: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:36:42: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:36:42: #1 total tags in treatment: 6881890 INFO @ Tue, 04 Sep 2018 10:36:42: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:36:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:36:42: #1 tags after filtering in treatment: 2832883 INFO @ Tue, 04 Sep 2018 10:36:42: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 04 Sep 2018 10:36:42: #1 finished! INFO @ Tue, 04 Sep 2018 10:36:42: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:36:42: #2 number of paired peaks: 2499 INFO @ Tue, 04 Sep 2018 10:36:42: start model_add_line... INFO @ Tue, 04 Sep 2018 10:36:42: start X-correlation... INFO @ Tue, 04 Sep 2018 10:36:42: end of X-cor INFO @ Tue, 04 Sep 2018 10:36:42: #2 finished! INFO @ Tue, 04 Sep 2018 10:36:42: #2 predicted fragment length is 243 bps INFO @ Tue, 04 Sep 2018 10:36:42: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 04 Sep 2018 10:36:42: #2.2 Generate R script for model : SRX4012474.20_model.r INFO @ Tue, 04 Sep 2018 10:36:42: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:36:55: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:36:59: #4 Write output xls file... SRX4012474.20_peaks.xls INFO @ Tue, 04 Sep 2018 10:36:59: #4 Write peak in narrowPeak format file... SRX4012474.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:36:59: #4 Write summits bed file... SRX4012474.20_summits.bed INFO @ Tue, 04 Sep 2018 10:36:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1314 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。