Job ID = 11158462 sra ファイルのダウンロード中... Completed: 2780869K bytes transferred in 349 seconds (65130K 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 32420082 spots for /home/okishinya/chipatlas/results/ce10/SRX4012476/SRR7082717.sra Written 32420082 spots for /home/okishinya/chipatlas/results/ce10/SRX4012476/SRR7082717.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: 01:42:37 32420082 reads; of these: 32420082 (100.00%) were paired; of these: 9005274 (27.78%) aligned concordantly 0 times 13149563 (40.56%) aligned concordantly exactly 1 time 10265245 (31.66%) aligned concordantly >1 times ---- 9005274 pairs aligned concordantly 0 times; of these: 617329 (6.86%) aligned discordantly 1 time ---- 8387945 pairs aligned 0 times concordantly or discordantly; of these: 16775890 mates make up the pairs; of these: 9454625 (56.36%) aligned 0 times 2050627 (12.22%) aligned exactly 1 time 5270638 (31.42%) aligned >1 times 85.42% overall alignment rate Time searching: 01:42:37 Overall time: 01:42:37 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 24 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] 4897376 / 23633774 = 0.2072 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 10:34:52: # Command line: callpeak -t SRX4012476.bam -f BAM -g ce -n SRX4012476.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4012476.05 # format = BAM # ChIP-seq file = ['SRX4012476.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 10:34:52: # Command line: callpeak -t SRX4012476.bam -f BAM -g ce -n SRX4012476.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4012476.20 # format = BAM # ChIP-seq file = ['SRX4012476.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 10:34:52: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:34:52: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:34:52: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:34:52: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:34:52: # Command line: callpeak -t SRX4012476.bam -f BAM -g ce -n SRX4012476.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4012476.10 # format = BAM # ChIP-seq file = ['SRX4012476.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 10:34:52: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:34:52: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:35:00: 1000000 INFO @ Tue, 04 Sep 2018 10:35:00: 1000000 INFO @ Tue, 04 Sep 2018 10:35:00: 1000000 INFO @ Tue, 04 Sep 2018 10:35:07: 2000000 INFO @ Tue, 04 Sep 2018 10:35:08: 2000000 INFO @ Tue, 04 Sep 2018 10:35:08: 2000000 INFO @ Tue, 04 Sep 2018 10:35:16: 3000000 INFO @ Tue, 04 Sep 2018 10:35:16: 3000000 INFO @ Tue, 04 Sep 2018 10:35:16: 3000000 INFO @ Tue, 04 Sep 2018 10:35:25: 4000000 INFO @ Tue, 04 Sep 2018 10:35:25: 4000000 INFO @ Tue, 04 Sep 2018 10:35:26: 4000000 INFO @ Tue, 04 Sep 2018 10:35:33: 5000000 INFO @ Tue, 04 Sep 2018 10:35:33: 5000000 INFO @ Tue, 04 Sep 2018 10:35:34: 5000000 INFO @ Tue, 04 Sep 2018 10:35:41: 6000000 INFO @ Tue, 04 Sep 2018 10:35:42: 6000000 INFO @ Tue, 04 Sep 2018 10:35:43: 6000000 INFO @ Tue, 04 Sep 2018 10:35:50: 7000000 INFO @ Tue, 04 Sep 2018 10:35:51: 7000000 INFO @ Tue, 04 Sep 2018 10:35:52: 7000000 INFO @ Tue, 04 Sep 2018 10:35:58: 8000000 INFO @ Tue, 04 Sep 2018 10:35:59: 8000000 INFO @ Tue, 04 Sep 2018 10:36:01: 8000000 INFO @ Tue, 04 Sep 2018 10:36:08: 9000000 INFO @ Tue, 04 Sep 2018 10:36:09: 9000000 INFO @ Tue, 04 Sep 2018 10:36:10: 9000000 INFO @ Tue, 04 Sep 2018 10:36:16: 10000000 INFO @ Tue, 04 Sep 2018 10:36:18: 10000000 INFO @ Tue, 04 Sep 2018 10:36:19: 10000000 INFO @ Tue, 04 Sep 2018 10:36:25: 11000000 INFO @ Tue, 04 Sep 2018 10:36:27: 11000000 INFO @ Tue, 04 Sep 2018 10:36:28: 11000000 INFO @ Tue, 04 Sep 2018 10:36:33: 12000000 INFO @ Tue, 04 Sep 2018 10:36:35: 12000000 INFO @ Tue, 04 Sep 2018 10:36:37: 12000000 INFO @ Tue, 04 Sep 2018 10:36:41: 13000000 INFO @ Tue, 04 Sep 2018 10:36:44: 13000000 INFO @ Tue, 04 Sep 2018 10:36:46: 13000000 INFO @ Tue, 04 Sep 2018 10:36:50: 14000000 INFO @ Tue, 04 Sep 2018 10:36:53: 14000000 INFO @ Tue, 04 Sep 2018 10:36:55: 14000000 INFO @ Tue, 04 Sep 2018 10:36:59: 15000000 INFO @ Tue, 04 Sep 2018 10:37:02: 15000000 INFO @ Tue, 04 Sep 2018 10:37:04: 15000000 INFO @ Tue, 04 Sep 2018 10:37:08: 16000000 INFO @ Tue, 04 Sep 2018 10:37:11: 16000000 INFO @ Tue, 04 Sep 2018 10:37:13: 16000000 INFO @ Tue, 04 Sep 2018 10:37:18: 17000000 INFO @ Tue, 04 Sep 2018 10:37:20: 17000000 INFO @ Tue, 04 Sep 2018 10:37:23: 17000000 INFO @ Tue, 04 Sep 2018 10:37:27: 18000000 INFO @ Tue, 04 Sep 2018 10:37:29: 18000000 INFO @ Tue, 04 Sep 2018 10:37:32: 18000000 INFO @ Tue, 04 Sep 2018 10:37:36: 19000000 INFO @ Tue, 04 Sep 2018 10:37:38: 19000000 INFO @ Tue, 04 Sep 2018 10:37:41: 19000000 INFO @ Tue, 04 Sep 2018 10:37:44: 20000000 INFO @ Tue, 04 Sep 2018 10:37:47: 20000000 INFO @ Tue, 04 Sep 2018 10:37:50: 20000000 INFO @ Tue, 04 Sep 2018 10:37:52: 21000000 INFO @ Tue, 04 Sep 2018 10:37:55: 21000000 INFO @ Tue, 04 Sep 2018 10:37:59: 21000000 INFO @ Tue, 04 Sep 2018 10:38:01: 22000000 INFO @ Tue, 04 Sep 2018 10:38:04: 22000000 INFO @ Tue, 04 Sep 2018 10:38:08: 22000000 INFO @ Tue, 04 Sep 2018 10:38:09: 23000000 INFO @ Tue, 04 Sep 2018 10:38:13: 23000000 INFO @ Tue, 04 Sep 2018 10:38:17: 23000000 INFO @ Tue, 04 Sep 2018 10:38:17: 24000000 INFO @ Tue, 04 Sep 2018 10:38:21: 24000000 INFO @ Tue, 04 Sep 2018 10:38:25: 24000000 INFO @ Tue, 04 Sep 2018 10:38:26: 25000000 INFO @ Tue, 04 Sep 2018 10:38:30: 25000000 INFO @ Tue, 04 Sep 2018 10:38:34: 25000000 INFO @ Tue, 04 Sep 2018 10:38:35: 26000000 INFO @ Tue, 04 Sep 2018 10:38:39: 26000000 INFO @ Tue, 04 Sep 2018 10:38:42: 26000000 INFO @ Tue, 04 Sep 2018 10:38:43: 27000000 INFO @ Tue, 04 Sep 2018 10:38:47: 27000000 INFO @ Tue, 04 Sep 2018 10:38:50: 27000000 INFO @ Tue, 04 Sep 2018 10:38:52: 28000000 INFO @ Tue, 04 Sep 2018 10:38:55: 28000000 INFO @ Tue, 04 Sep 2018 10:38:59: 28000000 INFO @ Tue, 04 Sep 2018 10:39:00: 29000000 INFO @ Tue, 04 Sep 2018 10:39:03: 29000000 INFO @ Tue, 04 Sep 2018 10:39:07: 29000000 INFO @ Tue, 04 Sep 2018 10:39:08: 30000000 INFO @ Tue, 04 Sep 2018 10:39:12: 30000000 INFO @ Tue, 04 Sep 2018 10:39:15: 30000000 INFO @ Tue, 04 Sep 2018 10:39:17: 31000000 INFO @ Tue, 04 Sep 2018 10:39:20: 31000000 INFO @ Tue, 04 Sep 2018 10:39:23: 31000000 INFO @ Tue, 04 Sep 2018 10:39:25: 32000000 INFO @ Tue, 04 Sep 2018 10:39:28: 32000000 INFO @ Tue, 04 Sep 2018 10:39:31: 32000000 INFO @ Tue, 04 Sep 2018 10:39:34: 33000000 INFO @ Tue, 04 Sep 2018 10:39:36: 33000000 INFO @ Tue, 04 Sep 2018 10:39:40: 33000000 INFO @ Tue, 04 Sep 2018 10:39:42: 34000000 INFO @ Tue, 04 Sep 2018 10:39:44: 34000000 INFO @ Tue, 04 Sep 2018 10:39:48: 34000000 INFO @ Tue, 04 Sep 2018 10:39:51: 35000000 INFO @ Tue, 04 Sep 2018 10:39:53: 35000000 INFO @ Tue, 04 Sep 2018 10:39:55: 35000000 INFO @ Tue, 04 Sep 2018 10:39:59: 36000000 INFO @ Tue, 04 Sep 2018 10:40:02: 36000000 INFO @ Tue, 04 Sep 2018 10:40:04: 36000000 INFO @ Tue, 04 Sep 2018 10:40:07: 37000000 INFO @ Tue, 04 Sep 2018 10:40:11: 37000000 INFO @ Tue, 04 Sep 2018 10:40:11: 37000000 INFO @ Tue, 04 Sep 2018 10:40:15: 38000000 INFO @ Tue, 04 Sep 2018 10:40:19: 38000000 INFO @ Tue, 04 Sep 2018 10:40:20: 38000000 INFO @ Tue, 04 Sep 2018 10:40:24: 39000000 INFO @ Tue, 04 Sep 2018 10:40:27: 39000000 INFO @ Tue, 04 Sep 2018 10:40:28: 39000000 INFO @ Tue, 04 Sep 2018 10:40:33: 40000000 INFO @ Tue, 04 Sep 2018 10:40:35: 40000000 INFO @ Tue, 04 Sep 2018 10:40:37: 40000000 INFO @ Tue, 04 Sep 2018 10:40:42: 41000000 INFO @ Tue, 04 Sep 2018 10:40:43: 41000000 INFO @ Tue, 04 Sep 2018 10:40:45: 41000000 INFO @ Tue, 04 Sep 2018 10:40:50: 42000000 INFO @ Tue, 04 Sep 2018 10:40:51: 42000000 INFO @ Tue, 04 Sep 2018 10:40:54: 42000000 INFO @ Tue, 04 Sep 2018 10:40:59: 43000000 INFO @ Tue, 04 Sep 2018 10:40:59: 43000000 INFO @ Tue, 04 Sep 2018 10:41:03: 43000000 INFO @ Tue, 04 Sep 2018 10:41:06: 44000000 INFO @ Tue, 04 Sep 2018 10:41:08: 44000000 INFO @ Tue, 04 Sep 2018 10:41:12: 44000000 INFO @ Tue, 04 Sep 2018 10:41:14: 45000000 INFO @ Tue, 04 Sep 2018 10:41:16: 45000000 INFO @ Tue, 04 Sep 2018 10:41:20: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:41:20: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:41:20: #1 total tags in treatment: 18548047 INFO @ Tue, 04 Sep 2018 10:41:20: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:41:20: #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 10:41:20: #1 tags after filtering in treatment: 8400710 INFO @ Tue, 04 Sep 2018 10:41:20: #1 Redundant rate of treatment: 0.55 INFO @ Tue, 04 Sep 2018 10:41:20: #1 finished! INFO @ Tue, 04 Sep 2018 10:41:20: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:41:21: 45000000 INFO @ Tue, 04 Sep 2018 10:41:21: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:41:21: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:41:21: #1 total tags in treatment: 18548047 INFO @ Tue, 04 Sep 2018 10:41:21: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:41:21: #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 10:41:21: #2 number of paired peaks: 5036 INFO @ Tue, 04 Sep 2018 10:41:21: start model_add_line... INFO @ Tue, 04 Sep 2018 10:41:21: start X-correlation... INFO @ Tue, 04 Sep 2018 10:41:21: #1 tags after filtering in treatment: 8400710 INFO @ Tue, 04 Sep 2018 10:41:21: #1 Redundant rate of treatment: 0.55 INFO @ Tue, 04 Sep 2018 10:41:21: #1 finished! INFO @ Tue, 04 Sep 2018 10:41:21: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:41:22: end of X-cor INFO @ Tue, 04 Sep 2018 10:41:22: #2 finished! INFO @ Tue, 04 Sep 2018 10:41:22: #2 predicted fragment length is 366 bps INFO @ Tue, 04 Sep 2018 10:41:22: #2 alternative fragment length(s) may be 366 bps INFO @ Tue, 04 Sep 2018 10:41:22: #2.2 Generate R script for model : SRX4012476.20_model.r INFO @ Tue, 04 Sep 2018 10:41:22: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:41:23: #2 number of paired peaks: 5036 INFO @ Tue, 04 Sep 2018 10:41:23: start model_add_line... INFO @ Tue, 04 Sep 2018 10:41:23: start X-correlation... INFO @ Tue, 04 Sep 2018 10:41:23: end of X-cor INFO @ Tue, 04 Sep 2018 10:41:23: #2 finished! INFO @ Tue, 04 Sep 2018 10:41:23: #2 predicted fragment length is 366 bps INFO @ Tue, 04 Sep 2018 10:41:23: #2 alternative fragment length(s) may be 366 bps INFO @ Tue, 04 Sep 2018 10:41:23: #2.2 Generate R script for model : SRX4012476.10_model.r INFO @ Tue, 04 Sep 2018 10:41:23: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:41:25: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:41:25: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:41:25: #1 total tags in treatment: 18548047 INFO @ Tue, 04 Sep 2018 10:41:25: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:41:25: #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 10:41:26: #1 tags after filtering in treatment: 8400710 INFO @ Tue, 04 Sep 2018 10:41:26: #1 Redundant rate of treatment: 0.55 INFO @ Tue, 04 Sep 2018 10:41:26: #1 finished! INFO @ Tue, 04 Sep 2018 10:41:26: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:41:27: #2 number of paired peaks: 5036 INFO @ Tue, 04 Sep 2018 10:41:27: start model_add_line... INFO @ Tue, 04 Sep 2018 10:41:27: start X-correlation... INFO @ Tue, 04 Sep 2018 10:41:27: end of X-cor INFO @ Tue, 04 Sep 2018 10:41:27: #2 finished! INFO @ Tue, 04 Sep 2018 10:41:27: #2 predicted fragment length is 366 bps INFO @ Tue, 04 Sep 2018 10:41:27: #2 alternative fragment length(s) may be 366 bps INFO @ Tue, 04 Sep 2018 10:41:27: #2.2 Generate R script for model : SRX4012476.05_model.r INFO @ Tue, 04 Sep 2018 10:41:27: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:42:15: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:42:19: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:42:27: #4 Write output xls file... SRX4012476.20_peaks.xls INFO @ Tue, 04 Sep 2018 10:42:27: #4 Write peak in narrowPeak format file... SRX4012476.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:42:27: #4 Write summits bed file... SRX4012476.20_summits.bed INFO @ Tue, 04 Sep 2018 10:42:27: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3893 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:42:29: #4 Write output xls file... SRX4012476.10_peaks.xls INFO @ Tue, 04 Sep 2018 10:42:29: #4 Write peak in narrowPeak format file... SRX4012476.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:42:29: #4 Write summits bed file... SRX4012476.10_summits.bed INFO @ Tue, 04 Sep 2018 10:42:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4934 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:42:32: #4 Write output xls file... SRX4012476.05_peaks.xls INFO @ Tue, 04 Sep 2018 10:42:33: #4 Write peak in narrowPeak format file... SRX4012476.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:42:33: #4 Write summits bed file... SRX4012476.05_summits.bed INFO @ Tue, 04 Sep 2018 10:42:33: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (6189 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。