Job ID = 11245132 sra ファイルのダウンロード中... Completed: 1332846K bytes transferred in 18 seconds (595149K 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 26676792 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669584/SRR7818158.sra Written 26676792 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669584/SRR7818158.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: 00:17:57 26676792 reads; of these: 26676792 (100.00%) were paired; of these: 4540628 (17.02%) aligned concordantly 0 times 19203141 (71.98%) aligned concordantly exactly 1 time 2933023 (10.99%) aligned concordantly >1 times ---- 4540628 pairs aligned concordantly 0 times; of these: 67859 (1.49%) aligned discordantly 1 time ---- 4472769 pairs aligned 0 times concordantly or discordantly; of these: 8945538 mates make up the pairs; of these: 8315060 (92.95%) aligned 0 times 425059 (4.75%) aligned exactly 1 time 205419 (2.30%) aligned >1 times 84.42% overall alignment rate Time searching: 00:17:57 Overall time: 00:17:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 3319722 / 22194903 = 0.1496 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 @ Wed, 10 Oct 2018 00:01:53: # Command line: callpeak -t SRX4669584.bam -f BAM -g 12100000 -n SRX4669584.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669584.10 # format = BAM # ChIP-seq file = ['SRX4669584.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 10 Oct 2018 00:01:53: # Command line: callpeak -t SRX4669584.bam -f BAM -g 12100000 -n SRX4669584.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669584.20 # format = BAM # ChIP-seq file = ['SRX4669584.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 10 Oct 2018 00:01:53: # Command line: callpeak -t SRX4669584.bam -f BAM -g 12100000 -n SRX4669584.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669584.05 # format = BAM # ChIP-seq file = ['SRX4669584.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 10 Oct 2018 00:01:53: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:53: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:53: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:53: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:53: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:53: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:02:00: 1000000 INFO @ Wed, 10 Oct 2018 00:02:00: 1000000 INFO @ Wed, 10 Oct 2018 00:02:00: 1000000 INFO @ Wed, 10 Oct 2018 00:02:07: 2000000 INFO @ Wed, 10 Oct 2018 00:02:08: 2000000 INFO @ Wed, 10 Oct 2018 00:02:08: 2000000 INFO @ Wed, 10 Oct 2018 00:02:14: 3000000 INFO @ Wed, 10 Oct 2018 00:02:15: 3000000 INFO @ Wed, 10 Oct 2018 00:02:15: 3000000 INFO @ Wed, 10 Oct 2018 00:02:21: 4000000 INFO @ Wed, 10 Oct 2018 00:02:22: 4000000 INFO @ Wed, 10 Oct 2018 00:02:22: 4000000 INFO @ Wed, 10 Oct 2018 00:02:28: 5000000 INFO @ Wed, 10 Oct 2018 00:02:29: 5000000 INFO @ Wed, 10 Oct 2018 00:02:29: 5000000 INFO @ Wed, 10 Oct 2018 00:02:35: 6000000 INFO @ Wed, 10 Oct 2018 00:02:36: 6000000 INFO @ Wed, 10 Oct 2018 00:02:36: 6000000 INFO @ Wed, 10 Oct 2018 00:02:42: 7000000 INFO @ Wed, 10 Oct 2018 00:02:43: 7000000 INFO @ Wed, 10 Oct 2018 00:02:43: 7000000 INFO @ Wed, 10 Oct 2018 00:02:49: 8000000 INFO @ Wed, 10 Oct 2018 00:02:50: 8000000 INFO @ Wed, 10 Oct 2018 00:02:50: 8000000 INFO @ Wed, 10 Oct 2018 00:02:56: 9000000 INFO @ Wed, 10 Oct 2018 00:02:57: 9000000 INFO @ Wed, 10 Oct 2018 00:02:57: 9000000 INFO @ Wed, 10 Oct 2018 00:03:03: 10000000 INFO @ Wed, 10 Oct 2018 00:03:04: 10000000 INFO @ Wed, 10 Oct 2018 00:03:04: 10000000 INFO @ Wed, 10 Oct 2018 00:03:10: 11000000 INFO @ Wed, 10 Oct 2018 00:03:11: 11000000 INFO @ Wed, 10 Oct 2018 00:03:11: 11000000 INFO @ Wed, 10 Oct 2018 00:03:17: 12000000 INFO @ Wed, 10 Oct 2018 00:03:18: 12000000 INFO @ Wed, 10 Oct 2018 00:03:18: 12000000 INFO @ Wed, 10 Oct 2018 00:03:24: 13000000 INFO @ Wed, 10 Oct 2018 00:03:25: 13000000 INFO @ Wed, 10 Oct 2018 00:03:25: 13000000 INFO @ Wed, 10 Oct 2018 00:03:31: 14000000 INFO @ Wed, 10 Oct 2018 00:03:32: 14000000 INFO @ Wed, 10 Oct 2018 00:03:32: 14000000 INFO @ Wed, 10 Oct 2018 00:03:38: 15000000 INFO @ Wed, 10 Oct 2018 00:03:39: 15000000 INFO @ Wed, 10 Oct 2018 00:03:39: 15000000 INFO @ Wed, 10 Oct 2018 00:03:45: 16000000 INFO @ Wed, 10 Oct 2018 00:03:46: 16000000 INFO @ Wed, 10 Oct 2018 00:03:46: 16000000 INFO @ Wed, 10 Oct 2018 00:03:52: 17000000 INFO @ Wed, 10 Oct 2018 00:03:53: 17000000 INFO @ Wed, 10 Oct 2018 00:03:53: 17000000 INFO @ Wed, 10 Oct 2018 00:03:59: 18000000 INFO @ Wed, 10 Oct 2018 00:04:00: 18000000 INFO @ Wed, 10 Oct 2018 00:04:00: 18000000 INFO @ Wed, 10 Oct 2018 00:04:06: 19000000 INFO @ Wed, 10 Oct 2018 00:04:07: 19000000 INFO @ Wed, 10 Oct 2018 00:04:07: 19000000 INFO @ Wed, 10 Oct 2018 00:04:13: 20000000 INFO @ Wed, 10 Oct 2018 00:04:14: 20000000 INFO @ Wed, 10 Oct 2018 00:04:14: 20000000 INFO @ Wed, 10 Oct 2018 00:04:20: 21000000 INFO @ Wed, 10 Oct 2018 00:04:21: 21000000 INFO @ Wed, 10 Oct 2018 00:04:21: 21000000 INFO @ Wed, 10 Oct 2018 00:04:27: 22000000 INFO @ Wed, 10 Oct 2018 00:04:28: 22000000 INFO @ Wed, 10 Oct 2018 00:04:28: 22000000 INFO @ Wed, 10 Oct 2018 00:04:34: 23000000 INFO @ Wed, 10 Oct 2018 00:04:35: 23000000 INFO @ Wed, 10 Oct 2018 00:04:35: 23000000 INFO @ Wed, 10 Oct 2018 00:04:42: 24000000 INFO @ Wed, 10 Oct 2018 00:04:42: 24000000 INFO @ Wed, 10 Oct 2018 00:04:42: 24000000 INFO @ Wed, 10 Oct 2018 00:04:49: 25000000 INFO @ Wed, 10 Oct 2018 00:04:49: 25000000 INFO @ Wed, 10 Oct 2018 00:04:49: 25000000 INFO @ Wed, 10 Oct 2018 00:04:56: 26000000 INFO @ Wed, 10 Oct 2018 00:04:56: 26000000 INFO @ Wed, 10 Oct 2018 00:04:57: 26000000 INFO @ Wed, 10 Oct 2018 00:05:03: 27000000 INFO @ Wed, 10 Oct 2018 00:05:03: 27000000 INFO @ Wed, 10 Oct 2018 00:05:05: 27000000 INFO @ Wed, 10 Oct 2018 00:05:11: 28000000 INFO @ Wed, 10 Oct 2018 00:05:11: 28000000 INFO @ Wed, 10 Oct 2018 00:05:13: 28000000 INFO @ Wed, 10 Oct 2018 00:05:18: 29000000 INFO @ Wed, 10 Oct 2018 00:05:18: 29000000 INFO @ Wed, 10 Oct 2018 00:05:21: 29000000 INFO @ Wed, 10 Oct 2018 00:05:25: 30000000 INFO @ Wed, 10 Oct 2018 00:05:25: 30000000 INFO @ Wed, 10 Oct 2018 00:05:29: 30000000 INFO @ Wed, 10 Oct 2018 00:05:32: 31000000 INFO @ Wed, 10 Oct 2018 00:05:32: 31000000 INFO @ Wed, 10 Oct 2018 00:05:37: 31000000 INFO @ Wed, 10 Oct 2018 00:05:40: 32000000 INFO @ Wed, 10 Oct 2018 00:05:40: 32000000 INFO @ Wed, 10 Oct 2018 00:05:45: 32000000 INFO @ Wed, 10 Oct 2018 00:05:47: 33000000 INFO @ Wed, 10 Oct 2018 00:05:47: 33000000 INFO @ Wed, 10 Oct 2018 00:05:53: 33000000 INFO @ Wed, 10 Oct 2018 00:05:54: 34000000 INFO @ Wed, 10 Oct 2018 00:05:54: 34000000 INFO @ Wed, 10 Oct 2018 00:06:01: 34000000 INFO @ Wed, 10 Oct 2018 00:06:01: 35000000 INFO @ Wed, 10 Oct 2018 00:06:01: 35000000 INFO @ Wed, 10 Oct 2018 00:06:09: 35000000 INFO @ Wed, 10 Oct 2018 00:06:09: 36000000 INFO @ Wed, 10 Oct 2018 00:06:09: 36000000 INFO @ Wed, 10 Oct 2018 00:06:16: 37000000 INFO @ Wed, 10 Oct 2018 00:06:16: 37000000 INFO @ Wed, 10 Oct 2018 00:06:17: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 10 Oct 2018 00:06:23: 38000000 INFO @ Wed, 10 Oct 2018 00:06:23: 38000000 INFO @ Wed, 10 Oct 2018 00:06:25: 37000000 INFO @ Wed, 10 Oct 2018 00:06:26: #1 tag size is determined as 50 bps INFO @ Wed, 10 Oct 2018 00:06:26: #1 tag size is determined as 50 bps INFO @ Wed, 10 Oct 2018 00:06:26: #1 tag size = 50 INFO @ Wed, 10 Oct 2018 00:06:26: #1 tag size = 50 INFO @ Wed, 10 Oct 2018 00:06:26: #1 total tags in treatment: 18822605 INFO @ Wed, 10 Oct 2018 00:06:26: #1 total tags in treatment: 18822605 INFO @ Wed, 10 Oct 2018 00:06:26: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:26: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:06:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:06:27: #1 tags after filtering in treatment: 11804574 INFO @ Wed, 10 Oct 2018 00:06:27: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 10 Oct 2018 00:06:27: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:27: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:27: #1 tags after filtering in treatment: 11804574 INFO @ Wed, 10 Oct 2018 00:06:27: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 10 Oct 2018 00:06:27: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:27: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:27: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:27: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 10 Oct 2018 00:06:27: Process for pairing-model is terminated! cat: SRX4669584.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669584.10_model.r': 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 `SRX4669584.10_*.xls': 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 `SRX4669584.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:06:27: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:27: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 10 Oct 2018 00:06:27: Process for pairing-model is terminated! cat: SRX4669584.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669584.05_model.r': 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 `SRX4669584.05_*.xls': 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 `SRX4669584.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:06:31: 38000000 INFO @ Wed, 10 Oct 2018 00:06:34: #1 tag size is determined as 50 bps INFO @ Wed, 10 Oct 2018 00:06:34: #1 tag size = 50 INFO @ Wed, 10 Oct 2018 00:06:34: #1 total tags in treatment: 18822605 INFO @ Wed, 10 Oct 2018 00:06:34: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:06:34: #1 tags after filtering in treatment: 11804574 INFO @ Wed, 10 Oct 2018 00:06:34: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 10 Oct 2018 00:06:34: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:34: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:35: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:35: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 10 Oct 2018 00:06:35: Process for pairing-model is terminated! cat: SRX4669584.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669584.20_model.r': 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 `SRX4669584.20_*.xls': 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 `SRX4669584.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BigWig に変換しました。