Job ID = 9161727 sra ファイルのダウンロード中... Completed: 2506960K bytes transferred in 25 seconds (821447K bits/sec), in 1 file, 2 directories. 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... Written 17277257 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1004421/SRR1986239.sra Written 17277257 spots total 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: 00:20:32 17277257 reads; of these: 17277257 (100.00%) were paired; of these: 8123730 (47.02%) aligned concordantly 0 times 8349258 (48.33%) aligned concordantly exactly 1 time 804269 (4.66%) aligned concordantly >1 times ---- 8123730 pairs aligned concordantly 0 times; of these: 2250912 (27.71%) aligned discordantly 1 time ---- 5872818 pairs aligned 0 times concordantly or discordantly; of these: 11745636 mates make up the pairs; of these: 10726770 (91.33%) aligned 0 times 533431 (4.54%) aligned exactly 1 time 485435 (4.13%) aligned >1 times 68.96% overall alignment rate Time searching: 00:20:32 Overall time: 00:20:32 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 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 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] 1122674 / 11293538 = 0.0994 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, 28 Jun 2017 04:59:14: # Command line: callpeak -t SRX1004421.bam -f BAM -g 12100000 -n SRX1004421.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1004421.20 # format = BAM # ChIP-seq file = ['SRX1004421.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, 28 Jun 2017 04:59:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:59:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:59:14: # Command line: callpeak -t SRX1004421.bam -f BAM -g 12100000 -n SRX1004421.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1004421.05 # format = BAM # ChIP-seq file = ['SRX1004421.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, 28 Jun 2017 04:59:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:59:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:59:14: # Command line: callpeak -t SRX1004421.bam -f BAM -g 12100000 -n SRX1004421.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1004421.10 # format = BAM # ChIP-seq file = ['SRX1004421.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, 28 Jun 2017 04:59:14: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:59:14: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:59:21: 1000000 INFO @ Wed, 28 Jun 2017 04:59:22: 1000000 INFO @ Wed, 28 Jun 2017 04:59:22: 1000000 INFO @ Wed, 28 Jun 2017 04:59:29: 2000000 INFO @ Wed, 28 Jun 2017 04:59:29: 2000000 INFO @ Wed, 28 Jun 2017 04:59:29: 2000000 INFO @ Wed, 28 Jun 2017 04:59:36: 3000000 INFO @ Wed, 28 Jun 2017 04:59:36: 3000000 INFO @ Wed, 28 Jun 2017 04:59:37: 3000000 INFO @ Wed, 28 Jun 2017 04:59:43: 4000000 INFO @ Wed, 28 Jun 2017 04:59:43: 4000000 INFO @ Wed, 28 Jun 2017 04:59:44: 4000000 INFO @ Wed, 28 Jun 2017 04:59:50: 5000000 INFO @ Wed, 28 Jun 2017 04:59:51: 5000000 INFO @ Wed, 28 Jun 2017 04:59:51: 5000000 INFO @ Wed, 28 Jun 2017 04:59:57: 6000000 INFO @ Wed, 28 Jun 2017 04:59:58: 6000000 INFO @ Wed, 28 Jun 2017 04:59:59: 6000000 INFO @ Wed, 28 Jun 2017 05:00:05: 7000000 INFO @ Wed, 28 Jun 2017 05:00:05: 7000000 INFO @ Wed, 28 Jun 2017 05:00:06: 7000000 INFO @ Wed, 28 Jun 2017 05:00:12: 8000000 INFO @ Wed, 28 Jun 2017 05:00:12: 8000000 INFO @ Wed, 28 Jun 2017 05:00:14: 8000000 INFO @ Wed, 28 Jun 2017 05:00:19: 9000000 INFO @ Wed, 28 Jun 2017 05:00:19: 9000000 INFO @ Wed, 28 Jun 2017 05:00:21: 9000000 INFO @ Wed, 28 Jun 2017 05:00:26: 10000000 INFO @ Wed, 28 Jun 2017 05:00:27: 10000000 INFO @ Wed, 28 Jun 2017 05:00:29: 10000000 INFO @ Wed, 28 Jun 2017 05:00:34: 11000000 INFO @ Wed, 28 Jun 2017 05:00:34: 11000000 INFO @ Wed, 28 Jun 2017 05:00:36: 11000000 INFO @ Wed, 28 Jun 2017 05:00:41: 12000000 INFO @ Wed, 28 Jun 2017 05:00:41: 12000000 INFO @ Wed, 28 Jun 2017 05:00:44: 12000000 INFO @ Wed, 28 Jun 2017 05:00:48: 13000000 INFO @ Wed, 28 Jun 2017 05:00:49: 13000000 INFO @ Wed, 28 Jun 2017 05:00:52: 13000000 INFO @ Wed, 28 Jun 2017 05:00:56: 14000000 INFO @ Wed, 28 Jun 2017 05:00:56: 14000000 INFO @ Wed, 28 Jun 2017 05:01:00: 14000000 INFO @ Wed, 28 Jun 2017 05:01:03: 15000000 INFO @ Wed, 28 Jun 2017 05:01:04: 15000000 INFO @ Wed, 28 Jun 2017 05:01:07: 15000000 INFO @ Wed, 28 Jun 2017 05:01:10: 16000000 INFO @ Wed, 28 Jun 2017 05:01:11: 16000000 INFO @ Wed, 28 Jun 2017 05:01:15: 16000000 INFO @ Wed, 28 Jun 2017 05:01:18: 17000000 INFO @ Wed, 28 Jun 2017 05:01:18: 17000000 INFO @ Wed, 28 Jun 2017 05:01:23: 17000000 INFO @ Wed, 28 Jun 2017 05:01:26: 18000000 INFO @ Wed, 28 Jun 2017 05:01:27: 18000000 INFO @ Wed, 28 Jun 2017 05:01:32: 18000000 INFO @ Wed, 28 Jun 2017 05:01:36: 19000000 INFO @ Wed, 28 Jun 2017 05:01:36: 19000000 INFO @ Wed, 28 Jun 2017 05:01:41: 19000000 INFO @ Wed, 28 Jun 2017 05:01:45: 20000000 INFO @ Wed, 28 Jun 2017 05:01:45: 20000000 INFO @ Wed, 28 Jun 2017 05:01:50: 20000000 INFO @ Wed, 28 Jun 2017 05:01:54: 21000000 INFO @ Wed, 28 Jun 2017 05:01:55: 21000000 INFO @ Wed, 28 Jun 2017 05:01:59: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 05:01:59: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 05:01:59: #1 total tags in treatment: 8223886 INFO @ Wed, 28 Jun 2017 05:01:59: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:01:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:01:59: 21000000 INFO @ Wed, 28 Jun 2017 05:02:00: #1 tags after filtering in treatment: 4980770 INFO @ Wed, 28 Jun 2017 05:02:00: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 28 Jun 2017 05:02:00: #1 finished! INFO @ Wed, 28 Jun 2017 05:02:00: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:02:00: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:02:00: 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, 28 Jun 2017 05:02:00: Process for pairing-model is terminated! cat: SRX1004421.20_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 `SRX1004421.20_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 `SRX1004421.20_*.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 `SRX1004421.20_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 INFO @ Wed, 28 Jun 2017 05:02:00: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 05:02:00: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 05:02:00: #1 total tags in treatment: 8223886 INFO @ Wed, 28 Jun 2017 05:02:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:02:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:02:00: #1 tags after filtering in treatment: 4980770 INFO @ Wed, 28 Jun 2017 05:02:00: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 28 Jun 2017 05:02:00: #1 finished! INFO @ Wed, 28 Jun 2017 05:02:00: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:02:01: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:02:01: 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, 28 Jun 2017 05:02:01: Process for pairing-model is terminated! cat: SRX1004421.05_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 `SRX1004421.05_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 `SRX1004421.05_*.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 `SRX1004421.05_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, 28 Jun 2017 05:02:04: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 05:02:04: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 05:02:04: #1 total tags in treatment: 8223886 INFO @ Wed, 28 Jun 2017 05:02:04: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:02:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:02:05: #1 tags after filtering in treatment: 4980770 INFO @ Wed, 28 Jun 2017 05:02:05: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 28 Jun 2017 05:02:05: #1 finished! INFO @ Wed, 28 Jun 2017 05:02:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:02:05: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:02:05: 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, 28 Jun 2017 05:02:05: Process for pairing-model is terminated! cat: SRX1004421.10_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 `SRX1004421.10_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 `SRX1004421.10_*.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 `SRX1004421.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。