Job ID = 11245210 sra ファイルのダウンロード中... Completed: 404750K bytes transferred in 7 seconds (430313K bits/sec), in 1 file. Completed: 351117K bytes transferred in 7 seconds (404439K 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 3430449 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669661/SRR7818293.sra Written 3430449 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669661/SRR7818293.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669661/SRR7818292.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669661/SRR7818292.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 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: 00:05:49 7430449 reads; of these: 7430449 (100.00%) were paired; of these: 2089897 (28.13%) aligned concordantly 0 times 4675420 (62.92%) aligned concordantly exactly 1 time 665132 (8.95%) aligned concordantly >1 times ---- 2089897 pairs aligned concordantly 0 times; of these: 44566 (2.13%) aligned discordantly 1 time ---- 2045331 pairs aligned 0 times concordantly or discordantly; of these: 4090662 mates make up the pairs; of these: 3767188 (92.09%) aligned 0 times 257579 (6.30%) aligned exactly 1 time 65895 (1.61%) aligned >1 times 74.65% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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 8 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] 62176 / 5372950 = 0.0116 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 00:00:03: # Command line: callpeak -t SRX4669661.bam -f BAM -g 12100000 -n SRX4669661.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669661.20 # format = BAM # ChIP-seq file = ['SRX4669661.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 00:00:03: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:00:03: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:00:03: # Command line: callpeak -t SRX4669661.bam -f BAM -g 12100000 -n SRX4669661.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669661.05 # format = BAM # ChIP-seq file = ['SRX4669661.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 00:00:03: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:00:03: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:00:03: # Command line: callpeak -t SRX4669661.bam -f BAM -g 12100000 -n SRX4669661.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669661.10 # format = BAM # ChIP-seq file = ['SRX4669661.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 00:00:03: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:00:03: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:00:09: 1000000 INFO @ Wed, 10 Oct 2018 00:00:09: 1000000 INFO @ Wed, 10 Oct 2018 00:00:10: 1000000 INFO @ Wed, 10 Oct 2018 00:00:16: 2000000 INFO @ Wed, 10 Oct 2018 00:00:16: 2000000 INFO @ Wed, 10 Oct 2018 00:00:16: 2000000 INFO @ Wed, 10 Oct 2018 00:00:22: 3000000 INFO @ Wed, 10 Oct 2018 00:00:22: 3000000 INFO @ Wed, 10 Oct 2018 00:00:22: 3000000 INFO @ Wed, 10 Oct 2018 00:00:29: 4000000 INFO @ Wed, 10 Oct 2018 00:00:29: 4000000 INFO @ Wed, 10 Oct 2018 00:00:29: 4000000 INFO @ Wed, 10 Oct 2018 00:00:35: 5000000 INFO @ Wed, 10 Oct 2018 00:00:35: 5000000 INFO @ Wed, 10 Oct 2018 00:00:36: 5000000 INFO @ Wed, 10 Oct 2018 00:00:42: 6000000 INFO @ Wed, 10 Oct 2018 00:00:42: 6000000 INFO @ Wed, 10 Oct 2018 00:00:42: 6000000 INFO @ Wed, 10 Oct 2018 00:00:48: 7000000 INFO @ Wed, 10 Oct 2018 00:00:48: 7000000 INFO @ Wed, 10 Oct 2018 00:00:49: 7000000 INFO @ Wed, 10 Oct 2018 00:00:54: 8000000 INFO @ Wed, 10 Oct 2018 00:00:55: 8000000 INFO @ Wed, 10 Oct 2018 00:00:56: 8000000 INFO @ Wed, 10 Oct 2018 00:01:01: 9000000 INFO @ Wed, 10 Oct 2018 00:01:01: 9000000 INFO @ Wed, 10 Oct 2018 00:01:02: 9000000 INFO @ Wed, 10 Oct 2018 00:01:07: 10000000 INFO @ Wed, 10 Oct 2018 00:01:08: 10000000 INFO @ Wed, 10 Oct 2018 00:01:09: 10000000 INFO @ Wed, 10 Oct 2018 00:01:13: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:01:13: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:01:13: #1 total tags in treatment: 5278583 INFO @ Wed, 10 Oct 2018 00:01:13: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:01:13: #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 00:01:13: #1 tags after filtering in treatment: 4319868 INFO @ Wed, 10 Oct 2018 00:01:13: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 10 Oct 2018 00:01:13: #1 finished! INFO @ Wed, 10 Oct 2018 00:01:13: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:01:14: #2 number of paired peaks: 36 WARNING @ Wed, 10 Oct 2018 00:01:14: Too few paired peaks (36) 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 00:01:14: Process for pairing-model is terminated! cat: SRX4669661.10_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 `SRX4669661.10_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 `SRX4669661.10_*.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 `SRX4669661.10_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 00:01:14: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:01:14: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:01:14: #1 total tags in treatment: 5278583 INFO @ Wed, 10 Oct 2018 00:01:14: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:01:14: #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 00:01:14: #1 tags after filtering in treatment: 4319868 INFO @ Wed, 10 Oct 2018 00:01:14: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 10 Oct 2018 00:01:14: #1 finished! INFO @ Wed, 10 Oct 2018 00:01:14: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:01:14: #2 number of paired peaks: 36 WARNING @ Wed, 10 Oct 2018 00:01:14: Too few paired peaks (36) 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 00:01:14: Process for pairing-model is terminated! cat: SRX4669661.05_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 `SRX4669661.05_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 `SRX4669661.05_*.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 `SRX4669661.05_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 00:01:15: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:01:15: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:01:15: #1 total tags in treatment: 5278583 INFO @ Wed, 10 Oct 2018 00:01:15: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:01:15: #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 00:01:15: #1 tags after filtering in treatment: 4319868 INFO @ Wed, 10 Oct 2018 00:01:15: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 10 Oct 2018 00:01:15: #1 finished! INFO @ Wed, 10 Oct 2018 00:01:15: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:01:15: #2 number of paired peaks: 36 WARNING @ Wed, 10 Oct 2018 00:01:15: Too few paired peaks (36) 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 00:01:15: Process for pairing-model is terminated! cat: SRX4669661.20_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 `SRX4669661.20_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 `SRX4669661.20_*.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 `SRX4669661.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。