Job ID = 11192765 sra ファイルのダウンロード中... Completed: 44822K bytes transferred in 3 seconds (97125K 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 1468695 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924880/SRR3824911.sra Written 1468695 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924880/SRR3824911.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: 00:00:59 1468695 reads; of these: 1468695 (100.00%) were paired; of these: 469475 (31.97%) aligned concordantly 0 times 931607 (63.43%) aligned concordantly exactly 1 time 67613 (4.60%) aligned concordantly >1 times ---- 469475 pairs aligned concordantly 0 times; of these: 104945 (22.35%) aligned discordantly 1 time ---- 364530 pairs aligned 0 times concordantly or discordantly; of these: 729060 mates make up the pairs; of these: 374764 (51.40%) aligned 0 times 316045 (43.35%) aligned exactly 1 time 38251 (5.25%) aligned >1 times 87.24% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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_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] 265457 / 1044902 = 0.2540 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 @ Sat, 15 Sep 2018 09:54:17: # Command line: callpeak -t SRX1924880.bam -f BAM -g 12100000 -n SRX1924880.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924880.10 # format = BAM # ChIP-seq file = ['SRX1924880.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 @ Sat, 15 Sep 2018 09:54:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:54:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:54:17: # Command line: callpeak -t SRX1924880.bam -f BAM -g 12100000 -n SRX1924880.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924880.20 # format = BAM # ChIP-seq file = ['SRX1924880.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 @ Sat, 15 Sep 2018 09:54:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:54:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:54:17: # Command line: callpeak -t SRX1924880.bam -f BAM -g 12100000 -n SRX1924880.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924880.05 # format = BAM # ChIP-seq file = ['SRX1924880.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 @ Sat, 15 Sep 2018 09:54:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:54:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:54:23: 1000000 INFO @ Sat, 15 Sep 2018 09:54:23: 1000000 INFO @ Sat, 15 Sep 2018 09:54:23: 1000000 INFO @ Sat, 15 Sep 2018 09:54:30: 2000000 INFO @ Sat, 15 Sep 2018 09:54:30: 2000000 INFO @ Sat, 15 Sep 2018 09:54:30: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:54:30: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:54:30: #1 total tags in treatment: 742075 INFO @ Sat, 15 Sep 2018 09:54:30: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:54:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:54:30: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:54:30: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:54:30: #1 total tags in treatment: 742075 INFO @ Sat, 15 Sep 2018 09:54:30: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:54:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:54:30: #1 tags after filtering in treatment: 677343 INFO @ Sat, 15 Sep 2018 09:54:30: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Sep 2018 09:54:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:54:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:54:30: #1 tags after filtering in treatment: 677343 INFO @ Sat, 15 Sep 2018 09:54:30: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Sep 2018 09:54:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:54:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:54:30: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 09:54:30: 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 @ Sat, 15 Sep 2018 09:54:30: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 09:54:30: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 09:54:30: 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 @ Sat, 15 Sep 2018 09:54:30: Process for pairing-model is terminated! cat: SRX1924880.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sat, 15 Sep 2018 09:54:30: 2000000 cat: SRX1924880.20_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) pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX1924880.05_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 `SRX1924880.05_*.xls': そのようなファイルやディレクトリはありません rm: needLargeMem: trying to allocate 0 bytes (limit: 17179869184)cannot remove `SRX1924880.05_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 rm: cannot remove `SRX1924880.20_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 `SRX1924880.20_*.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 `SRX1924880.20_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 @ Sat, 15 Sep 2018 09:54:30: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:54:30: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:54:30: #1 total tags in treatment: 742075 INFO @ Sat, 15 Sep 2018 09:54:30: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:54:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:54:30: #1 tags after filtering in treatment: 677343 INFO @ Sat, 15 Sep 2018 09:54:30: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Sep 2018 09:54:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:54:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:54:30: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 09:54:30: 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 @ Sat, 15 Sep 2018 09:54:30: Process for pairing-model is terminated! cat: SRX1924880.10_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 `SRX1924880.10_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 `SRX1924880.10_*.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 `SRX1924880.10_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。