Job ID = 11193142 sra ファイルのダウンロード中... Completed: 665414K bytes transferred in 12 seconds (422581K 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 20082528 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337734/SRR7467869.sra Written 20082528 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337734/SRR7467869.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: 00:03:57 20082528 reads; of these: 20082528 (100.00%) were paired; of these: 18986506 (94.54%) aligned concordantly 0 times 958027 (4.77%) aligned concordantly exactly 1 time 137995 (0.69%) aligned concordantly >1 times ---- 18986506 pairs aligned concordantly 0 times; of these: 835970 (4.40%) aligned discordantly 1 time ---- 18150536 pairs aligned 0 times concordantly or discordantly; of these: 36301072 mates make up the pairs; of these: 34646209 (95.44%) aligned 0 times 1316465 (3.63%) aligned exactly 1 time 338398 (0.93%) aligned >1 times 13.74% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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_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] 536267 / 1845536 = 0.2906 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 11:07:23: # Command line: callpeak -t SRX4337734.bam -f BAM -g 12100000 -n SRX4337734.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337734.05 # format = BAM # ChIP-seq file = ['SRX4337734.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 11:07:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:23: # Command line: callpeak -t SRX4337734.bam -f BAM -g 12100000 -n SRX4337734.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337734.20 # format = BAM # ChIP-seq file = ['SRX4337734.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 11:07:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:23: # Command line: callpeak -t SRX4337734.bam -f BAM -g 12100000 -n SRX4337734.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337734.10 # format = BAM # ChIP-seq file = ['SRX4337734.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 11:07:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:28: 1000000 INFO @ Sat, 15 Sep 2018 11:07:28: 1000000 INFO @ Sat, 15 Sep 2018 11:07:28: 1000000 INFO @ Sat, 15 Sep 2018 11:07:32: 2000000 INFO @ Sat, 15 Sep 2018 11:07:32: 2000000 INFO @ Sat, 15 Sep 2018 11:07:33: 2000000 INFO @ Sat, 15 Sep 2018 11:07:37: 3000000 INFO @ Sat, 15 Sep 2018 11:07:37: 3000000 INFO @ Sat, 15 Sep 2018 11:07:37: 3000000 INFO @ Sat, 15 Sep 2018 11:07:41: 4000000 INFO @ Sat, 15 Sep 2018 11:07:42: 4000000 INFO @ Sat, 15 Sep 2018 11:07:42: 4000000 INFO @ Sat, 15 Sep 2018 11:07:43: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:07:43: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:07:43: #1 total tags in treatment: 807714 INFO @ Sat, 15 Sep 2018 11:07:43: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:43: #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 11:07:43: #1 tags after filtering in treatment: 703991 INFO @ Sat, 15 Sep 2018 11:07:43: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 11:07:43: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:43: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:43: #2 number of paired peaks: 49 WARNING @ Sat, 15 Sep 2018 11:07:43: Too few paired peaks (49) 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 11:07:43: Process for pairing-model is terminated! cat: SRX4337734.05_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 `SRX4337734.05_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 `SRX4337734.05_*.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 `SRX4337734.05_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 @ Sat, 15 Sep 2018 11:07:44: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:07:44: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:07:44: #1 total tags in treatment: 807714 INFO @ Sat, 15 Sep 2018 11:07:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:44: #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 11:07:44: #1 tags after filtering in treatment: 703991 INFO @ Sat, 15 Sep 2018 11:07:44: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 11:07:44: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:44: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:44: #2 number of paired peaks: 49 WARNING @ Sat, 15 Sep 2018 11:07:44: Too few paired peaks (49) 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 11:07:44: Process for pairing-model is terminated! cat: SRX4337734.20_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 `SRX4337734.20_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 `SRX4337734.20_*.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 `SRX4337734.20_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 11:07:44: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:07:44: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:07:44: #1 total tags in treatment: 807714 INFO @ Sat, 15 Sep 2018 11:07:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:44: #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 11:07:44: #1 tags after filtering in treatment: 703991 INFO @ Sat, 15 Sep 2018 11:07:44: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 11:07:44: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:44: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:44: #2 number of paired peaks: 49 WARNING @ Sat, 15 Sep 2018 11:07:44: Too few paired peaks (49) 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 11:07:44: Process for pairing-model is terminated! cat: SRX4337734.10_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 `SRX4337734.10_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 `SRX4337734.10_*.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 `SRX4337734.10_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。