Job ID = 11245123 sra ファイルのダウンロード中... Completed: 318561K bytes transferred in 7 seconds (353155K 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 6482925 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669579/SRR7818153.sra Written 6482925 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669579/SRR7818153.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: 00:04:30 6482925 reads; of these: 6482925 (100.00%) were paired; of these: 578351 (8.92%) aligned concordantly 0 times 5136010 (79.22%) aligned concordantly exactly 1 time 768564 (11.86%) aligned concordantly >1 times ---- 578351 pairs aligned concordantly 0 times; of these: 12640 (2.19%) aligned discordantly 1 time ---- 565711 pairs aligned 0 times concordantly or discordantly; of these: 1131422 mates make up the pairs; of these: 984051 (86.97%) aligned 0 times 96834 (8.56%) aligned exactly 1 time 50537 (4.47%) aligned >1 times 92.41% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 116721 / 5909400 = 0.0198 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 @ Tue, 09 Oct 2018 23:36:45: # Command line: callpeak -t SRX4669579.bam -f BAM -g 12100000 -n SRX4669579.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669579.05 # format = BAM # ChIP-seq file = ['SRX4669579.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 @ Tue, 09 Oct 2018 23:36:45: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:36:45: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:36:45: # Command line: callpeak -t SRX4669579.bam -f BAM -g 12100000 -n SRX4669579.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669579.20 # format = BAM # ChIP-seq file = ['SRX4669579.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 @ Tue, 09 Oct 2018 23:36:45: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:36:45: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:36:45: # Command line: callpeak -t SRX4669579.bam -f BAM -g 12100000 -n SRX4669579.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669579.10 # format = BAM # ChIP-seq file = ['SRX4669579.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 @ Tue, 09 Oct 2018 23:36:45: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:36:45: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:36:51: 1000000 INFO @ Tue, 09 Oct 2018 23:36:51: 1000000 INFO @ Tue, 09 Oct 2018 23:36:51: 1000000 INFO @ Tue, 09 Oct 2018 23:36:56: 2000000 INFO @ Tue, 09 Oct 2018 23:36:56: 2000000 INFO @ Tue, 09 Oct 2018 23:36:57: 2000000 INFO @ Tue, 09 Oct 2018 23:37:02: 3000000 INFO @ Tue, 09 Oct 2018 23:37:02: 3000000 INFO @ Tue, 09 Oct 2018 23:37:02: 3000000 INFO @ Tue, 09 Oct 2018 23:37:08: 4000000 INFO @ Tue, 09 Oct 2018 23:37:08: 4000000 INFO @ Tue, 09 Oct 2018 23:37:08: 4000000 INFO @ Tue, 09 Oct 2018 23:37:14: 5000000 INFO @ Tue, 09 Oct 2018 23:37:14: 5000000 INFO @ Tue, 09 Oct 2018 23:37:14: 5000000 INFO @ Tue, 09 Oct 2018 23:37:19: 6000000 INFO @ Tue, 09 Oct 2018 23:37:20: 6000000 INFO @ Tue, 09 Oct 2018 23:37:20: 6000000 INFO @ Tue, 09 Oct 2018 23:37:25: 7000000 INFO @ Tue, 09 Oct 2018 23:37:26: 7000000 INFO @ Tue, 09 Oct 2018 23:37:26: 7000000 INFO @ Tue, 09 Oct 2018 23:37:31: 8000000 INFO @ Tue, 09 Oct 2018 23:37:32: 8000000 INFO @ Tue, 09 Oct 2018 23:37:32: 8000000 INFO @ Tue, 09 Oct 2018 23:37:36: 9000000 INFO @ Tue, 09 Oct 2018 23:37:38: 9000000 INFO @ Tue, 09 Oct 2018 23:37:39: 9000000 INFO @ Tue, 09 Oct 2018 23:37:42: 10000000 INFO @ Tue, 09 Oct 2018 23:37:43: 10000000 INFO @ Tue, 09 Oct 2018 23:37:45: 10000000 INFO @ Tue, 09 Oct 2018 23:37:48: 11000000 INFO @ Tue, 09 Oct 2018 23:37:49: 11000000 INFO @ Tue, 09 Oct 2018 23:37:51: 11000000 INFO @ Tue, 09 Oct 2018 23:37:52: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:37:52: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:37:52: #1 total tags in treatment: 5787939 INFO @ Tue, 09 Oct 2018 23:37:52: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:37:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:37:52: #1 tags after filtering in treatment: 4431056 INFO @ Tue, 09 Oct 2018 23:37:52: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 09 Oct 2018 23:37:52: #1 finished! INFO @ Tue, 09 Oct 2018 23:37:52: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:37:52: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:37:52: Too few paired peaks (31) 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 @ Tue, 09 Oct 2018 23:37:52: Process for pairing-model is terminated! cat: SRX4669579.20_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 `SRX4669579.20_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 `SRX4669579.20_*.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 `SRX4669579.20_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 @ Tue, 09 Oct 2018 23:37:54: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:37:54: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:37:54: #1 total tags in treatment: 5787939 INFO @ Tue, 09 Oct 2018 23:37:54: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:37:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:37:54: #1 tags after filtering in treatment: 4431056 INFO @ Tue, 09 Oct 2018 23:37:54: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 09 Oct 2018 23:37:54: #1 finished! INFO @ Tue, 09 Oct 2018 23:37:54: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:37:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:37:54: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:37:54: Too few paired peaks (31) 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 @ Tue, 09 Oct 2018 23:37:54: Process for pairing-model is terminated! cat: SRX4669579.05_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 `SRX4669579.05_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 `SRX4669579.05_*.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 `SRX4669579.05_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 @ Tue, 09 Oct 2018 23:37:55: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:37:55: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:37:55: #1 total tags in treatment: 5787939 INFO @ Tue, 09 Oct 2018 23:37:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:37:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:37:55: #1 tags after filtering in treatment: 4431056 INFO @ Tue, 09 Oct 2018 23:37:55: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 09 Oct 2018 23:37:55: #1 finished! INFO @ Tue, 09 Oct 2018 23:37:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:37:56: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:37:56: Too few paired peaks (31) 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 @ Tue, 09 Oct 2018 23:37:56: Process for pairing-model is terminated! cat: SRX4669579.10_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 `SRX4669579.10_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 `SRX4669579.10_*.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 `SRX4669579.10_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。