Job ID = 11245215 sra ファイルのダウンロード中... Completed: 412062K bytes transferred in 7 seconds (481221K bits/sec), in 1 file. Completed: 412536K bytes transferred in 7 seconds (458923K bits/sec), in 1 file. Completed: 415426K bytes transferred in 6 seconds (486719K bits/sec), in 1 file. Completed: 85540K bytes transferred in 3 seconds (177900K 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 800994 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818308.sra Written 800994 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818308.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818307.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818307.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818306.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818306.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818305.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669665/SRR7818305.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: 00:11:33 12800994 reads; of these: 12800994 (100.00%) were paired; of these: 1993137 (15.57%) aligned concordantly 0 times 9522355 (74.39%) aligned concordantly exactly 1 time 1285502 (10.04%) aligned concordantly >1 times ---- 1993137 pairs aligned concordantly 0 times; of these: 161661 (8.11%) aligned discordantly 1 time ---- 1831476 pairs aligned 0 times concordantly or discordantly; of these: 3662952 mates make up the pairs; of these: 3154142 (86.11%) aligned 0 times 373249 (10.19%) aligned exactly 1 time 135561 (3.70%) aligned >1 times 87.68% overall alignment rate Time searching: 00:11:33 Overall time: 00:11:33 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] 180248 / 10937300 = 0.0165 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 00:11:16: # Command line: callpeak -t SRX4669665.bam -f BAM -g 12100000 -n SRX4669665.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669665.10 # format = BAM # ChIP-seq file = ['SRX4669665.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 00:11:16: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:11:16: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:11:16: # Command line: callpeak -t SRX4669665.bam -f BAM -g 12100000 -n SRX4669665.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669665.05 # format = BAM # ChIP-seq file = ['SRX4669665.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 00:11:16: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:11:16: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:11:16: # Command line: callpeak -t SRX4669665.bam -f BAM -g 12100000 -n SRX4669665.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669665.20 # format = BAM # ChIP-seq file = ['SRX4669665.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 00:11:16: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:11:16: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:11:24: 1000000 INFO @ Wed, 10 Oct 2018 00:11:24: 1000000 INFO @ Wed, 10 Oct 2018 00:11:24: 1000000 INFO @ Wed, 10 Oct 2018 00:11:31: 2000000 INFO @ Wed, 10 Oct 2018 00:11:31: 2000000 INFO @ Wed, 10 Oct 2018 00:11:31: 2000000 INFO @ Wed, 10 Oct 2018 00:11:38: 3000000 INFO @ Wed, 10 Oct 2018 00:11:38: 3000000 INFO @ Wed, 10 Oct 2018 00:11:38: 3000000 INFO @ Wed, 10 Oct 2018 00:11:45: 4000000 INFO @ Wed, 10 Oct 2018 00:11:46: 4000000 INFO @ Wed, 10 Oct 2018 00:11:46: 4000000 INFO @ Wed, 10 Oct 2018 00:11:53: 5000000 INFO @ Wed, 10 Oct 2018 00:11:53: 5000000 INFO @ Wed, 10 Oct 2018 00:11:53: 5000000 INFO @ Wed, 10 Oct 2018 00:12:00: 6000000 INFO @ Wed, 10 Oct 2018 00:12:00: 6000000 INFO @ Wed, 10 Oct 2018 00:12:00: 6000000 INFO @ Wed, 10 Oct 2018 00:12:07: 7000000 INFO @ Wed, 10 Oct 2018 00:12:07: 7000000 INFO @ Wed, 10 Oct 2018 00:12:07: 7000000 INFO @ Wed, 10 Oct 2018 00:12:15: 8000000 INFO @ Wed, 10 Oct 2018 00:12:15: 8000000 INFO @ Wed, 10 Oct 2018 00:12:15: 8000000 INFO @ Wed, 10 Oct 2018 00:12:22: 9000000 INFO @ Wed, 10 Oct 2018 00:12:22: 9000000 INFO @ Wed, 10 Oct 2018 00:12:22: 9000000 INFO @ Wed, 10 Oct 2018 00:12:29: 10000000 INFO @ Wed, 10 Oct 2018 00:12:29: 10000000 INFO @ Wed, 10 Oct 2018 00:12:29: 10000000 INFO @ Wed, 10 Oct 2018 00:12:36: 11000000 INFO @ Wed, 10 Oct 2018 00:12:36: 11000000 INFO @ Wed, 10 Oct 2018 00:12:36: 11000000 INFO @ Wed, 10 Oct 2018 00:12:43: 12000000 INFO @ Wed, 10 Oct 2018 00:12:44: 12000000 INFO @ Wed, 10 Oct 2018 00:12:44: 12000000 INFO @ Wed, 10 Oct 2018 00:12:50: 13000000 INFO @ Wed, 10 Oct 2018 00:12:51: 13000000 INFO @ Wed, 10 Oct 2018 00:12:52: 13000000 INFO @ Wed, 10 Oct 2018 00:12:57: 14000000 INFO @ Wed, 10 Oct 2018 00:12:58: 14000000 INFO @ Wed, 10 Oct 2018 00:12:59: 14000000 INFO @ Wed, 10 Oct 2018 00:13:04: 15000000 INFO @ Wed, 10 Oct 2018 00:13:06: 15000000 INFO @ Wed, 10 Oct 2018 00:13:07: 15000000 INFO @ Wed, 10 Oct 2018 00:13:11: 16000000 INFO @ Wed, 10 Oct 2018 00:13:13: 16000000 INFO @ Wed, 10 Oct 2018 00:13:15: 16000000 INFO @ Wed, 10 Oct 2018 00:13:18: 17000000 INFO @ Wed, 10 Oct 2018 00:13:21: 17000000 INFO @ Wed, 10 Oct 2018 00:13:22: 17000000 INFO @ Wed, 10 Oct 2018 00:13:25: 18000000 INFO @ Wed, 10 Oct 2018 00:13:28: 18000000 INFO @ Wed, 10 Oct 2018 00:13:30: 18000000 INFO @ Wed, 10 Oct 2018 00:13:32: 19000000 INFO @ Wed, 10 Oct 2018 00:13:36: 19000000 INFO @ Wed, 10 Oct 2018 00:13:38: 19000000 INFO @ Wed, 10 Oct 2018 00:13:39: 20000000 INFO @ Wed, 10 Oct 2018 00:13:44: 20000000 INFO @ Wed, 10 Oct 2018 00:13:46: 20000000 INFO @ Wed, 10 Oct 2018 00:13:46: 21000000 INFO @ Wed, 10 Oct 2018 00:13:51: 21000000 INFO @ Wed, 10 Oct 2018 00:13:53: 22000000 INFO @ Wed, 10 Oct 2018 00:13:53: 21000000 INFO @ Wed, 10 Oct 2018 00:13:53: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:53: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:53: #1 total tags in treatment: 10628752 INFO @ Wed, 10 Oct 2018 00:13:53: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:53: #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 00:13:54: #1 tags after filtering in treatment: 7955344 INFO @ Wed, 10 Oct 2018 00:13:54: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:54: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:54: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:54: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:54: 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, 10 Oct 2018 00:13:54: Process for pairing-model is terminated! cat: SRX4669665.10_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 `SRX4669665.10_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 `SRX4669665.10_*.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 `SRX4669665.10_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 00:13:59: 22000000 INFO @ Wed, 10 Oct 2018 00:13:59: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:59: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:59: #1 total tags in treatment: 10628752 INFO @ Wed, 10 Oct 2018 00:13:59: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:59: #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 00:14:00: #1 tags after filtering in treatment: 7955344 INFO @ Wed, 10 Oct 2018 00:14:00: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:14:00: #1 finished! INFO @ Wed, 10 Oct 2018 00:14:00: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:14:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:14:00: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:14:00: 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, 10 Oct 2018 00:14:00: Process for pairing-model is terminated! cat: SRX4669665.05_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 `SRX4669665.05_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 `SRX4669665.05_*.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 `SRX4669665.05_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 00:14:01: 22000000 INFO @ Wed, 10 Oct 2018 00:14:01: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:14:01: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:14:01: #1 total tags in treatment: 10628752 INFO @ Wed, 10 Oct 2018 00:14:01: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:14:01: #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 00:14:01: #1 tags after filtering in treatment: 7955344 INFO @ Wed, 10 Oct 2018 00:14:01: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:14:01: #1 finished! INFO @ Wed, 10 Oct 2018 00:14:01: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:14:02: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:14:02: 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, 10 Oct 2018 00:14:02: Process for pairing-model is terminated! cat: SRX4669665.20_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 `SRX4669665.20_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 `SRX4669665.20_*.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 `SRX4669665.20_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。