Job ID = 11245149 sra ファイルのダウンロード中... Completed: 26887K bytes transferred in 3 seconds (70997K bits/sec), in 1 file. Completed: 211249K bytes transferred in 5 seconds (311241K 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 574876 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669598/SRR7818176.sra Written 574876 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669598/SRR7818176.sra Read 5668457 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669598/SRR7818177.sra Written 5668457 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669598/SRR7818177.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: 00:05:01 6243333 reads; of these: 6243333 (100.00%) were paired; of these: 522717 (8.37%) aligned concordantly 0 times 4964311 (79.51%) aligned concordantly exactly 1 time 756305 (12.11%) aligned concordantly >1 times ---- 522717 pairs aligned concordantly 0 times; of these: 20196 (3.86%) aligned discordantly 1 time ---- 502521 pairs aligned 0 times concordantly or discordantly; of these: 1005042 mates make up the pairs; of these: 837286 (83.31%) aligned 0 times 93465 (9.30%) aligned exactly 1 time 74291 (7.39%) aligned >1 times 93.29% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 1094475 / 5735985 = 0.1908 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 23:43:08: # Command line: callpeak -t SRX4669598.bam -f BAM -g 12100000 -n SRX4669598.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669598.10 # format = BAM # ChIP-seq file = ['SRX4669598.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 23:43:08: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:43:08: # Command line: callpeak -t SRX4669598.bam -f BAM -g 12100000 -n SRX4669598.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669598.05 # format = BAM # ChIP-seq file = ['SRX4669598.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 23:43:08: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:43:08: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:43:08: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:43:08: # Command line: callpeak -t SRX4669598.bam -f BAM -g 12100000 -n SRX4669598.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669598.20 # format = BAM # ChIP-seq file = ['SRX4669598.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 23:43:08: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:43:08: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:43:14: 1000000 INFO @ Tue, 09 Oct 2018 23:43:14: 1000000 INFO @ Tue, 09 Oct 2018 23:43:14: 1000000 INFO @ Tue, 09 Oct 2018 23:43:20: 2000000 INFO @ Tue, 09 Oct 2018 23:43:20: 2000000 INFO @ Tue, 09 Oct 2018 23:43:20: 2000000 INFO @ Tue, 09 Oct 2018 23:43:26: 3000000 INFO @ Tue, 09 Oct 2018 23:43:26: 3000000 INFO @ Tue, 09 Oct 2018 23:43:27: 3000000 INFO @ Tue, 09 Oct 2018 23:43:32: 4000000 INFO @ Tue, 09 Oct 2018 23:43:33: 4000000 INFO @ Tue, 09 Oct 2018 23:43:34: 4000000 INFO @ Tue, 09 Oct 2018 23:43:39: 5000000 INFO @ Tue, 09 Oct 2018 23:43:40: 5000000 INFO @ Tue, 09 Oct 2018 23:43:40: 5000000 INFO @ Tue, 09 Oct 2018 23:43:45: 6000000 INFO @ Tue, 09 Oct 2018 23:43:46: 6000000 INFO @ Tue, 09 Oct 2018 23:43:47: 6000000 INFO @ Tue, 09 Oct 2018 23:43:51: 7000000 INFO @ Tue, 09 Oct 2018 23:43:53: 7000000 INFO @ Tue, 09 Oct 2018 23:43:54: 7000000 INFO @ Tue, 09 Oct 2018 23:43:58: 8000000 INFO @ Tue, 09 Oct 2018 23:44:00: 8000000 INFO @ Tue, 09 Oct 2018 23:44:01: 8000000 INFO @ Tue, 09 Oct 2018 23:44:04: 9000000 INFO @ Tue, 09 Oct 2018 23:44:06: 9000000 INFO @ Tue, 09 Oct 2018 23:44:07: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:44:07: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:44:07: #1 total tags in treatment: 4629674 INFO @ Tue, 09 Oct 2018 23:44:07: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:44:07: #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 23:44:08: #1 tags after filtering in treatment: 3789514 INFO @ Tue, 09 Oct 2018 23:44:08: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:44:08: #1 finished! INFO @ Tue, 09 Oct 2018 23:44:08: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:44:08: #2 number of paired peaks: 35 WARNING @ Tue, 09 Oct 2018 23:44:08: Too few paired peaks (35) 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 23:44:08: Process for pairing-model is terminated! cat: SRX4669598.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Tue, 09 Oct 2018 23:44:08: 9000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669598.10_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 `SRX4669598.10_*.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 `SRX4669598.10_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 @ Tue, 09 Oct 2018 23:44:09: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:44:09: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:44:09: #1 total tags in treatment: 4629674 INFO @ Tue, 09 Oct 2018 23:44:09: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:44:09: #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 23:44:09: #1 tags after filtering in treatment: 3789514 INFO @ Tue, 09 Oct 2018 23:44:09: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:44:09: #1 finished! INFO @ Tue, 09 Oct 2018 23:44:09: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:44:10: #2 number of paired peaks: 35 WARNING @ Tue, 09 Oct 2018 23:44:10: Too few paired peaks (35) 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 23:44:10: Process for pairing-model is terminated! cat: SRX4669598.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669598.20_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 `SRX4669598.20_*.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 `SRX4669598.20_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 23:44:11: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:44:11: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:44:11: #1 total tags in treatment: 4629674 INFO @ Tue, 09 Oct 2018 23:44:11: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:44:11: #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 23:44:11: #1 tags after filtering in treatment: 3789514 INFO @ Tue, 09 Oct 2018 23:44:11: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:44:11: #1 finished! INFO @ Tue, 09 Oct 2018 23:44:11: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:44:11: #2 number of paired peaks: 35 WARNING @ Tue, 09 Oct 2018 23:44:11: Too few paired peaks (35) 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 23:44:11: Process for pairing-model is terminated! cat: SRX4669598.05_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 `SRX4669598.05_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 `SRX4669598.05_*.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 `SRX4669598.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。