Job ID = 11245211 sra ファイルのダウンロード中... Completed: 411089K bytes transferred in 7 seconds (459904K bits/sec), in 1 file. Completed: 411388K bytes transferred in 7 seconds (462455K bits/sec), in 1 file. Completed: 414116K bytes transferred in 7 seconds (468974K bits/sec), in 1 file. Completed: 65559K bytes transferred in 3 seconds (137901K 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 612700 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818297.sra Written 612700 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818297.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818295.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818295.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818296.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818296.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818294.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669662/SRR7818294.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: 00:11:39 12612700 reads; of these: 12612700 (100.00%) were paired; of these: 2272140 (18.01%) aligned concordantly 0 times 9074298 (71.95%) aligned concordantly exactly 1 time 1266262 (10.04%) aligned concordantly >1 times ---- 2272140 pairs aligned concordantly 0 times; of these: 134277 (5.91%) aligned discordantly 1 time ---- 2137863 pairs aligned 0 times concordantly or discordantly; of these: 4275726 mates make up the pairs; of these: 3719490 (86.99%) aligned 0 times 425338 (9.95%) aligned exactly 1 time 130898 (3.06%) aligned >1 times 85.25% overall alignment rate Time searching: 00:11:39 Overall time: 00:11:39 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] 191652 / 10443798 = 0.0184 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 00:10:31: # Command line: callpeak -t SRX4669662.bam -f BAM -g 12100000 -n SRX4669662.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669662.05 # format = BAM # ChIP-seq file = ['SRX4669662.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 00:10:31: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:10:31: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:10:31: # Command line: callpeak -t SRX4669662.bam -f BAM -g 12100000 -n SRX4669662.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669662.10 # format = BAM # ChIP-seq file = ['SRX4669662.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 00:10:31: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:10:31: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:10:31: # Command line: callpeak -t SRX4669662.bam -f BAM -g 12100000 -n SRX4669662.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669662.20 # format = BAM # ChIP-seq file = ['SRX4669662.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 00:10:31: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:10:31: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:10:39: 1000000 INFO @ Wed, 10 Oct 2018 00:10:39: 1000000 INFO @ Wed, 10 Oct 2018 00:10:39: 1000000 INFO @ Wed, 10 Oct 2018 00:10:47: 2000000 INFO @ Wed, 10 Oct 2018 00:10:47: 2000000 INFO @ Wed, 10 Oct 2018 00:10:47: 2000000 INFO @ Wed, 10 Oct 2018 00:10:55: 3000000 INFO @ Wed, 10 Oct 2018 00:10:55: 3000000 INFO @ Wed, 10 Oct 2018 00:10:55: 3000000 INFO @ Wed, 10 Oct 2018 00:11:03: 4000000 INFO @ Wed, 10 Oct 2018 00:11:03: 4000000 INFO @ Wed, 10 Oct 2018 00:11:03: 4000000 INFO @ Wed, 10 Oct 2018 00:11:11: 5000000 INFO @ Wed, 10 Oct 2018 00:11:11: 5000000 INFO @ Wed, 10 Oct 2018 00:11:11: 5000000 INFO @ Wed, 10 Oct 2018 00:11:19: 6000000 INFO @ Wed, 10 Oct 2018 00:11:19: 6000000 INFO @ Wed, 10 Oct 2018 00:11:19: 6000000 INFO @ Wed, 10 Oct 2018 00:11:27: 7000000 INFO @ Wed, 10 Oct 2018 00:11:27: 7000000 INFO @ Wed, 10 Oct 2018 00:11:27: 7000000 INFO @ Wed, 10 Oct 2018 00:11:35: 8000000 INFO @ Wed, 10 Oct 2018 00:11:35: 8000000 INFO @ Wed, 10 Oct 2018 00:11:35: 8000000 INFO @ Wed, 10 Oct 2018 00:11:43: 9000000 INFO @ Wed, 10 Oct 2018 00:11:43: 9000000 INFO @ Wed, 10 Oct 2018 00:11:43: 9000000 INFO @ Wed, 10 Oct 2018 00:11:51: 10000000 INFO @ Wed, 10 Oct 2018 00:11:51: 10000000 INFO @ Wed, 10 Oct 2018 00:11:51: 10000000 INFO @ Wed, 10 Oct 2018 00:11:59: 11000000 INFO @ Wed, 10 Oct 2018 00:11:59: 11000000 INFO @ Wed, 10 Oct 2018 00:11:59: 11000000 INFO @ Wed, 10 Oct 2018 00:12:06: 12000000 INFO @ Wed, 10 Oct 2018 00:12:06: 12000000 INFO @ Wed, 10 Oct 2018 00:12:06: 12000000 INFO @ Wed, 10 Oct 2018 00:12:14: 13000000 INFO @ Wed, 10 Oct 2018 00:12:14: 13000000 INFO @ Wed, 10 Oct 2018 00:12:14: 13000000 INFO @ Wed, 10 Oct 2018 00:12:22: 14000000 INFO @ Wed, 10 Oct 2018 00:12:22: 14000000 INFO @ Wed, 10 Oct 2018 00:12:22: 14000000 INFO @ Wed, 10 Oct 2018 00:12:30: 15000000 INFO @ Wed, 10 Oct 2018 00:12:30: 15000000 INFO @ Wed, 10 Oct 2018 00:12:30: 15000000 INFO @ Wed, 10 Oct 2018 00:12:38: 16000000 INFO @ Wed, 10 Oct 2018 00:12:38: 16000000 INFO @ Wed, 10 Oct 2018 00:12:38: 16000000 INFO @ Wed, 10 Oct 2018 00:12:46: 17000000 INFO @ Wed, 10 Oct 2018 00:12:46: 17000000 INFO @ Wed, 10 Oct 2018 00:12:46: 17000000 INFO @ Wed, 10 Oct 2018 00:12:54: 18000000 INFO @ Wed, 10 Oct 2018 00:12:54: 18000000 INFO @ Wed, 10 Oct 2018 00:12:54: 18000000 INFO @ Wed, 10 Oct 2018 00:13:02: 19000000 INFO @ Wed, 10 Oct 2018 00:13:02: 19000000 INFO @ Wed, 10 Oct 2018 00:13:02: 19000000 INFO @ Wed, 10 Oct 2018 00:13:10: 20000000 INFO @ Wed, 10 Oct 2018 00:13:10: 20000000 INFO @ Wed, 10 Oct 2018 00:13:10: 20000000 INFO @ Wed, 10 Oct 2018 00:13:18: 21000000 INFO @ Wed, 10 Oct 2018 00:13:18: 21000000 INFO @ Wed, 10 Oct 2018 00:13:18: 21000000 INFO @ Wed, 10 Oct 2018 00:13:19: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:19: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:19: #1 total tags in treatment: 10149927 INFO @ Wed, 10 Oct 2018 00:13:19: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:19: #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 00:13:19: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:19: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:19: #1 total tags in treatment: 10149927 INFO @ Wed, 10 Oct 2018 00:13:19: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:19: #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 00:13:19: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:19: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:19: #1 total tags in treatment: 10149927 INFO @ Wed, 10 Oct 2018 00:13:19: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:19: #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 00:13:19: #1 tags after filtering in treatment: 7609243 INFO @ Wed, 10 Oct 2018 00:13:19: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:19: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:19: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:19: #1 tags after filtering in treatment: 7609243 INFO @ Wed, 10 Oct 2018 00:13:19: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:19: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:19: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:19: #1 tags after filtering in treatment: 7609243 INFO @ Wed, 10 Oct 2018 00:13:19: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:19: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:19: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:19: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:19: 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 00:13:19: Process for pairing-model is terminated! INFO @ Wed, 10 Oct 2018 00:13:19: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:19: 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 00:13:19: Process for pairing-model is terminated! cat: SRX4669662.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4669662.20_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 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669662.10_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 `SRX4669662.10_*.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 `SRX4669662.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669662.20_model.r': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `SRX4669662.20_*.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 `SRX4669662.20_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 @ Wed, 10 Oct 2018 00:13:19: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:19: 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 00:13:19: Process for pairing-model is terminated! cat: SRX4669662.05_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 `SRX4669662.05_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 `SRX4669662.05_*.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 `SRX4669662.05_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。