Job ID = 11245134 sra ファイルのダウンロード中... Completed: 552772K bytes transferred in 9 seconds (453665K 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 9702969 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669585/SRR7818159.sra Written 9702969 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669585/SRR7818159.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: 00:06:15 9702969 reads; of these: 9702969 (100.00%) were paired; of these: 2489076 (25.65%) aligned concordantly 0 times 6131308 (63.19%) aligned concordantly exactly 1 time 1082585 (11.16%) aligned concordantly >1 times ---- 2489076 pairs aligned concordantly 0 times; of these: 13238 (0.53%) aligned discordantly 1 time ---- 2475838 pairs aligned 0 times concordantly or discordantly; of these: 4951676 mates make up the pairs; of these: 4769983 (96.33%) aligned 0 times 95650 (1.93%) aligned exactly 1 time 86043 (1.74%) aligned >1 times 75.42% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 2789343 / 7224979 = 0.3861 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 23:41:00: # Command line: callpeak -t SRX4669585.bam -f BAM -g 12100000 -n SRX4669585.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669585.10 # format = BAM # ChIP-seq file = ['SRX4669585.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 23:41:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:41:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:41:00: # Command line: callpeak -t SRX4669585.bam -f BAM -g 12100000 -n SRX4669585.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669585.05 # format = BAM # ChIP-seq file = ['SRX4669585.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 23:41:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:41:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:41:00: # Command line: callpeak -t SRX4669585.bam -f BAM -g 12100000 -n SRX4669585.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669585.20 # format = BAM # ChIP-seq file = ['SRX4669585.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 23:41:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:41:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:41:07: 1000000 INFO @ Tue, 09 Oct 2018 23:41:07: 1000000 INFO @ Tue, 09 Oct 2018 23:41:08: 1000000 INFO @ Tue, 09 Oct 2018 23:41:14: 2000000 INFO @ Tue, 09 Oct 2018 23:41:14: 2000000 INFO @ Tue, 09 Oct 2018 23:41:15: 2000000 INFO @ Tue, 09 Oct 2018 23:41:20: 3000000 INFO @ Tue, 09 Oct 2018 23:41:20: 3000000 INFO @ Tue, 09 Oct 2018 23:41:22: 3000000 INFO @ Tue, 09 Oct 2018 23:41:27: 4000000 INFO @ Tue, 09 Oct 2018 23:41:27: 4000000 INFO @ Tue, 09 Oct 2018 23:41:29: 4000000 INFO @ Tue, 09 Oct 2018 23:41:34: 5000000 INFO @ Tue, 09 Oct 2018 23:41:34: 5000000 INFO @ Tue, 09 Oct 2018 23:41:37: 5000000 INFO @ Tue, 09 Oct 2018 23:41:41: 6000000 INFO @ Tue, 09 Oct 2018 23:41:41: 6000000 INFO @ Tue, 09 Oct 2018 23:41:44: 6000000 INFO @ Tue, 09 Oct 2018 23:41:48: 7000000 INFO @ Tue, 09 Oct 2018 23:41:48: 7000000 INFO @ Tue, 09 Oct 2018 23:41:51: 7000000 INFO @ Tue, 09 Oct 2018 23:41:54: 8000000 INFO @ Tue, 09 Oct 2018 23:41:54: 8000000 INFO @ Tue, 09 Oct 2018 23:41:58: 8000000 INFO @ Tue, 09 Oct 2018 23:42:01: 9000000 INFO @ Tue, 09 Oct 2018 23:42:01: 9000000 INFO @ Tue, 09 Oct 2018 23:42:01: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:42:01: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:42:01: #1 total tags in treatment: 4428151 INFO @ Tue, 09 Oct 2018 23:42:01: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:42:01: #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 23:42:01: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:42:01: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:42:01: #1 total tags in treatment: 4428151 INFO @ Tue, 09 Oct 2018 23:42:01: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:42:01: #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 23:42:01: #1 tags after filtering in treatment: 3485253 INFO @ Tue, 09 Oct 2018 23:42:01: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:42:01: #1 finished! INFO @ Tue, 09 Oct 2018 23:42:01: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:42:01: #1 tags after filtering in treatment: 3485253 INFO @ Tue, 09 Oct 2018 23:42:01: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:42:01: #1 finished! INFO @ Tue, 09 Oct 2018 23:42:01: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:42:02: #2 number of paired peaks: 38 WARNING @ Tue, 09 Oct 2018 23:42:02: Too few paired peaks (38) 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 23:42:02: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:42:02: #2 number of paired peaks: 38 WARNING @ Tue, 09 Oct 2018 23:42:02: Too few paired peaks (38) 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 23:42:02: Process for pairing-model is terminated! cat: SRX4669585.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4669585.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669585.20_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 `SRX4669585.20_*.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 `SRX4669585.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4669585.05_model.r'CompletedMACS2peakCalling : 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 `SRX4669585.05_*.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 `SRX4669585.05_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 23:42:05: 9000000 INFO @ Tue, 09 Oct 2018 23:42:06: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:42:06: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:42:06: #1 total tags in treatment: 4428151 INFO @ Tue, 09 Oct 2018 23:42:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:42:06: #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 23:42:06: #1 tags after filtering in treatment: 3485253 INFO @ Tue, 09 Oct 2018 23:42:06: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:42:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:42:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:42:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:42:06: #2 number of paired peaks: 38 WARNING @ Tue, 09 Oct 2018 23:42:06: Too few paired peaks (38) 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 23:42:06: Process for pairing-model is terminated! cat: SRX4669585.10_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 `SRX4669585.10_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 `SRX4669585.10_*.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 `SRX4669585.10_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。