Job ID = 2007714 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:21:05 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 2,202 reads read : 4,404 reads written : 4,404 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR467434.sra.cache’: No such file or directory 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: 00:00:01 2202 reads; of these: 2202 (100.00%) were paired; of these: 403 (18.30%) aligned concordantly 0 times 1642 (74.57%) aligned concordantly exactly 1 time 157 (7.13%) aligned concordantly >1 times ---- 403 pairs aligned concordantly 0 times; of these: 40 (9.93%) aligned discordantly 1 time ---- 363 pairs aligned 0 times concordantly or discordantly; of these: 726 mates make up the pairs; of these: 682 (93.94%) aligned 0 times 28 (3.86%) aligned exactly 1 time 16 (2.20%) aligned >1 times 84.51% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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_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] 3 / 1837 = 0.0016 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.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 @ Fri, 05 Jul 2019 16:22:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:27: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:27: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:27: #1 total tags in treatment: 1796 INFO @ Fri, 05 Jul 2019 16:22:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:22:27: #1 tags after filtering in treatment: 1796 INFO @ Fri, 05 Jul 2019 16:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:27: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:27: #2 number of paired peaks: 42 WARNING @ Fri, 05 Jul 2019 16:22:27: Too few paired peaks (42) 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 @ Fri, 05 Jul 2019 16:22:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.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 @ Fri, 05 Jul 2019 16:22:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:28: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:28: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:28: #1 total tags in treatment: 1796 INFO @ Fri, 05 Jul 2019 16:22:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:22:28: #1 tags after filtering in treatment: 1796 INFO @ Fri, 05 Jul 2019 16:22:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:28: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:28: #2 number of paired peaks: 42 WARNING @ Fri, 05 Jul 2019 16:22:28: Too few paired peaks (42) 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 @ Fri, 05 Jul 2019 16:22:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.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 @ Fri, 05 Jul 2019 16:22:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:29: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:29: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:29: #1 total tags in treatment: 1796 INFO @ Fri, 05 Jul 2019 16:22:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:22:29: #1 tags after filtering in treatment: 1796 INFO @ Fri, 05 Jul 2019 16:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:29: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:29: #2 number of paired peaks: 42 WARNING @ Fri, 05 Jul 2019 16:22:29: Too few paired peaks (42) 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 @ Fri, 05 Jul 2019 16:22:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433669/ERX433669.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling