Job ID = 2007955 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:51 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:51 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506391/ERR506391.1' 2019-07-05T07:40:51 fasterq-dump.2.9.6 err: invalid accession 'ERR506391' 2019-07-05T07:41:06 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:41:06 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506391/ERR506391.1' 2019-07-05T07:41:06 fasterq-dump.2.9.6 err: invalid accession 'ERR506391' 2019-07-05T07:41:21 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:41:21 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506391/ERR506391.1' 2019-07-05T07:41:21 fasterq-dump.2.9.6 err: invalid accession 'ERR506391' 2019-07-05T07:48:47 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 : 1,943,819 reads read : 3,887,638 reads written : 3,887,638 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:46 1943819 reads; of these: 1943819 (100.00%) were paired; of these: 294490 (15.15%) aligned concordantly 0 times 1516605 (78.02%) aligned concordantly exactly 1 time 132724 (6.83%) aligned concordantly >1 times ---- 294490 pairs aligned concordantly 0 times; of these: 173775 (59.01%) aligned discordantly 1 time ---- 120715 pairs aligned 0 times concordantly or discordantly; of these: 241430 mates make up the pairs; of these: 166500 (68.96%) aligned 0 times 39109 (16.20%) aligned exactly 1 time 35821 (14.84%) aligned >1 times 95.72% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 12031 / 1802660 = 0.0067 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 @ Fri, 05 Jul 2019 16:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.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 16:56:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:56:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.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 16:56:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:56:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:56:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.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 16:56:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:56:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:56:32: 1000000 INFO @ Fri, 05 Jul 2019 16:56:37: 1000000 INFO @ Fri, 05 Jul 2019 16:56:38: 1000000 INFO @ Fri, 05 Jul 2019 16:56:41: 2000000 INFO @ Fri, 05 Jul 2019 16:56:50: 3000000 INFO @ Fri, 05 Jul 2019 16:56:50: 2000000 INFO @ Fri, 05 Jul 2019 16:56:52: 2000000 INFO @ Fri, 05 Jul 2019 16:56:56: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:56:56: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:56:56: #1 total tags in treatment: 1637838 INFO @ Fri, 05 Jul 2019 16:56:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:56:56: #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 16:56:56: #1 tags after filtering in treatment: 1571837 INFO @ Fri, 05 Jul 2019 16:56:56: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:56:56: #1 finished! INFO @ Fri, 05 Jul 2019 16:56:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:56:56: #2 number of paired peaks: 12 WARNING @ Fri, 05 Jul 2019 16:56:56: Too few paired peaks (12) 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 16:56:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.05_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/ERX471748/ERX471748.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:57:04: 3000000 INFO @ Fri, 05 Jul 2019 16:57:05: 3000000 INFO @ Fri, 05 Jul 2019 16:57:13: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:57:13: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:57:13: #1 total tags in treatment: 1637838 INFO @ Fri, 05 Jul 2019 16:57:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:57:13: #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 16:57:13: #1 tags after filtering in treatment: 1571837 INFO @ Fri, 05 Jul 2019 16:57:13: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:57:13: #1 finished! INFO @ Fri, 05 Jul 2019 16:57:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:57:13: #2 number of paired peaks: 12 WARNING @ Fri, 05 Jul 2019 16:57:13: Too few paired peaks (12) 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 16:57:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.10_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/ERX471748/ERX471748.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:57:14: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:57:14: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:57:14: #1 total tags in treatment: 1637838 INFO @ Fri, 05 Jul 2019 16:57:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:57:14: #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 16:57:14: #1 tags after filtering in treatment: 1571837 INFO @ Fri, 05 Jul 2019 16:57:14: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:57:14: #1 finished! INFO @ Fri, 05 Jul 2019 16:57:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:57:14: #2 number of paired peaks: 12 WARNING @ Fri, 05 Jul 2019 16:57:14: Too few paired peaks (12) 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 16:57:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.20_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/ERX471748/ERX471748.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471748/ERX471748.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。