Job ID = 2010521 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:49:53 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' 2019-07-05T13:49:53 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/traces/sra15/SRR/001011/SRR1035326' 2019-07-05T13:49:53 fasterq-dump.2.9.6 err: invalid accession 'SRR1035326' 2019-07-05T13:50:08 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' 2019-07-05T13:50:08 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/traces/sra15/SRR/001011/SRR1035326' 2019-07-05T13:50:08 fasterq-dump.2.9.6 err: invalid accession 'SRR1035326' 2019-07-05T13:50:23 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' 2019-07-05T13:50:23 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/traces/sra15/SRR/001011/SRR1035326' 2019-07-05T13:50:23 fasterq-dump.2.9.6 err: invalid accession 'SRR1035326' 2019-07-05T13:56:56 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 ) 2019-07-05T14:02:36 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 ) 2019-07-05T14:02:36 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 : 12,767,158 reads read : 25,534,316 reads written : 25,534,316 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: 00:07:27 12767158 reads; of these: 12767158 (100.00%) were paired; of these: 4873396 (38.17%) aligned concordantly 0 times 6928525 (54.27%) aligned concordantly exactly 1 time 965237 (7.56%) aligned concordantly >1 times ---- 4873396 pairs aligned concordantly 0 times; of these: 96664 (1.98%) aligned discordantly 1 time ---- 4776732 pairs aligned 0 times concordantly or discordantly; of these: 9553464 mates make up the pairs; of these: 9033094 (94.55%) aligned 0 times 373432 (3.91%) aligned exactly 1 time 146938 (1.54%) aligned >1 times 64.62% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:34 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] 2513761 / 7981252 = 0.3150 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 23:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.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 23:20:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.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 23:20:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:40: 1000000 INFO @ Fri, 05 Jul 2019 23:20:41: 1000000 INFO @ Fri, 05 Jul 2019 23:20:47: 2000000 INFO @ Fri, 05 Jul 2019 23:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.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 23:20:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:48: 2000000 INFO @ Fri, 05 Jul 2019 23:20:55: 3000000 INFO @ Fri, 05 Jul 2019 23:20:56: 3000000 INFO @ Fri, 05 Jul 2019 23:20:57: 1000000 INFO @ Fri, 05 Jul 2019 23:21:02: 4000000 INFO @ Fri, 05 Jul 2019 23:21:03: 4000000 INFO @ Fri, 05 Jul 2019 23:21:05: 2000000 INFO @ Fri, 05 Jul 2019 23:21:09: 5000000 INFO @ Fri, 05 Jul 2019 23:21:10: 5000000 INFO @ Fri, 05 Jul 2019 23:21:14: 3000000 INFO @ Fri, 05 Jul 2019 23:21:16: 6000000 INFO @ Fri, 05 Jul 2019 23:21:18: 6000000 INFO @ Fri, 05 Jul 2019 23:21:22: 4000000 INFO @ Fri, 05 Jul 2019 23:21:24: 7000000 INFO @ Fri, 05 Jul 2019 23:21:25: 7000000 INFO @ Fri, 05 Jul 2019 23:21:31: 5000000 INFO @ Fri, 05 Jul 2019 23:21:31: 8000000 INFO @ Fri, 05 Jul 2019 23:21:32: 8000000 INFO @ Fri, 05 Jul 2019 23:21:39: 6000000 INFO @ Fri, 05 Jul 2019 23:21:39: 9000000 INFO @ Fri, 05 Jul 2019 23:21:40: 9000000 INFO @ Fri, 05 Jul 2019 23:21:46: 10000000 INFO @ Fri, 05 Jul 2019 23:21:47: 7000000 INFO @ Fri, 05 Jul 2019 23:21:47: 10000000 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 23:21:54: 11000000 INFO @ Fri, 05 Jul 2019 23:21:55: 11000000 INFO @ Fri, 05 Jul 2019 23:21:55: 8000000 INFO @ Fri, 05 Jul 2019 23:21:57: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:57: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:57: #1 total tags in treatment: 5398203 INFO @ Fri, 05 Jul 2019 23:21:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:57: #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 23:21:57: #1 tags after filtering in treatment: 1606907 INFO @ Fri, 05 Jul 2019 23:21:57: #1 Redundant rate of treatment: 0.70 INFO @ Fri, 05 Jul 2019 23:21:57: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:57: #2 number of paired peaks: 1128 INFO @ Fri, 05 Jul 2019 23:21:57: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:57: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:57: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:57: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:57: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:21:57: #2 alternative fragment length(s) may be 0,102,117,123,142,165,172,188 bps INFO @ Fri, 05 Jul 2019 23:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381225/SRX381225.05_model.r WARNING @ Fri, 05 Jul 2019 23:21:57: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:21:57: #2 You may need to consider one of the other alternative d(s): 0,102,117,123,142,165,172,188 WARNING @ Fri, 05 Jul 2019 23:21:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:21:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:57: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381225.05.bed: No such file or directory mv: cannot stat ‘SRX381225.05.bed’: No such file or directory /var/spool/uge/at076/job_scripts/2010521: line 335: 26100 Terminated MACS $i /var/spool/uge/at076/job_scripts/2010521: line 335: 26121 Terminated MACS $i /var/spool/uge/at076/job_scripts/2010521: line 335: 26135 Terminated MACS $i mv: cannot stat ‘SRX381225.05.bb’: No such file or directory ls: cannot access SRX381225.10.bed: No such file or directory mv: cannot stat ‘SRX381225.10.bed’: No such file or directory mv: cannot stat ‘SRX381225.10.bb’: No such file or directory ls: cannot access SRX381225.20.bed: No such file or directory mv: cannot stat ‘SRX381225.20.bed’: No such file or directory mv: cannot stat ‘SRX381225.20.bb’: No such file or directory