Job ID = 2010588 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:23:30 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 ) 2019-07-05T14:23:30 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 ) 2019-07-05T14:24:21 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 ) 2019-07-05T14:24:56 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:24:56 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.84' 2019-07-05T14:24:56 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.24) from '172.19.7.84' 2019-07-05T14:26:01 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 ) 2019-07-05T14:26:01 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 ) 2019-07-05T14:26:42 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 ) 2019-07-05T14:26:42 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 ) 2019-07-05T14:28:12 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 ) 2019-07-05T14:30:21 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 ) 2019-07-05T14:30:22 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 ) 2019-07-05T14:32:27 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 ) 2019-07-05T14:32:58 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 : 5,720,336 reads read : 11,440,672 reads written : 11,440,672 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: 00:04:57 5720336 reads; of these: 5720336 (100.00%) were paired; of these: 848909 (14.84%) aligned concordantly 0 times 3823531 (66.84%) aligned concordantly exactly 1 time 1047896 (18.32%) aligned concordantly >1 times ---- 848909 pairs aligned concordantly 0 times; of these: 50332 (5.93%) aligned discordantly 1 time ---- 798577 pairs aligned 0 times concordantly or discordantly; of these: 1597154 mates make up the pairs; of these: 1421891 (89.03%) aligned 0 times 109053 (6.83%) aligned exactly 1 time 66210 (4.15%) aligned >1 times 87.57% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 181769 / 4917621 = 0.0370 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 23:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.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 23:42:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:42:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.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 23:42:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:42:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.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 23:42:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:42:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:42:20: 1000000 INFO @ Fri, 05 Jul 2019 23:42:22: 1000000 INFO @ Fri, 05 Jul 2019 23:42:26: 1000000 INFO @ Fri, 05 Jul 2019 23:42:27: 2000000 INFO @ Fri, 05 Jul 2019 23:42:30: 2000000 INFO @ Fri, 05 Jul 2019 23:42:34: 3000000 INFO @ Fri, 05 Jul 2019 23:42:37: 2000000 INFO @ Fri, 05 Jul 2019 23:42:38: 3000000 INFO @ Fri, 05 Jul 2019 23:42:41: 4000000 INFO @ Fri, 05 Jul 2019 23:42:46: 4000000 INFO @ Fri, 05 Jul 2019 23:42:48: 3000000 INFO @ Fri, 05 Jul 2019 23:42:48: 5000000 INFO @ Fri, 05 Jul 2019 23:42:54: 5000000 INFO @ Fri, 05 Jul 2019 23:42:55: 6000000 INFO @ Fri, 05 Jul 2019 23:42:59: 4000000 INFO @ Fri, 05 Jul 2019 23:43:02: 7000000 INFO @ Fri, 05 Jul 2019 23:43:02: 6000000 INFO @ Fri, 05 Jul 2019 23:43:09: 8000000 INFO @ Fri, 05 Jul 2019 23:43:09: 5000000 INFO @ Fri, 05 Jul 2019 23:43:10: 7000000 INFO @ Fri, 05 Jul 2019 23:43:16: 9000000 INFO @ Fri, 05 Jul 2019 23:43:18: 8000000 INFO @ Fri, 05 Jul 2019 23:43:20: 6000000 INFO @ Fri, 05 Jul 2019 23:43:20: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:43:20: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:43:20: #1 total tags in treatment: 4690331 INFO @ Fri, 05 Jul 2019 23:43:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:43:20: #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 23:43:20: #1 tags after filtering in treatment: 2924634 INFO @ Fri, 05 Jul 2019 23:43:20: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:43:20: #1 finished! INFO @ Fri, 05 Jul 2019 23:43:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:43:21: #2 number of paired peaks: 185 WARNING @ Fri, 05 Jul 2019 23:43:21: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 05 Jul 2019 23:43:21: start model_add_line... INFO @ Fri, 05 Jul 2019 23:43:21: start X-correlation... INFO @ Fri, 05 Jul 2019 23:43:21: end of X-cor INFO @ Fri, 05 Jul 2019 23:43:21: #2 finished! INFO @ Fri, 05 Jul 2019 23:43:21: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:43:21: #2 alternative fragment length(s) may be 0,11,42,57,91,106,112,115,127,147,193,221,251,297,373 bps INFO @ Fri, 05 Jul 2019 23:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.05_model.r INFO @ Fri, 05 Jul 2019 23:43:26: 9000000 WARNING @ Fri, 05 Jul 2019 23:43:28: #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 23:43:28: #2 You may need to consider one of the other alternative d(s): 0,11,42,57,91,106,112,115,127,147,193,221,251,297,373 WARNING @ Fri, 05 Jul 2019 23:43:28: #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 23:43:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:43:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:43:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:43:31: #1 total tags in treatment: 4690331 INFO @ Fri, 05 Jul 2019 23:43:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:43:31: #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 23:43:31: 7000000 INFO @ Fri, 05 Jul 2019 23:43:31: #1 tags after filtering in treatment: 2924634 INFO @ Fri, 05 Jul 2019 23:43:31: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:43:31: #1 finished! INFO @ Fri, 05 Jul 2019 23:43:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:43:31: #2 number of paired peaks: 185 WARNING @ Fri, 05 Jul 2019 23:43:31: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 05 Jul 2019 23:43:31: start model_add_line... INFO @ Fri, 05 Jul 2019 23:43:31: start X-correlation... INFO @ Fri, 05 Jul 2019 23:43:31: end of X-cor INFO @ Fri, 05 Jul 2019 23:43:31: #2 finished! INFO @ Fri, 05 Jul 2019 23:43:31: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:43:31: #2 alternative fragment length(s) may be 0,11,42,57,91,106,112,115,127,147,193,221,251,297,373 bps INFO @ Fri, 05 Jul 2019 23:43:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381289/SRX381289.10_model.r WARNING @ Fri, 05 Jul 2019 23:43:31: #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 23:43:31: #2 You may need to consider one of the other alternative d(s): 0,11,42,57,91,106,112,115,127,147,193,221,251,297,373 WARNING @ Fri, 05 Jul 2019 23:43:31: #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 23:43:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:43:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:43:41: 8000000 BigWig に変換しました。 ls: cannot access SRX381289.05.bed: No such file or directory mv: cannot stat ‘SRX381289.05.bed’: No such file or directory /var/spool/uge/at116/job_scripts/2010588: line 335: 36202 Terminated MACS $i /var/spool/uge/at116/job_scripts/2010588: line 335: 36223 Terminated MACS $i /var/spool/uge/at116/job_scripts/2010588: line 335: 36238 Terminated MACS $i mv: cannot stat ‘SRX381289.05.bb’: No such file or directory ls: cannot access SRX381289.10.bed: No such file or directory mv: cannot stat ‘SRX381289.10.bed’: No such file or directory mv: cannot stat ‘SRX381289.10.bb’: No such file or directory ls: cannot access SRX381289.20.bed: No such file or directory mv: cannot stat ‘SRX381289.20.bed’: No such file or directory mv: cannot stat ‘SRX381289.20.bb’: No such file or directory