Job ID = 2010576 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:17:22 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 ) 2019-07-05T14:17:22 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 ) 2019-07-05T14:21:44 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 ) 2019-07-05T14:21:44 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 ) 2019-07-05T14:22:45 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 ) 2019-07-05T14:23:45 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 ) 2019-07-05T14:24:22 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 ) 2019-07-05T14:26:01 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 ) 2019-07-05T14:29:20 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 ) 2019-07-05T14:32:27 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 ) spots read : 19,146,688 reads read : 38,293,376 reads written : 38,293,376 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: 00:16:15 19146688 reads; of these: 19146688 (100.00%) were paired; of these: 4820559 (25.18%) aligned concordantly 0 times 11607827 (60.63%) aligned concordantly exactly 1 time 2718302 (14.20%) aligned concordantly >1 times ---- 4820559 pairs aligned concordantly 0 times; of these: 177255 (3.68%) aligned discordantly 1 time ---- 4643304 pairs aligned 0 times concordantly or discordantly; of these: 9286608 mates make up the pairs; of these: 9020632 (97.14%) aligned 0 times 117784 (1.27%) aligned exactly 1 time 148192 (1.60%) aligned >1 times 76.44% overall alignment rate Time searching: 00:16:15 Overall time: 00:16:15 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 12 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] 3233545 / 14489027 = 0.2232 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 @ Sat, 06 Jul 2019 00:04:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.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 @ Sat, 06 Jul 2019 00:04:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.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 @ Sat, 06 Jul 2019 00:04:57: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:57: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.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 @ Sat, 06 Jul 2019 00:04:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:05:05: 1000000 INFO @ Sat, 06 Jul 2019 00:05:06: 1000000 INFO @ Sat, 06 Jul 2019 00:05:07: 1000000 INFO @ Sat, 06 Jul 2019 00:05:14: 2000000 INFO @ Sat, 06 Jul 2019 00:05:16: 2000000 INFO @ Sat, 06 Jul 2019 00:05:17: 2000000 INFO @ Sat, 06 Jul 2019 00:05:24: 3000000 INFO @ Sat, 06 Jul 2019 00:05:26: 3000000 INFO @ Sat, 06 Jul 2019 00:05:26: 3000000 INFO @ Sat, 06 Jul 2019 00:05:33: 4000000 INFO @ Sat, 06 Jul 2019 00:05:35: 4000000 INFO @ Sat, 06 Jul 2019 00:05:35: 4000000 INFO @ Sat, 06 Jul 2019 00:05:42: 5000000 INFO @ Sat, 06 Jul 2019 00:05:45: 5000000 INFO @ Sat, 06 Jul 2019 00:05:45: 5000000 INFO @ Sat, 06 Jul 2019 00:05:52: 6000000 INFO @ Sat, 06 Jul 2019 00:05:54: 6000000 INFO @ Sat, 06 Jul 2019 00:05:55: 6000000 INFO @ Sat, 06 Jul 2019 00:06:01: 7000000 INFO @ Sat, 06 Jul 2019 00:06:04: 7000000 INFO @ Sat, 06 Jul 2019 00:06:04: 7000000 INFO @ Sat, 06 Jul 2019 00:06:10: 8000000 INFO @ Sat, 06 Jul 2019 00:06:13: 8000000 INFO @ Sat, 06 Jul 2019 00:06:14: 8000000 INFO @ Sat, 06 Jul 2019 00:06:20: 9000000 INFO @ Sat, 06 Jul 2019 00:06:23: 9000000 INFO @ Sat, 06 Jul 2019 00:06:23: 9000000 INFO @ Sat, 06 Jul 2019 00:06:29: 10000000 INFO @ Sat, 06 Jul 2019 00:06:33: 10000000 INFO @ Sat, 06 Jul 2019 00:06:33: 10000000 INFO @ Sat, 06 Jul 2019 00:06:38: 11000000 INFO @ Sat, 06 Jul 2019 00:06:42: 11000000 INFO @ Sat, 06 Jul 2019 00:06:42: 11000000 INFO @ Sat, 06 Jul 2019 00:06:47: 12000000 INFO @ Sat, 06 Jul 2019 00:06:52: 12000000 INFO @ Sat, 06 Jul 2019 00:06:52: 12000000 INFO @ Sat, 06 Jul 2019 00:06:56: 13000000 INFO @ Sat, 06 Jul 2019 00:07:01: 13000000 INFO @ Sat, 06 Jul 2019 00:07:01: 13000000 INFO @ Sat, 06 Jul 2019 00:07:05: 14000000 INFO @ Sat, 06 Jul 2019 00:07:11: 14000000 INFO @ Sat, 06 Jul 2019 00:07:11: 14000000 INFO @ Sat, 06 Jul 2019 00:07:14: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:07:20: 15000000 INFO @ Sat, 06 Jul 2019 00:07:20: 15000000 INFO @ Sat, 06 Jul 2019 00:07:23: 16000000 INFO @ Sat, 06 Jul 2019 00:07:29: 16000000 INFO @ Sat, 06 Jul 2019 00:07:29: 16000000 INFO @ Sat, 06 Jul 2019 00:07:31: 17000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:07:38: 17000000 INFO @ Sat, 06 Jul 2019 00:07:38: 17000000 INFO @ Sat, 06 Jul 2019 00:07:40: 18000000 INFO @ Sat, 06 Jul 2019 00:07:47: 18000000 INFO @ Sat, 06 Jul 2019 00:07:47: 18000000 INFO @ Sat, 06 Jul 2019 00:07:49: 19000000 INFO @ Sat, 06 Jul 2019 00:07:56: 19000000 INFO @ Sat, 06 Jul 2019 00:07:56: 19000000 INFO @ Sat, 06 Jul 2019 00:07:57: 20000000 INFO @ Sat, 06 Jul 2019 00:08:05: 20000000 INFO @ Sat, 06 Jul 2019 00:08:05: 20000000 INFO @ Sat, 06 Jul 2019 00:08:06: 21000000 INFO @ Sat, 06 Jul 2019 00:08:14: 21000000 INFO @ Sat, 06 Jul 2019 00:08:14: 21000000 INFO @ Sat, 06 Jul 2019 00:08:14: 22000000 INFO @ Sat, 06 Jul 2019 00:08:21: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:08:21: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:08:21: #1 total tags in treatment: 11120158 INFO @ Sat, 06 Jul 2019 00:08:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:08:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:08:22: #1 tags after filtering in treatment: 4839077 INFO @ Sat, 06 Jul 2019 00:08:22: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 06 Jul 2019 00:08:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:08:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:08:22: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 00:08:22: Too few paired peaks (1) 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 @ Sat, 06 Jul 2019 00:08:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.05_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/SRX381277/SRX381277.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:08:23: 22000000 INFO @ Sat, 06 Jul 2019 00:08:23: 22000000 INFO @ Sat, 06 Jul 2019 00:08:30: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:08:30: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:08:30: #1 total tags in treatment: 11120158 INFO @ Sat, 06 Jul 2019 00:08:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:08:30: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:08:30: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:08:30: #1 total tags in treatment: 11120158 INFO @ Sat, 06 Jul 2019 00:08:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:08:30: #1 tags after filtering in treatment: 4839077 INFO @ Sat, 06 Jul 2019 00:08:30: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 06 Jul 2019 00:08:30: #1 finished! INFO @ Sat, 06 Jul 2019 00:08:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:08:30: #1 tags after filtering in treatment: 4839077 INFO @ Sat, 06 Jul 2019 00:08:30: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 06 Jul 2019 00:08:30: #1 finished! INFO @ Sat, 06 Jul 2019 00:08:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:08:30: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 00:08:30: Too few paired peaks (1) 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 @ Sat, 06 Jul 2019 00:08:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.10_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/SRX381277/SRX381277.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:08:31: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 00:08:31: Too few paired peaks (1) 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 @ Sat, 06 Jul 2019 00:08:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.20_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/SRX381277/SRX381277.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381277/SRX381277.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling