Job ID = 2010582 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:21:09 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 ) 2019-07-05T14:21:09 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 ) 2019-07-05T14:23:45 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 ) 2019-07-05T14:24:30 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 ) 2019-07-05T14:25:40 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:25:40 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:26:05 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 ) 2019-07-05T14:27:57 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 ) 2019-07-05T14:27:57 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 ) 2019-07-05T14:28:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:29:28 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 : 11,101,428 reads read : 22,202,856 reads written : 22,202,856 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: 00:10:02 11101428 reads; of these: 11101428 (100.00%) were paired; of these: 999903 (9.01%) aligned concordantly 0 times 8452800 (76.14%) aligned concordantly exactly 1 time 1648725 (14.85%) aligned concordantly >1 times ---- 999903 pairs aligned concordantly 0 times; of these: 218284 (21.83%) aligned discordantly 1 time ---- 781619 pairs aligned 0 times concordantly or discordantly; of these: 1563238 mates make up the pairs; of these: 1338451 (85.62%) aligned 0 times 107353 (6.87%) aligned exactly 1 time 117434 (7.51%) aligned >1 times 93.97% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 186702 / 10269020 = 0.0182 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 23:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.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 23:51:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:51:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.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 23:51:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:51:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.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 23:51:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:51:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:51:56: 1000000 INFO @ Fri, 05 Jul 2019 23:51:58: 1000000 INFO @ Fri, 05 Jul 2019 23:51:59: 1000000 INFO @ Fri, 05 Jul 2019 23:52:03: 2000000 INFO @ Fri, 05 Jul 2019 23:52:06: 2000000 INFO @ Fri, 05 Jul 2019 23:52:08: 2000000 INFO @ Fri, 05 Jul 2019 23:52:11: 3000000 INFO @ Fri, 05 Jul 2019 23:52:14: 3000000 INFO @ Fri, 05 Jul 2019 23:52:18: 3000000 INFO @ Fri, 05 Jul 2019 23:52:18: 4000000 INFO @ Fri, 05 Jul 2019 23:52:22: 4000000 INFO @ Fri, 05 Jul 2019 23:52:26: 5000000 INFO @ Fri, 05 Jul 2019 23:52:28: 4000000 INFO @ Fri, 05 Jul 2019 23:52:29: 5000000 INFO @ Fri, 05 Jul 2019 23:52:34: 6000000 INFO @ Fri, 05 Jul 2019 23:52:37: 5000000 INFO @ Fri, 05 Jul 2019 23:52:37: 6000000 INFO @ Fri, 05 Jul 2019 23:52:41: 7000000 INFO @ Fri, 05 Jul 2019 23:52:45: 7000000 INFO @ Fri, 05 Jul 2019 23:52:46: 6000000 INFO @ Fri, 05 Jul 2019 23:52:49: 8000000 INFO @ Fri, 05 Jul 2019 23:52:52: 8000000 INFO @ Fri, 05 Jul 2019 23:52:55: 7000000 INFO @ Fri, 05 Jul 2019 23:52:57: 9000000 INFO @ Fri, 05 Jul 2019 23:53:00: 9000000 INFO @ Fri, 05 Jul 2019 23:53:04: 10000000 INFO @ Fri, 05 Jul 2019 23:53:04: 8000000 INFO @ Fri, 05 Jul 2019 23:53:08: 10000000 INFO @ Fri, 05 Jul 2019 23:53:12: 11000000 INFO @ Fri, 05 Jul 2019 23:53:14: 9000000 INFO @ Fri, 05 Jul 2019 23:53:15: 11000000 INFO @ Fri, 05 Jul 2019 23:53:19: 12000000 INFO @ Fri, 05 Jul 2019 23:53:23: 10000000 INFO @ Fri, 05 Jul 2019 23:53:23: 12000000 INFO @ Fri, 05 Jul 2019 23:53:27: 13000000 INFO @ Fri, 05 Jul 2019 23:53:30: 13000000 INFO @ Fri, 05 Jul 2019 23:53:32: 11000000 INFO @ Fri, 05 Jul 2019 23:53:35: 14000000 INFO @ Fri, 05 Jul 2019 23:53:38: 14000000 INFO @ Fri, 05 Jul 2019 23:53:41: 12000000 INFO @ Fri, 05 Jul 2019 23:53:42: 15000000 INFO @ Fri, 05 Jul 2019 23:53:46: 15000000 INFO @ Fri, 05 Jul 2019 23:53:50: 13000000 INFO @ Fri, 05 Jul 2019 23:53:50: 16000000 INFO @ Fri, 05 Jul 2019 23:53:53: 16000000 INFO @ Fri, 05 Jul 2019 23:53:57: 17000000 INFO @ Fri, 05 Jul 2019 23:53:59: 14000000 INFO @ Fri, 05 Jul 2019 23:54:01: 17000000 INFO @ Fri, 05 Jul 2019 23:54:05: 18000000 INFO @ Fri, 05 Jul 2019 23:54:08: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:54:09: 15000000 INFO @ Fri, 05 Jul 2019 23:54:12: 19000000 INFO @ Fri, 05 Jul 2019 23:54:16: 19000000 INFO @ Fri, 05 Jul 2019 23:54:18: 16000000 INFO @ Fri, 05 Jul 2019 23:54:20: 20000000 INFO @ Fri, 05 Jul 2019 23:54:23: 20000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:54:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:54:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:54:23: #1 total tags in treatment: 9915322 INFO @ Fri, 05 Jul 2019 23:54:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:54:23: #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 23:54:24: #1 tags after filtering in treatment: 6590632 INFO @ Fri, 05 Jul 2019 23:54:24: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:54:24: #1 finished! INFO @ Fri, 05 Jul 2019 23:54:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:54:24: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:54:24: Too few paired peaks (0) 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 23:54:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.05_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/SRX381283/SRX381283.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:54:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:54:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:54:27: #1 total tags in treatment: 9915322 INFO @ Fri, 05 Jul 2019 23:54:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:54:27: #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 23:54:27: #1 tags after filtering in treatment: 6590632 INFO @ Fri, 05 Jul 2019 23:54:27: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:54:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:54:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:54:28: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:54:28: Too few paired peaks (0) 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 23:54:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.20_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 23:54:28: 17000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:54:37: 18000000 INFO @ Fri, 05 Jul 2019 23:54:47: 19000000 INFO @ Fri, 05 Jul 2019 23:54:56: 20000000 INFO @ Fri, 05 Jul 2019 23:55:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:55:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:55:00: #1 total tags in treatment: 9915322 INFO @ Fri, 05 Jul 2019 23:55:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:00: #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 23:55:01: #1 tags after filtering in treatment: 6590632 INFO @ Fri, 05 Jul 2019 23:55:01: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:55:01: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:01: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:55:01: Too few paired peaks (0) 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 23:55:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.10_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/SRX381283/SRX381283.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381283/SRX381283.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling