Job ID = 2010581 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:23:34 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 ) 2019-07-05T14:24:30 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 ) 2019-07-05T14:25:18 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 ) 2019-07-05T14:26:05 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 ) 2019-07-05T14:27:58 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 ) 2019-07-05T14:28:51 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 ) 2019-07-05T14:33:47 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 : 13,858,581 reads read : 27,717,162 reads written : 27,717,162 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: 00:11:39 13858581 reads; of these: 13858581 (100.00%) were paired; of these: 1344160 (9.70%) aligned concordantly 0 times 9742971 (70.30%) aligned concordantly exactly 1 time 2771450 (20.00%) aligned concordantly >1 times ---- 1344160 pairs aligned concordantly 0 times; of these: 524837 (39.05%) aligned discordantly 1 time ---- 819323 pairs aligned 0 times concordantly or discordantly; of these: 1638646 mates make up the pairs; of these: 994992 (60.72%) aligned 0 times 301117 (18.38%) aligned exactly 1 time 342537 (20.90%) aligned >1 times 96.41% overall alignment rate Time searching: 00:11:39 Overall time: 00:11:39 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] 577001 / 12798974 = 0.0451 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 23:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.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 23:57:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.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 23:57:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:26: 1000000 INFO @ Fri, 05 Jul 2019 23:57:28: 1000000 INFO @ Fri, 05 Jul 2019 23:57:32: 2000000 INFO @ Fri, 05 Jul 2019 23:57:35: 2000000 INFO @ Fri, 05 Jul 2019 23:57:38: 3000000 INFO @ Fri, 05 Jul 2019 23:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.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 23:57:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:41: 3000000 INFO @ Fri, 05 Jul 2019 23:57:45: 4000000 INFO @ Fri, 05 Jul 2019 23:57:48: 1000000 INFO @ Fri, 05 Jul 2019 23:57:48: 4000000 INFO @ Fri, 05 Jul 2019 23:57:51: 5000000 INFO @ Fri, 05 Jul 2019 23:57:55: 2000000 INFO @ Fri, 05 Jul 2019 23:57:55: 5000000 INFO @ Fri, 05 Jul 2019 23:57:56: 6000000 INFO @ Fri, 05 Jul 2019 23:58:01: 3000000 INFO @ Fri, 05 Jul 2019 23:58:01: 6000000 INFO @ Fri, 05 Jul 2019 23:58:02: 7000000 INFO @ Fri, 05 Jul 2019 23:58:08: 7000000 INFO @ Fri, 05 Jul 2019 23:58:08: 4000000 INFO @ Fri, 05 Jul 2019 23:58:08: 8000000 INFO @ Fri, 05 Jul 2019 23:58:14: 9000000 INFO @ Fri, 05 Jul 2019 23:58:15: 8000000 INFO @ Fri, 05 Jul 2019 23:58:15: 5000000 INFO @ Fri, 05 Jul 2019 23:58:20: 10000000 INFO @ Fri, 05 Jul 2019 23:58:21: 9000000 INFO @ Fri, 05 Jul 2019 23:58:21: 6000000 INFO @ Fri, 05 Jul 2019 23:58:26: 11000000 INFO @ Fri, 05 Jul 2019 23:58:28: 10000000 INFO @ Fri, 05 Jul 2019 23:58:28: 7000000 INFO @ Fri, 05 Jul 2019 23:58:32: 12000000 INFO @ Fri, 05 Jul 2019 23:58:35: 11000000 INFO @ Fri, 05 Jul 2019 23:58:35: 8000000 INFO @ Fri, 05 Jul 2019 23:58:38: 13000000 INFO @ Fri, 05 Jul 2019 23:58:41: 12000000 INFO @ Fri, 05 Jul 2019 23:58:41: 9000000 INFO @ Fri, 05 Jul 2019 23:58:44: 14000000 INFO @ Fri, 05 Jul 2019 23:58:48: 13000000 INFO @ Fri, 05 Jul 2019 23:58:48: 10000000 INFO @ Fri, 05 Jul 2019 23:58:50: 15000000 INFO @ Fri, 05 Jul 2019 23:58:54: 14000000 INFO @ Fri, 05 Jul 2019 23:58:55: 11000000 INFO @ Fri, 05 Jul 2019 23:58:56: 16000000 INFO @ Fri, 05 Jul 2019 23:59:01: 15000000 INFO @ Fri, 05 Jul 2019 23:59:02: 12000000 INFO @ Fri, 05 Jul 2019 23:59:02: 17000000 INFO @ Fri, 05 Jul 2019 23:59:08: 16000000 INFO @ Fri, 05 Jul 2019 23:59:08: 18000000 INFO @ Fri, 05 Jul 2019 23:59:08: 13000000 INFO @ Fri, 05 Jul 2019 23:59:14: 17000000 INFO @ Fri, 05 Jul 2019 23:59:15: 19000000 INFO @ Fri, 05 Jul 2019 23:59:15: 14000000 INFO @ Fri, 05 Jul 2019 23:59:20: 18000000 INFO @ Fri, 05 Jul 2019 23:59:21: 20000000 INFO @ Fri, 05 Jul 2019 23:59:22: 15000000 INFO @ Fri, 05 Jul 2019 23:59:27: 19000000 INFO @ Fri, 05 Jul 2019 23:59:27: 21000000 INFO @ Fri, 05 Jul 2019 23:59:29: 16000000 INFO @ Fri, 05 Jul 2019 23:59:33: 22000000 INFO @ Fri, 05 Jul 2019 23:59:34: 20000000 INFO @ Fri, 05 Jul 2019 23:59:35: 17000000 INFO @ Fri, 05 Jul 2019 23:59:39: 23000000 INFO @ Fri, 05 Jul 2019 23:59:40: 21000000 INFO @ Fri, 05 Jul 2019 23:59:42: 18000000 INFO @ Fri, 05 Jul 2019 23:59:45: 24000000 INFO @ Fri, 05 Jul 2019 23:59:47: 22000000 INFO @ Fri, 05 Jul 2019 23:59:49: 19000000 INFO @ Fri, 05 Jul 2019 23:59:51: 25000000 INFO @ Fri, 05 Jul 2019 23:59:53: 23000000 INFO @ Fri, 05 Jul 2019 23:59:54: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:59:54: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:59:54: #1 total tags in treatment: 11938273 INFO @ Fri, 05 Jul 2019 23:59:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:54: #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 23:59:55: #1 tags after filtering in treatment: 8012910 INFO @ Fri, 05 Jul 2019 23:59:55: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:59:55: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:55: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:59:55: 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 23:59:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.05_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/SRX381282/SRX381282.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:59:56: 20000000 INFO @ Sat, 06 Jul 2019 00:00:00: 24000000 INFO @ Sat, 06 Jul 2019 00:00:03: 21000000 INFO @ Sat, 06 Jul 2019 00:00:06: 25000000 INFO @ Sat, 06 Jul 2019 00:00:10: 22000000 INFO @ Sat, 06 Jul 2019 00:00:10: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:00:10: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:00:10: #1 total tags in treatment: 11938273 INFO @ Sat, 06 Jul 2019 00:00:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:10: #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 00:00:11: #1 tags after filtering in treatment: 8012910 INFO @ Sat, 06 Jul 2019 00:00:11: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 00:00:11: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:00:11: 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 @ Sat, 06 Jul 2019 00:00:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.10_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/SRX381282/SRX381282.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:16: 23000000 INFO @ Sat, 06 Jul 2019 00:00:23: 24000000 INFO @ Sat, 06 Jul 2019 00:00:30: 25000000 INFO @ Sat, 06 Jul 2019 00:00:34: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:00:34: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:00:34: #1 total tags in treatment: 11938273 INFO @ Sat, 06 Jul 2019 00:00:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:34: #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 00:00:34: #1 tags after filtering in treatment: 8012910 INFO @ Sat, 06 Jul 2019 00:00:34: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 00:00:34: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:35: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:00:35: 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 @ Sat, 06 Jul 2019 00:00:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.20_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/SRX381282/SRX381282.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381282/SRX381282.20_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。