Job ID = 2010921 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T16:16:05 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 ) 2019-07-05T16:16:05 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 ) 2019-07-05T16:17:17 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 ) 2019-07-05T16:17:17 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 : 16,247,197 reads read : 32,494,394 reads written : 32,494,394 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1105633.sra.cache’: 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: 00:17:27 16247197 reads; of these: 16247197 (100.00%) were paired; of these: 4365330 (26.87%) aligned concordantly 0 times 9996470 (61.53%) aligned concordantly exactly 1 time 1885397 (11.60%) aligned concordantly >1 times ---- 4365330 pairs aligned concordantly 0 times; of these: 373915 (8.57%) aligned discordantly 1 time ---- 3991415 pairs aligned 0 times concordantly or discordantly; of these: 7982830 mates make up the pairs; of these: 7454906 (93.39%) aligned 0 times 277092 (3.47%) aligned exactly 1 time 250832 (3.14%) aligned >1 times 77.06% overall alignment rate Time searching: 00:17:27 Overall time: 00:17:27 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] 652469 / 12221198 = 0.0534 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 01:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.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 01:50:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:50:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.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 01:50:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:50:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.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 01:50:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:50:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:50:45: 1000000 INFO @ Sat, 06 Jul 2019 01:50:47: 1000000 INFO @ Sat, 06 Jul 2019 01:50:48: 1000000 INFO @ Sat, 06 Jul 2019 01:50:53: 2000000 INFO @ Sat, 06 Jul 2019 01:50:55: 2000000 INFO @ Sat, 06 Jul 2019 01:50:56: 2000000 INFO @ Sat, 06 Jul 2019 01:51:00: 3000000 INFO @ Sat, 06 Jul 2019 01:51:04: 3000000 INFO @ Sat, 06 Jul 2019 01:51:05: 3000000 INFO @ Sat, 06 Jul 2019 01:51:08: 4000000 INFO @ Sat, 06 Jul 2019 01:51:12: 4000000 INFO @ Sat, 06 Jul 2019 01:51:13: 4000000 INFO @ Sat, 06 Jul 2019 01:51:16: 5000000 INFO @ Sat, 06 Jul 2019 01:51:21: 5000000 INFO @ Sat, 06 Jul 2019 01:51:22: 5000000 INFO @ Sat, 06 Jul 2019 01:51:23: 6000000 INFO @ Sat, 06 Jul 2019 01:51:29: 6000000 INFO @ Sat, 06 Jul 2019 01:51:30: 6000000 INFO @ Sat, 06 Jul 2019 01:51:31: 7000000 INFO @ Sat, 06 Jul 2019 01:51:38: 7000000 INFO @ Sat, 06 Jul 2019 01:51:38: 8000000 INFO @ Sat, 06 Jul 2019 01:51:39: 7000000 INFO @ Sat, 06 Jul 2019 01:51:46: 9000000 INFO @ Sat, 06 Jul 2019 01:51:46: 8000000 INFO @ Sat, 06 Jul 2019 01:51:47: 8000000 INFO @ Sat, 06 Jul 2019 01:51:54: 10000000 INFO @ Sat, 06 Jul 2019 01:51:56: 9000000 INFO @ Sat, 06 Jul 2019 01:51:56: 9000000 INFO @ Sat, 06 Jul 2019 01:52:01: 11000000 INFO @ Sat, 06 Jul 2019 01:52:04: 10000000 INFO @ Sat, 06 Jul 2019 01:52:05: 10000000 INFO @ Sat, 06 Jul 2019 01:52:09: 12000000 INFO @ Sat, 06 Jul 2019 01:52:13: 11000000 INFO @ Sat, 06 Jul 2019 01:52:14: 11000000 INFO @ Sat, 06 Jul 2019 01:52:17: 13000000 INFO @ Sat, 06 Jul 2019 01:52:22: 12000000 INFO @ Sat, 06 Jul 2019 01:52:23: 12000000 INFO @ Sat, 06 Jul 2019 01:52:24: 14000000 INFO @ Sat, 06 Jul 2019 01:52:30: 13000000 INFO @ Sat, 06 Jul 2019 01:52:31: 13000000 INFO @ Sat, 06 Jul 2019 01:52:32: 15000000 INFO @ Sat, 06 Jul 2019 01:52:39: 14000000 INFO @ Sat, 06 Jul 2019 01:52:39: 16000000 INFO @ Sat, 06 Jul 2019 01:52:40: 14000000 INFO @ Sat, 06 Jul 2019 01:52:47: 17000000 INFO @ Sat, 06 Jul 2019 01:52:47: 15000000 INFO @ Sat, 06 Jul 2019 01:52:48: 15000000 INFO @ Sat, 06 Jul 2019 01:52:55: 18000000 INFO @ Sat, 06 Jul 2019 01:52:56: 16000000 INFO @ Sat, 06 Jul 2019 01:52:57: 16000000 INFO @ Sat, 06 Jul 2019 01:53:03: 19000000 INFO @ Sat, 06 Jul 2019 01:53:04: 17000000 INFO @ Sat, 06 Jul 2019 01:53:05: 17000000 INFO @ Sat, 06 Jul 2019 01:53:10: 20000000 INFO @ Sat, 06 Jul 2019 01:53:12: 18000000 INFO @ Sat, 06 Jul 2019 01:53:14: 18000000 INFO @ Sat, 06 Jul 2019 01:53:18: 21000000 INFO @ Sat, 06 Jul 2019 01:53:21: 19000000 INFO @ Sat, 06 Jul 2019 01:53:22: 19000000 INFO @ Sat, 06 Jul 2019 01:53:25: 22000000 INFO @ Sat, 06 Jul 2019 01:53:29: 20000000 INFO @ Sat, 06 Jul 2019 01:53:31: 20000000 INFO @ Sat, 06 Jul 2019 01:53:33: 23000000 INFO @ Sat, 06 Jul 2019 01:53:38: 21000000 INFO @ Sat, 06 Jul 2019 01:53:39: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:53:39: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:53:39: #1 total tags in treatment: 11234236 INFO @ Sat, 06 Jul 2019 01:53:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:53:39: #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 01:53:39: #1 tags after filtering in treatment: 7938440 INFO @ Sat, 06 Jul 2019 01:53:39: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 01:53:39: #1 finished! INFO @ Sat, 06 Jul 2019 01:53:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:53:39: 21000000 INFO @ Sat, 06 Jul 2019 01:53:40: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:53:40: 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 01:53:40: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:53:46: 22000000 INFO @ Sat, 06 Jul 2019 01:53:48: 22000000 BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 01:53:55: 23000000 INFO @ Sat, 06 Jul 2019 01:53:56: 23000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.05_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:54:01: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:54:01: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:54:01: #1 total tags in treatment: 11234236 INFO @ Sat, 06 Jul 2019 01:54:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:54:01: #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 01:54:01: #1 tags after filtering in treatment: 7938440 INFO @ Sat, 06 Jul 2019 01:54:01: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 01:54:01: #1 finished! INFO @ Sat, 06 Jul 2019 01:54:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:54:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:54:02: 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 01:54:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.20_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/SRX424392/SRX424392.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:54:03: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:54:03: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:54:03: #1 total tags in treatment: 11234236 INFO @ Sat, 06 Jul 2019 01:54:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:54:03: #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 01:54:03: #1 tags after filtering in treatment: 7938440 INFO @ Sat, 06 Jul 2019 01:54:03: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 01:54:03: #1 finished! INFO @ Sat, 06 Jul 2019 01:54:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:54:03: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:54:03: 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 01:54:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.10_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/SRX424392/SRX424392.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424392/SRX424392.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。