Job ID = 2010740 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:10:45 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 ) 2019-07-05T15:10:45 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 ) 2019-07-05T15:23:18 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 ) spots read : 10,000,626 reads read : 20,001,252 reads written : 20,001,252 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: 00:08:50 10000626 reads; of these: 10000626 (100.00%) were paired; of these: 1764981 (17.65%) aligned concordantly 0 times 7292851 (72.92%) aligned concordantly exactly 1 time 942794 (9.43%) aligned concordantly >1 times ---- 1764981 pairs aligned concordantly 0 times; of these: 123465 (7.00%) aligned discordantly 1 time ---- 1641516 pairs aligned 0 times concordantly or discordantly; of these: 3283032 mates make up the pairs; of these: 2843940 (86.63%) aligned 0 times 335160 (10.21%) aligned exactly 1 time 103932 (3.17%) aligned >1 times 85.78% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 112132 / 8333609 = 0.0135 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 00:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.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 00:42:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:42:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.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 00:42:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:42:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.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 00:42:21: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:42:21: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:42:33: 1000000 INFO @ Sat, 06 Jul 2019 00:42:35: 1000000 INFO @ Sat, 06 Jul 2019 00:42:35: 1000000 INFO @ Sat, 06 Jul 2019 00:42:47: 2000000 INFO @ Sat, 06 Jul 2019 00:42:48: 2000000 INFO @ Sat, 06 Jul 2019 00:42:48: 2000000 INFO @ Sat, 06 Jul 2019 00:43:01: 3000000 INFO @ Sat, 06 Jul 2019 00:43:02: 3000000 INFO @ Sat, 06 Jul 2019 00:43:02: 3000000 INFO @ Sat, 06 Jul 2019 00:43:12: 4000000 INFO @ Sat, 06 Jul 2019 00:43:14: 4000000 INFO @ Sat, 06 Jul 2019 00:43:15: 4000000 INFO @ Sat, 06 Jul 2019 00:43:25: 5000000 INFO @ Sat, 06 Jul 2019 00:43:26: 5000000 INFO @ Sat, 06 Jul 2019 00:43:29: 5000000 INFO @ Sat, 06 Jul 2019 00:43:38: 6000000 INFO @ Sat, 06 Jul 2019 00:43:39: 6000000 INFO @ Sat, 06 Jul 2019 00:43:43: 6000000 INFO @ Sat, 06 Jul 2019 00:43:50: 7000000 INFO @ Sat, 06 Jul 2019 00:43:52: 7000000 INFO @ Sat, 06 Jul 2019 00:43:57: 7000000 INFO @ Sat, 06 Jul 2019 00:44:04: 8000000 INFO @ Sat, 06 Jul 2019 00:44:07: 8000000 INFO @ Sat, 06 Jul 2019 00:44:12: 8000000 INFO @ Sat, 06 Jul 2019 00:44:20: 9000000 INFO @ Sat, 06 Jul 2019 00:44:22: 9000000 INFO @ Sat, 06 Jul 2019 00:44:28: 9000000 INFO @ Sat, 06 Jul 2019 00:44:35: 10000000 INFO @ Sat, 06 Jul 2019 00:44:36: 10000000 INFO @ Sat, 06 Jul 2019 00:44:43: 10000000 INFO @ Sat, 06 Jul 2019 00:44:48: 11000000 INFO @ Sat, 06 Jul 2019 00:44:49: 11000000 INFO @ Sat, 06 Jul 2019 00:44:58: 11000000 INFO @ Sat, 06 Jul 2019 00:45:00: 12000000 INFO @ Sat, 06 Jul 2019 00:45:02: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:45:11: 13000000 INFO @ Sat, 06 Jul 2019 00:45:13: 12000000 INFO @ Sat, 06 Jul 2019 00:45:16: 13000000 INFO @ Sat, 06 Jul 2019 00:45:20: 14000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:45:28: 13000000 INFO @ Sat, 06 Jul 2019 00:45:29: 14000000 INFO @ Sat, 06 Jul 2019 00:45:29: 15000000 INFO @ Sat, 06 Jul 2019 00:45:38: 16000000 INFO @ Sat, 06 Jul 2019 00:45:41: 15000000 INFO @ Sat, 06 Jul 2019 00:45:43: 14000000 INFO @ Sat, 06 Jul 2019 00:45:46: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:45:46: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:45:46: #1 total tags in treatment: 8124401 INFO @ Sat, 06 Jul 2019 00:45:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:45:46: #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 00:45:47: #1 tags after filtering in treatment: 6379322 INFO @ Sat, 06 Jul 2019 00:45:47: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 00:45:47: #1 finished! INFO @ Sat, 06 Jul 2019 00:45:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:45:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:45:47: 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 00:45:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.10_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/SRX386920/SRX386920.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:45:53: 16000000 INFO @ Sat, 06 Jul 2019 00:45:57: 15000000 INFO @ Sat, 06 Jul 2019 00:46:05: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:46:05: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:46:05: #1 total tags in treatment: 8124401 INFO @ Sat, 06 Jul 2019 00:46:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:46:05: #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 00:46:06: #1 tags after filtering in treatment: 6379322 INFO @ Sat, 06 Jul 2019 00:46:06: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 00:46:06: #1 finished! INFO @ Sat, 06 Jul 2019 00:46:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:46:06: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:46:06: 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 00:46:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.20_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/SRX386920/SRX386920.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:46:12: 16000000 INFO @ Sat, 06 Jul 2019 00:46:24: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:46:24: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:46:24: #1 total tags in treatment: 8124401 INFO @ Sat, 06 Jul 2019 00:46:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:46:24: #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 00:46:25: #1 tags after filtering in treatment: 6379322 INFO @ Sat, 06 Jul 2019 00:46:25: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 00:46:25: #1 finished! INFO @ Sat, 06 Jul 2019 00:46:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:46:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:46:25: 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 00:46:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.05_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/SRX386920/SRX386920.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386920/SRX386920.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling