Job ID = 2011741 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:19:15 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 ) 2019-07-05T17:19:15 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 : 12,260,148 reads read : 24,520,296 reads written : 24,520,296 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: 00:08:29 12260148 reads; of these: 12260148 (100.00%) were paired; of these: 1580204 (12.89%) aligned concordantly 0 times 9239421 (75.36%) aligned concordantly exactly 1 time 1440523 (11.75%) aligned concordantly >1 times ---- 1580204 pairs aligned concordantly 0 times; of these: 398089 (25.19%) aligned discordantly 1 time ---- 1182115 pairs aligned 0 times concordantly or discordantly; of these: 2364230 mates make up the pairs; of these: 1931278 (81.69%) aligned 0 times 213651 (9.04%) aligned exactly 1 time 219301 (9.28%) aligned >1 times 92.12% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 706010 / 11075294 = 0.0637 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 02:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.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 02:39:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.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 02:39:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.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 02:39:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:12: 1000000 INFO @ Sat, 06 Jul 2019 02:39:14: 1000000 INFO @ Sat, 06 Jul 2019 02:39:15: 1000000 INFO @ Sat, 06 Jul 2019 02:39:20: 2000000 INFO @ Sat, 06 Jul 2019 02:39:23: 2000000 INFO @ Sat, 06 Jul 2019 02:39:23: 2000000 INFO @ Sat, 06 Jul 2019 02:39:28: 3000000 INFO @ Sat, 06 Jul 2019 02:39:31: 3000000 INFO @ Sat, 06 Jul 2019 02:39:32: 3000000 INFO @ Sat, 06 Jul 2019 02:39:36: 4000000 INFO @ Sat, 06 Jul 2019 02:39:39: 4000000 INFO @ Sat, 06 Jul 2019 02:39:40: 4000000 INFO @ Sat, 06 Jul 2019 02:39:44: 5000000 INFO @ Sat, 06 Jul 2019 02:39:47: 5000000 INFO @ Sat, 06 Jul 2019 02:39:48: 5000000 INFO @ Sat, 06 Jul 2019 02:39:51: 6000000 INFO @ Sat, 06 Jul 2019 02:39:56: 6000000 INFO @ Sat, 06 Jul 2019 02:39:56: 6000000 INFO @ Sat, 06 Jul 2019 02:39:59: 7000000 INFO @ Sat, 06 Jul 2019 02:40:04: 7000000 INFO @ Sat, 06 Jul 2019 02:40:04: 7000000 INFO @ Sat, 06 Jul 2019 02:40:06: 8000000 INFO @ Sat, 06 Jul 2019 02:40:11: 8000000 INFO @ Sat, 06 Jul 2019 02:40:12: 8000000 INFO @ Sat, 06 Jul 2019 02:40:14: 9000000 INFO @ Sat, 06 Jul 2019 02:40:19: 9000000 INFO @ Sat, 06 Jul 2019 02:40:20: 9000000 INFO @ Sat, 06 Jul 2019 02:40:21: 10000000 INFO @ Sat, 06 Jul 2019 02:40:27: 10000000 INFO @ Sat, 06 Jul 2019 02:40:28: 10000000 INFO @ Sat, 06 Jul 2019 02:40:29: 11000000 INFO @ Sat, 06 Jul 2019 02:40:34: 11000000 INFO @ Sat, 06 Jul 2019 02:40:36: 12000000 INFO @ Sat, 06 Jul 2019 02:40:37: 11000000 INFO @ Sat, 06 Jul 2019 02:40:42: 12000000 INFO @ Sat, 06 Jul 2019 02:40:44: 13000000 INFO @ Sat, 06 Jul 2019 02:40:45: 12000000 INFO @ Sat, 06 Jul 2019 02:40:49: 13000000 INFO @ Sat, 06 Jul 2019 02:40:51: 14000000 INFO @ Sat, 06 Jul 2019 02:40:53: 13000000 INFO @ Sat, 06 Jul 2019 02:40:57: 14000000 INFO @ Sat, 06 Jul 2019 02:40:58: 15000000 INFO @ Sat, 06 Jul 2019 02:41:01: 14000000 INFO @ Sat, 06 Jul 2019 02:41:04: 15000000 INFO @ Sat, 06 Jul 2019 02:41:06: 16000000 INFO @ Sat, 06 Jul 2019 02:41:08: 15000000 INFO @ Sat, 06 Jul 2019 02:41:12: 16000000 INFO @ Sat, 06 Jul 2019 02:41:13: 17000000 INFO @ Sat, 06 Jul 2019 02:41:16: 16000000 INFO @ Sat, 06 Jul 2019 02:41:20: 17000000 INFO @ Sat, 06 Jul 2019 02:41:21: 18000000 INFO @ Sat, 06 Jul 2019 02:41:23: 17000000 INFO @ Sat, 06 Jul 2019 02:41:28: 18000000 INFO @ Sat, 06 Jul 2019 02:41:29: 19000000 INFO @ Sat, 06 Jul 2019 02:41:31: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:41:36: 20000000 INFO @ Sat, 06 Jul 2019 02:41:36: 19000000 INFO @ Sat, 06 Jul 2019 02:41:38: 19000000 INFO @ Sat, 06 Jul 2019 02:41:44: 21000000 INFO @ Sat, 06 Jul 2019 02:41:44: 20000000 INFO @ Sat, 06 Jul 2019 02:41:45: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:41:45: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:41:45: #1 total tags in treatment: 9990416 INFO @ Sat, 06 Jul 2019 02:41:45: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:41:45: #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 02:41:45: #1 tags after filtering in treatment: 7078862 INFO @ Sat, 06 Jul 2019 02:41:45: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 02:41:45: #1 finished! INFO @ Sat, 06 Jul 2019 02:41:45: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:41:46: 20000000 INFO @ Sat, 06 Jul 2019 02:41:46: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:41:46: 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 02:41:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.05_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/SRX4915181/SRX4915181.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:41:52: 21000000 INFO @ Sat, 06 Jul 2019 02:41:53: 21000000 INFO @ Sat, 06 Jul 2019 02:41:54: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:41:54: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:41:54: #1 total tags in treatment: 9990416 INFO @ Sat, 06 Jul 2019 02:41:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:41:54: #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 02:41:54: #1 tags after filtering in treatment: 7078862 INFO @ Sat, 06 Jul 2019 02:41:54: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 02:41:54: #1 finished! INFO @ Sat, 06 Jul 2019 02:41:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:41:54: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:41:54: 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 02:41:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Sat, 06 Jul 2019 02:41:55: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:41:55: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:41:55: #1 total tags in treatment: 9990416 INFO @ Sat, 06 Jul 2019 02:41:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:41:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:41:55: #1 tags after filtering in treatment: 7078862 INFO @ Sat, 06 Jul 2019 02:41:55: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 02:41:55: #1 finished! INFO @ Sat, 06 Jul 2019 02:41:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:41:55: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:41:55: 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 @ Sat, 06 Jul 2019 02:41:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.10_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/SRX4915181/SRX4915181.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915181/SRX4915181.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。