Job ID = 2640986 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:13:26 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 ) 2019-08-24T11:13:43 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 : 10,063,946 reads read : 20,127,892 reads written : 20,127,892 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: 00:12:53 10063946 reads; of these: 10063946 (100.00%) were paired; of these: 385303 (3.83%) aligned concordantly 0 times 8534527 (84.80%) aligned concordantly exactly 1 time 1144116 (11.37%) aligned concordantly >1 times ---- 385303 pairs aligned concordantly 0 times; of these: 156879 (40.72%) aligned discordantly 1 time ---- 228424 pairs aligned 0 times concordantly or discordantly; of these: 456848 mates make up the pairs; of these: 380371 (83.26%) aligned 0 times 29121 (6.37%) aligned exactly 1 time 47356 (10.37%) aligned >1 times 98.11% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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] 100412 / 9833192 = 0.0102 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.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, 24 Aug 2019 20:52:54: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:52:54: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:53:03: 1000000 INFO @ Sat, 24 Aug 2019 20:53:13: 2000000 INFO @ Sat, 24 Aug 2019 20:53:23: 3000000 INFO @ Sat, 24 Aug 2019 20:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.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, 24 Aug 2019 20:53:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:53:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:53:32: 4000000 INFO @ Sat, 24 Aug 2019 20:53:33: 1000000 INFO @ Sat, 24 Aug 2019 20:53:42: 5000000 INFO @ Sat, 24 Aug 2019 20:53:43: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:53:52: 6000000 INFO @ Sat, 24 Aug 2019 20:53:53: 3000000 INFO @ Sat, 24 Aug 2019 20:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.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, 24 Aug 2019 20:53:54: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:53:54: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:54:01: 7000000 INFO @ Sat, 24 Aug 2019 20:54:03: 4000000 INFO @ Sat, 24 Aug 2019 20:54:03: 1000000 INFO @ Sat, 24 Aug 2019 20:54:11: 8000000 INFO @ Sat, 24 Aug 2019 20:54:13: 5000000 INFO @ Sat, 24 Aug 2019 20:54:13: 2000000 INFO @ Sat, 24 Aug 2019 20:54:21: 9000000 INFO @ Sat, 24 Aug 2019 20:54:22: 6000000 INFO @ Sat, 24 Aug 2019 20:54:23: 3000000 INFO @ Sat, 24 Aug 2019 20:54:31: 10000000 INFO @ Sat, 24 Aug 2019 20:54:32: 7000000 INFO @ Sat, 24 Aug 2019 20:54:33: 4000000 INFO @ Sat, 24 Aug 2019 20:54:41: 11000000 INFO @ Sat, 24 Aug 2019 20:54:42: 8000000 INFO @ Sat, 24 Aug 2019 20:54:43: 5000000 INFO @ Sat, 24 Aug 2019 20:54:51: 12000000 INFO @ Sat, 24 Aug 2019 20:54:52: 9000000 INFO @ Sat, 24 Aug 2019 20:54:54: 6000000 INFO @ Sat, 24 Aug 2019 20:55:01: 13000000 INFO @ Sat, 24 Aug 2019 20:55:02: 10000000 INFO @ Sat, 24 Aug 2019 20:55:04: 7000000 INFO @ Sat, 24 Aug 2019 20:55:12: 14000000 INFO @ Sat, 24 Aug 2019 20:55:12: 11000000 INFO @ Sat, 24 Aug 2019 20:55:14: 8000000 INFO @ Sat, 24 Aug 2019 20:55:22: 15000000 INFO @ Sat, 24 Aug 2019 20:55:22: 12000000 INFO @ Sat, 24 Aug 2019 20:55:24: 9000000 INFO @ Sat, 24 Aug 2019 20:55:32: 16000000 INFO @ Sat, 24 Aug 2019 20:55:33: 13000000 INFO @ Sat, 24 Aug 2019 20:55:35: 10000000 INFO @ Sat, 24 Aug 2019 20:55:43: 17000000 INFO @ Sat, 24 Aug 2019 20:55:43: 14000000 INFO @ Sat, 24 Aug 2019 20:55:46: 11000000 INFO @ Sat, 24 Aug 2019 20:55:54: 15000000 INFO @ Sat, 24 Aug 2019 20:55:54: 18000000 INFO @ Sat, 24 Aug 2019 20:55:58: 12000000 INFO @ Sat, 24 Aug 2019 20:56:04: 16000000 INFO @ Sat, 24 Aug 2019 20:56:05: 19000000 INFO @ Sat, 24 Aug 2019 20:56:08: 13000000 INFO @ Sat, 24 Aug 2019 20:56:11: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:56:11: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:56:11: #1 total tags in treatment: 9579090 INFO @ Sat, 24 Aug 2019 20:56:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:56:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:56:12: #1 tags after filtering in treatment: 7497421 INFO @ Sat, 24 Aug 2019 20:56:12: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 20:56:12: #1 finished! INFO @ Sat, 24 Aug 2019 20:56:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:56:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:56:12: 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, 24 Aug 2019 20:56:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.05_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/SRX4936092/SRX4936092.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:56:14: 17000000 INFO @ Sat, 24 Aug 2019 20:56:18: 14000000 INFO @ Sat, 24 Aug 2019 20:56:24: 18000000 INFO @ Sat, 24 Aug 2019 20:56:28: 15000000 INFO @ Sat, 24 Aug 2019 20:56:34: 19000000 INFO @ Sat, 24 Aug 2019 20:56:38: 16000000 INFO @ Sat, 24 Aug 2019 20:56:40: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:56:40: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:56:40: #1 total tags in treatment: 9579090 INFO @ Sat, 24 Aug 2019 20:56:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:56:40: #1 tags after filtering in treatment: 7497421 INFO @ Sat, 24 Aug 2019 20:56:40: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 20:56:40: #1 finished! INFO @ Sat, 24 Aug 2019 20:56:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:56:40: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:56:40: 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, 24 Aug 2019 20:56:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.10_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/SRX4936092/SRX4936092.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:56:48: 17000000 INFO @ Sat, 24 Aug 2019 20:56:57: 18000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:57:07: 19000000 INFO @ Sat, 24 Aug 2019 20:57:12: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:57:12: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:57:12: #1 total tags in treatment: 9579090 INFO @ Sat, 24 Aug 2019 20:57:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:57:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:57:12: #1 tags after filtering in treatment: 7497421 INFO @ Sat, 24 Aug 2019 20:57:12: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 20:57:12: #1 finished! INFO @ Sat, 24 Aug 2019 20:57:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:57:13: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:57:13: 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, 24 Aug 2019 20:57:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.20_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/SRX4936092/SRX4936092.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936092/SRX4936092.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling