Job ID = 2641214 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:48:28 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 ) 2019-08-24T12:48:28 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 : 20,978,890 reads read : 41,957,780 reads written : 41,957,780 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: 00:18:07 20978890 reads; of these: 20978890 (100.00%) were paired; of these: 14412737 (68.70%) aligned concordantly 0 times 5465776 (26.05%) aligned concordantly exactly 1 time 1100377 (5.25%) aligned concordantly >1 times ---- 14412737 pairs aligned concordantly 0 times; of these: 5269258 (36.56%) aligned discordantly 1 time ---- 9143479 pairs aligned 0 times concordantly or discordantly; of these: 18286958 mates make up the pairs; of these: 8909502 (48.72%) aligned 0 times 6511023 (35.60%) aligned exactly 1 time 2866433 (15.67%) aligned >1 times 78.77% overall alignment rate Time searching: 00:18:07 Overall time: 00:18:07 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 16 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] 805047 / 7033022 = 0.1145 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.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 22:30:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:30:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:30:41: 1000000 INFO @ Sat, 24 Aug 2019 22:30:48: 2000000 INFO @ Sat, 24 Aug 2019 22:30:55: 3000000 INFO @ Sat, 24 Aug 2019 22:31:03: 4000000 INFO @ Sat, 24 Aug 2019 22:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.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 22:31:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:31:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:31:10: 5000000 INFO @ Sat, 24 Aug 2019 22:31:11: 1000000 INFO @ Sat, 24 Aug 2019 22:31:17: 6000000 INFO @ Sat, 24 Aug 2019 22:31:18: 2000000 INFO @ Sat, 24 Aug 2019 22:31:24: 7000000 INFO @ Sat, 24 Aug 2019 22:31:25: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:31:32: 8000000 INFO @ Sat, 24 Aug 2019 22:31:33: 4000000 INFO @ Sat, 24 Aug 2019 22:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.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 22:31:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:31:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:31:39: 9000000 INFO @ Sat, 24 Aug 2019 22:31:40: 5000000 INFO @ Sat, 24 Aug 2019 22:31:41: 1000000 INFO @ Sat, 24 Aug 2019 22:31:47: 10000000 INFO @ Sat, 24 Aug 2019 22:31:47: 6000000 INFO @ Sat, 24 Aug 2019 22:31:48: 2000000 INFO @ Sat, 24 Aug 2019 22:31:54: 11000000 INFO @ Sat, 24 Aug 2019 22:31:54: 7000000 INFO @ Sat, 24 Aug 2019 22:31:55: 3000000 INFO @ Sat, 24 Aug 2019 22:32:01: 12000000 INFO @ Sat, 24 Aug 2019 22:32:01: 8000000 INFO @ Sat, 24 Aug 2019 22:32:03: 4000000 INFO @ Sat, 24 Aug 2019 22:32:09: 9000000 INFO @ Sat, 24 Aug 2019 22:32:09: 13000000 INFO @ Sat, 24 Aug 2019 22:32:10: 5000000 INFO @ Sat, 24 Aug 2019 22:32:16: 10000000 INFO @ Sat, 24 Aug 2019 22:32:17: 6000000 INFO @ Sat, 24 Aug 2019 22:32:18: 14000000 INFO @ Sat, 24 Aug 2019 22:32:23: 11000000 INFO @ Sat, 24 Aug 2019 22:32:25: 7000000 INFO @ Sat, 24 Aug 2019 22:32:27: 15000000 INFO @ Sat, 24 Aug 2019 22:32:31: 12000000 INFO @ Sat, 24 Aug 2019 22:32:32: 8000000 INFO @ Sat, 24 Aug 2019 22:32:35: 16000000 INFO @ Sat, 24 Aug 2019 22:32:38: 13000000 INFO @ Sat, 24 Aug 2019 22:32:39: 9000000 INFO @ Sat, 24 Aug 2019 22:32:42: 17000000 INFO @ Sat, 24 Aug 2019 22:32:45: 14000000 INFO @ Sat, 24 Aug 2019 22:32:46: 10000000 INFO @ Sat, 24 Aug 2019 22:32:50: 18000000 INFO @ Sat, 24 Aug 2019 22:32:53: 15000000 INFO @ Sat, 24 Aug 2019 22:32:54: 11000000 INFO @ Sat, 24 Aug 2019 22:32:57: 19000000 INFO @ Sat, 24 Aug 2019 22:33:00: 16000000 INFO @ Sat, 24 Aug 2019 22:33:01: 12000000 INFO @ Sat, 24 Aug 2019 22:33:04: 20000000 INFO @ Sat, 24 Aug 2019 22:33:07: 17000000 INFO @ Sat, 24 Aug 2019 22:33:08: 13000000 INFO @ Sat, 24 Aug 2019 22:33:11: 21000000 INFO @ Sat, 24 Aug 2019 22:33:14: 18000000 INFO @ Sat, 24 Aug 2019 22:33:15: 14000000 INFO @ Sat, 24 Aug 2019 22:33:18: 22000000 INFO @ Sat, 24 Aug 2019 22:33:21: 19000000 INFO @ Sat, 24 Aug 2019 22:33:23: 15000000 INFO @ Sat, 24 Aug 2019 22:33:25: 23000000 INFO @ Sat, 24 Aug 2019 22:33:29: 20000000 INFO @ Sat, 24 Aug 2019 22:33:30: 16000000 INFO @ Sat, 24 Aug 2019 22:33:33: 24000000 INFO @ Sat, 24 Aug 2019 22:33:36: 21000000 INFO @ Sat, 24 Aug 2019 22:33:37: 17000000 INFO @ Sat, 24 Aug 2019 22:33:41: 25000000 INFO @ Sat, 24 Aug 2019 22:33:43: 22000000 INFO @ Sat, 24 Aug 2019 22:33:44: 18000000 INFO @ Sat, 24 Aug 2019 22:33:48: 26000000 INFO @ Sat, 24 Aug 2019 22:33:50: 23000000 INFO @ Sat, 24 Aug 2019 22:33:52: 19000000 INFO @ Sat, 24 Aug 2019 22:33:55: 27000000 INFO @ Sat, 24 Aug 2019 22:33:57: 24000000 INFO @ Sat, 24 Aug 2019 22:34:00: 20000000 INFO @ Sat, 24 Aug 2019 22:34:02: 28000000 INFO @ Sat, 24 Aug 2019 22:34:04: 25000000 INFO @ Sat, 24 Aug 2019 22:34:09: 21000000 INFO @ Sat, 24 Aug 2019 22:34:10: 29000000 INFO @ Sat, 24 Aug 2019 22:34:12: 26000000 INFO @ Sat, 24 Aug 2019 22:34:17: 30000000 INFO @ Sat, 24 Aug 2019 22:34:17: 22000000 INFO @ Sat, 24 Aug 2019 22:34:19: 27000000 INFO @ Sat, 24 Aug 2019 22:34:24: 31000000 INFO @ Sat, 24 Aug 2019 22:34:26: 23000000 INFO @ Sat, 24 Aug 2019 22:34:26: 28000000 INFO @ Sat, 24 Aug 2019 22:34:28: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:34:28: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:34:28: #1 total tags in treatment: 5768031 INFO @ Sat, 24 Aug 2019 22:34:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:34:28: #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 22:34:28: #1 tags after filtering in treatment: 3635651 INFO @ Sat, 24 Aug 2019 22:34:28: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 24 Aug 2019 22:34:28: #1 finished! INFO @ Sat, 24 Aug 2019 22:34:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:34:28: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:34:28: Too few paired peaks (27) 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 22:34:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.05_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/SRX5811111/SRX5811111.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:34:33: 29000000 INFO @ Sat, 24 Aug 2019 22:34:35: 24000000 INFO @ Sat, 24 Aug 2019 22:34:41: 30000000 INFO @ Sat, 24 Aug 2019 22:34:43: 25000000 INFO @ Sat, 24 Aug 2019 22:34:48: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:34:51: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:34:51: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:34:51: #1 total tags in treatment: 5768031 INFO @ Sat, 24 Aug 2019 22:34:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:34:51: #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 22:34:51: #1 tags after filtering in treatment: 3635651 INFO @ Sat, 24 Aug 2019 22:34:51: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 24 Aug 2019 22:34:51: #1 finished! INFO @ Sat, 24 Aug 2019 22:34:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:34:51: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:34:51: Too few paired peaks (27) 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 22:34:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.10_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/SRX5811111/SRX5811111.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:34:52: 26000000 INFO @ Sat, 24 Aug 2019 22:35:00: 27000000 INFO @ Sat, 24 Aug 2019 22:35:09: 28000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:35:17: 29000000 INFO @ Sat, 24 Aug 2019 22:35:26: 30000000 INFO @ Sat, 24 Aug 2019 22:35:34: 31000000 INFO @ Sat, 24 Aug 2019 22:35:38: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 22:35:38: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 22:35:38: #1 total tags in treatment: 5768031 INFO @ Sat, 24 Aug 2019 22:35:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:35:38: #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 22:35:38: #1 tags after filtering in treatment: 3635651 INFO @ Sat, 24 Aug 2019 22:35:38: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 24 Aug 2019 22:35:38: #1 finished! INFO @ Sat, 24 Aug 2019 22:35:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:35:39: #2 number of paired peaks: 27 WARNING @ Sat, 24 Aug 2019 22:35:39: Too few paired peaks (27) 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 22:35:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.20_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/SRX5811111/SRX5811111.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5811111/SRX5811111.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling