Job ID = 2009803 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T10:56:07 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 ) 2019-07-05T10:56:07 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 ) 2019-07-05T10:59:01 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 ) 2019-07-05T11:20:51 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 ) 2019-07-05T11:22:44 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 ) 2019-07-05T11:22:44 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 : 49,563,110 reads read : 99,126,220 reads written : 99,126,220 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: 00:23:34 49563110 reads; of these: 49563110 (100.00%) were paired; of these: 17088150 (34.48%) aligned concordantly 0 times 25575270 (51.60%) aligned concordantly exactly 1 time 6899690 (13.92%) aligned concordantly >1 times ---- 17088150 pairs aligned concordantly 0 times; of these: 4504226 (26.36%) aligned discordantly 1 time ---- 12583924 pairs aligned 0 times concordantly or discordantly; of these: 25167848 mates make up the pairs; of these: 20587102 (81.80%) aligned 0 times 1865418 (7.41%) aligned exactly 1 time 2715328 (10.79%) aligned >1 times 79.23% overall alignment rate Time searching: 00:23:34 Overall time: 00:23:34 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 20 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] 14330971 / 36949135 = 0.3879 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 @ Fri, 05 Jul 2019 21:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.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 @ Fri, 05 Jul 2019 21:28:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:28:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.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 @ Fri, 05 Jul 2019 21:28:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:28:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.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 @ Fri, 05 Jul 2019 21:28:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:28:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:28:43: 1000000 INFO @ Fri, 05 Jul 2019 21:28:43: 1000000 INFO @ Fri, 05 Jul 2019 21:28:44: 1000000 INFO @ Fri, 05 Jul 2019 21:28:52: 2000000 INFO @ Fri, 05 Jul 2019 21:28:52: 2000000 INFO @ Fri, 05 Jul 2019 21:28:54: 2000000 INFO @ Fri, 05 Jul 2019 21:29:02: 3000000 INFO @ Fri, 05 Jul 2019 21:29:02: 3000000 INFO @ Fri, 05 Jul 2019 21:29:03: 3000000 INFO @ Fri, 05 Jul 2019 21:29:11: 4000000 INFO @ Fri, 05 Jul 2019 21:29:12: 4000000 INFO @ Fri, 05 Jul 2019 21:29:13: 4000000 INFO @ Fri, 05 Jul 2019 21:29:21: 5000000 INFO @ Fri, 05 Jul 2019 21:29:22: 5000000 INFO @ Fri, 05 Jul 2019 21:29:23: 5000000 INFO @ Fri, 05 Jul 2019 21:29:31: 6000000 INFO @ Fri, 05 Jul 2019 21:29:32: 6000000 INFO @ Fri, 05 Jul 2019 21:29:32: 6000000 INFO @ Fri, 05 Jul 2019 21:29:40: 7000000 INFO @ Fri, 05 Jul 2019 21:29:41: 7000000 INFO @ Fri, 05 Jul 2019 21:29:42: 7000000 INFO @ Fri, 05 Jul 2019 21:29:48: 8000000 INFO @ Fri, 05 Jul 2019 21:29:50: 8000000 INFO @ Fri, 05 Jul 2019 21:29:51: 8000000 INFO @ Fri, 05 Jul 2019 21:29:57: 9000000 INFO @ Fri, 05 Jul 2019 21:30:00: 9000000 INFO @ Fri, 05 Jul 2019 21:30:00: 9000000 INFO @ Fri, 05 Jul 2019 21:30:05: 10000000 INFO @ Fri, 05 Jul 2019 21:30:09: 10000000 INFO @ Fri, 05 Jul 2019 21:30:09: 10000000 INFO @ Fri, 05 Jul 2019 21:30:13: 11000000 INFO @ Fri, 05 Jul 2019 21:30:18: 11000000 INFO @ Fri, 05 Jul 2019 21:30:18: 11000000 INFO @ Fri, 05 Jul 2019 21:30:22: 12000000 INFO @ Fri, 05 Jul 2019 21:30:27: 12000000 INFO @ Fri, 05 Jul 2019 21:30:28: 12000000 INFO @ Fri, 05 Jul 2019 21:30:30: 13000000 INFO @ Fri, 05 Jul 2019 21:30:36: 13000000 INFO @ Fri, 05 Jul 2019 21:30:37: 13000000 INFO @ Fri, 05 Jul 2019 21:30:38: 14000000 INFO @ Fri, 05 Jul 2019 21:30:45: 14000000 INFO @ Fri, 05 Jul 2019 21:30:46: 14000000 INFO @ Fri, 05 Jul 2019 21:30:47: 15000000 INFO @ Fri, 05 Jul 2019 21:30:54: 15000000 INFO @ Fri, 05 Jul 2019 21:30:54: 15000000 INFO @ Fri, 05 Jul 2019 21:30:55: 16000000 INFO @ Fri, 05 Jul 2019 21:31:03: 16000000 INFO @ Fri, 05 Jul 2019 21:31:03: 16000000 INFO @ Fri, 05 Jul 2019 21:31:03: 17000000 INFO @ Fri, 05 Jul 2019 21:31:12: 18000000 INFO @ Fri, 05 Jul 2019 21:31:12: 17000000 INFO @ Fri, 05 Jul 2019 21:31:12: 17000000 INFO @ Fri, 05 Jul 2019 21:31:20: 19000000 INFO @ Fri, 05 Jul 2019 21:31:21: 18000000 INFO @ Fri, 05 Jul 2019 21:31:21: 18000000 INFO @ Fri, 05 Jul 2019 21:31:28: 20000000 INFO @ Fri, 05 Jul 2019 21:31:29: 19000000 INFO @ Fri, 05 Jul 2019 21:31:30: 19000000 INFO @ Fri, 05 Jul 2019 21:31:36: 21000000 INFO @ Fri, 05 Jul 2019 21:31:38: 20000000 INFO @ Fri, 05 Jul 2019 21:31:38: 20000000 INFO @ Fri, 05 Jul 2019 21:31:44: 22000000 INFO @ Fri, 05 Jul 2019 21:31:47: 21000000 INFO @ Fri, 05 Jul 2019 21:31:48: 21000000 INFO @ Fri, 05 Jul 2019 21:31:53: 23000000 INFO @ Fri, 05 Jul 2019 21:31:57: 22000000 INFO @ Fri, 05 Jul 2019 21:31:58: 22000000 INFO @ Fri, 05 Jul 2019 21:32:02: 24000000 INFO @ Fri, 05 Jul 2019 21:32:07: 23000000 INFO @ Fri, 05 Jul 2019 21:32:08: 23000000 INFO @ Fri, 05 Jul 2019 21:32:11: 25000000 INFO @ Fri, 05 Jul 2019 21:32:18: 24000000 INFO @ Fri, 05 Jul 2019 21:32:18: 24000000 INFO @ Fri, 05 Jul 2019 21:32:20: 26000000 INFO @ Fri, 05 Jul 2019 21:32:28: 25000000 INFO @ Fri, 05 Jul 2019 21:32:28: 25000000 INFO @ Fri, 05 Jul 2019 21:32:28: 27000000 INFO @ Fri, 05 Jul 2019 21:32:37: 28000000 INFO @ Fri, 05 Jul 2019 21:32:38: 26000000 INFO @ Fri, 05 Jul 2019 21:32:38: 26000000 INFO @ Fri, 05 Jul 2019 21:32:46: 29000000 INFO @ Fri, 05 Jul 2019 21:32:48: 27000000 INFO @ Fri, 05 Jul 2019 21:32:48: 27000000 INFO @ Fri, 05 Jul 2019 21:32:54: 30000000 INFO @ Fri, 05 Jul 2019 21:32:57: 28000000 INFO @ Fri, 05 Jul 2019 21:32:58: 28000000 INFO @ Fri, 05 Jul 2019 21:33:03: 31000000 INFO @ Fri, 05 Jul 2019 21:33:07: 29000000 INFO @ Fri, 05 Jul 2019 21:33:07: 29000000 INFO @ Fri, 05 Jul 2019 21:33:11: 32000000 INFO @ Fri, 05 Jul 2019 21:33:17: 30000000 INFO @ Fri, 05 Jul 2019 21:33:17: 30000000 INFO @ Fri, 05 Jul 2019 21:33:19: 33000000 INFO @ Fri, 05 Jul 2019 21:33:27: 31000000 INFO @ Fri, 05 Jul 2019 21:33:27: 31000000 INFO @ Fri, 05 Jul 2019 21:33:28: 34000000 INFO @ Fri, 05 Jul 2019 21:33:36: 32000000 INFO @ Fri, 05 Jul 2019 21:33:36: 32000000 INFO @ Fri, 05 Jul 2019 21:33:37: 35000000 INFO @ Fri, 05 Jul 2019 21:33:46: 36000000 INFO @ Fri, 05 Jul 2019 21:33:46: 33000000 INFO @ Fri, 05 Jul 2019 21:33:46: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:33:54: 37000000 INFO @ Fri, 05 Jul 2019 21:33:55: 34000000 INFO @ Fri, 05 Jul 2019 21:33:56: 34000000 INFO @ Fri, 05 Jul 2019 21:34:03: 38000000 INFO @ Fri, 05 Jul 2019 21:34:06: 35000000 INFO @ Fri, 05 Jul 2019 21:34:06: 35000000 INFO @ Fri, 05 Jul 2019 21:34:11: 39000000 INFO @ Fri, 05 Jul 2019 21:34:16: 36000000 INFO @ Fri, 05 Jul 2019 21:34:16: 36000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:34:20: 40000000 INFO @ Fri, 05 Jul 2019 21:34:26: 37000000 INFO @ Fri, 05 Jul 2019 21:34:26: 37000000 INFO @ Fri, 05 Jul 2019 21:34:28: 41000000 INFO @ Fri, 05 Jul 2019 21:34:36: 38000000 INFO @ Fri, 05 Jul 2019 21:34:36: 38000000 INFO @ Fri, 05 Jul 2019 21:34:37: 42000000 INFO @ Fri, 05 Jul 2019 21:34:46: 43000000 INFO @ Fri, 05 Jul 2019 21:34:46: 39000000 INFO @ Fri, 05 Jul 2019 21:34:46: 39000000 INFO @ Fri, 05 Jul 2019 21:34:54: 44000000 INFO @ Fri, 05 Jul 2019 21:34:55: 40000000 INFO @ Fri, 05 Jul 2019 21:34:55: 40000000 INFO @ Fri, 05 Jul 2019 21:35:03: 45000000 INFO @ Fri, 05 Jul 2019 21:35:05: 41000000 INFO @ Fri, 05 Jul 2019 21:35:05: 41000000 INFO @ Fri, 05 Jul 2019 21:35:11: 46000000 INFO @ Fri, 05 Jul 2019 21:35:13: 42000000 INFO @ Fri, 05 Jul 2019 21:35:13: 42000000 INFO @ Fri, 05 Jul 2019 21:35:20: 47000000 INFO @ Fri, 05 Jul 2019 21:35:22: 43000000 INFO @ Fri, 05 Jul 2019 21:35:23: 43000000 INFO @ Fri, 05 Jul 2019 21:35:29: 48000000 INFO @ Fri, 05 Jul 2019 21:35:31: 44000000 INFO @ Fri, 05 Jul 2019 21:35:32: 44000000 INFO @ Fri, 05 Jul 2019 21:35:37: 49000000 INFO @ Fri, 05 Jul 2019 21:35:41: 45000000 INFO @ Fri, 05 Jul 2019 21:35:42: 45000000 INFO @ Fri, 05 Jul 2019 21:35:45: #1 tag size is determined as 24 bps INFO @ Fri, 05 Jul 2019 21:35:45: #1 tag size = 24 INFO @ Fri, 05 Jul 2019 21:35:45: #1 total tags in treatment: 18827125 INFO @ Fri, 05 Jul 2019 21:35:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:35:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:35:45: #1 tags after filtering in treatment: 6989983 INFO @ Fri, 05 Jul 2019 21:35:45: #1 Redundant rate of treatment: 0.63 INFO @ Fri, 05 Jul 2019 21:35:45: #1 finished! INFO @ Fri, 05 Jul 2019 21:35:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:35:46: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:35:46: 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 @ Fri, 05 Jul 2019 21:35:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.10_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/SRX160483/SRX160483.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:35:50: 46000000 INFO @ Fri, 05 Jul 2019 21:35:51: 46000000 INFO @ Fri, 05 Jul 2019 21:35:59: 47000000 INFO @ Fri, 05 Jul 2019 21:36:00: 47000000 INFO @ Fri, 05 Jul 2019 21:36:08: 48000000 INFO @ Fri, 05 Jul 2019 21:36:10: 48000000 INFO @ Fri, 05 Jul 2019 21:36:18: 49000000 INFO @ Fri, 05 Jul 2019 21:36:20: 49000000 INFO @ Fri, 05 Jul 2019 21:36:25: #1 tag size is determined as 24 bps INFO @ Fri, 05 Jul 2019 21:36:25: #1 tag size = 24 INFO @ Fri, 05 Jul 2019 21:36:25: #1 total tags in treatment: 18827125 INFO @ Fri, 05 Jul 2019 21:36:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:36:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:36:26: #1 tags after filtering in treatment: 6989983 INFO @ Fri, 05 Jul 2019 21:36:26: #1 Redundant rate of treatment: 0.63 INFO @ Fri, 05 Jul 2019 21:36:26: #1 finished! INFO @ Fri, 05 Jul 2019 21:36:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:36:26: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:36:26: 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 @ Fri, 05 Jul 2019 21:36:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.20_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/SRX160483/SRX160483.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:36:28: #1 tag size is determined as 24 bps INFO @ Fri, 05 Jul 2019 21:36:28: #1 tag size = 24 INFO @ Fri, 05 Jul 2019 21:36:28: #1 total tags in treatment: 18827125 INFO @ Fri, 05 Jul 2019 21:36:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:36:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:36:28: #1 tags after filtering in treatment: 6989983 INFO @ Fri, 05 Jul 2019 21:36:28: #1 Redundant rate of treatment: 0.63 INFO @ Fri, 05 Jul 2019 21:36:28: #1 finished! INFO @ Fri, 05 Jul 2019 21:36:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:36:29: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:36:29: 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 @ Fri, 05 Jul 2019 21:36:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.05_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/SRX160483/SRX160483.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX160483/SRX160483.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling