Job ID = 2641250 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,057,728 reads read : 16,115,456 reads written : 16,115,456 spots read : 8,050,297 reads read : 16,100,594 reads written : 16,100,594 spots read : 8,334,513 reads read : 16,669,026 reads written : 16,669,026 2019-08-24T13:25:33 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 ) 2019-08-24T13:25:33 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 ) 2019-08-24T13:25:33 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 ) 2019-08-24T13:25:33 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 : 8,182,631 reads read : 16,365,262 reads written : 16,365,262 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: 00:14:33 32625169 reads; of these: 32625169 (100.00%) were paired; of these: 12110658 (37.12%) aligned concordantly 0 times 18148325 (55.63%) aligned concordantly exactly 1 time 2366186 (7.25%) aligned concordantly >1 times ---- 12110658 pairs aligned concordantly 0 times; of these: 87222 (0.72%) aligned discordantly 1 time ---- 12023436 pairs aligned 0 times concordantly or discordantly; of these: 24046872 mates make up the pairs; of these: 20067936 (83.45%) aligned 0 times 3420327 (14.22%) aligned exactly 1 time 558609 (2.32%) aligned >1 times 69.24% overall alignment rate Time searching: 00:14:33 Overall time: 00:14:33 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] 864016 / 20595799 = 0.0420 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:56:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.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 22:56:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:56:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:56:16: 1000000 INFO @ Sat, 24 Aug 2019 22:56:23: 2000000 INFO @ Sat, 24 Aug 2019 22:56:31: 3000000 INFO @ Sat, 24 Aug 2019 22:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.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 22:56:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:56:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:56:38: 4000000 INFO @ Sat, 24 Aug 2019 22:56:47: 1000000 INFO @ Sat, 24 Aug 2019 22:56:47: 5000000 INFO @ Sat, 24 Aug 2019 22:56:56: 2000000 INFO @ Sat, 24 Aug 2019 22:56:56: 6000000 INFO @ Sat, 24 Aug 2019 22:57:05: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:57:06: 7000000 INFO @ Sat, 24 Aug 2019 22:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.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 22:57:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:57:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:57:14: 1000000 INFO @ Sat, 24 Aug 2019 22:57:14: 4000000 INFO @ Sat, 24 Aug 2019 22:57:15: 8000000 INFO @ Sat, 24 Aug 2019 22:57:21: 2000000 INFO @ Sat, 24 Aug 2019 22:57:24: 5000000 INFO @ Sat, 24 Aug 2019 22:57:24: 9000000 INFO @ Sat, 24 Aug 2019 22:57:27: 3000000 INFO @ Sat, 24 Aug 2019 22:57:33: 6000000 INFO @ Sat, 24 Aug 2019 22:57:33: 10000000 INFO @ Sat, 24 Aug 2019 22:57:34: 4000000 INFO @ Sat, 24 Aug 2019 22:57:40: 5000000 INFO @ Sat, 24 Aug 2019 22:57:42: 7000000 INFO @ Sat, 24 Aug 2019 22:57:42: 11000000 INFO @ Sat, 24 Aug 2019 22:57:47: 6000000 INFO @ Sat, 24 Aug 2019 22:57:51: 8000000 INFO @ Sat, 24 Aug 2019 22:57:52: 12000000 INFO @ Sat, 24 Aug 2019 22:57:53: 7000000 INFO @ Sat, 24 Aug 2019 22:58:00: 8000000 INFO @ Sat, 24 Aug 2019 22:58:00: 9000000 INFO @ Sat, 24 Aug 2019 22:58:01: 13000000 INFO @ Sat, 24 Aug 2019 22:58:06: 9000000 INFO @ Sat, 24 Aug 2019 22:58:10: 10000000 INFO @ Sat, 24 Aug 2019 22:58:10: 14000000 INFO @ Sat, 24 Aug 2019 22:58:13: 10000000 INFO @ Sat, 24 Aug 2019 22:58:19: 11000000 INFO @ Sat, 24 Aug 2019 22:58:19: 15000000 INFO @ Sat, 24 Aug 2019 22:58:19: 11000000 INFO @ Sat, 24 Aug 2019 22:58:26: 12000000 INFO @ Sat, 24 Aug 2019 22:58:28: 12000000 INFO @ Sat, 24 Aug 2019 22:58:28: 16000000 INFO @ Sat, 24 Aug 2019 22:58:32: 13000000 INFO @ Sat, 24 Aug 2019 22:58:37: 13000000 INFO @ Sat, 24 Aug 2019 22:58:37: 17000000 INFO @ Sat, 24 Aug 2019 22:58:38: 14000000 INFO @ Sat, 24 Aug 2019 22:58:45: 15000000 INFO @ Sat, 24 Aug 2019 22:58:46: 14000000 INFO @ Sat, 24 Aug 2019 22:58:46: 18000000 INFO @ Sat, 24 Aug 2019 22:58:51: 16000000 INFO @ Sat, 24 Aug 2019 22:58:55: 15000000 INFO @ Sat, 24 Aug 2019 22:58:56: 19000000 INFO @ Sat, 24 Aug 2019 22:58:58: 17000000 INFO @ Sat, 24 Aug 2019 22:59:04: 18000000 INFO @ Sat, 24 Aug 2019 22:59:04: 16000000 INFO @ Sat, 24 Aug 2019 22:59:05: 20000000 INFO @ Sat, 24 Aug 2019 22:59:11: 19000000 INFO @ Sat, 24 Aug 2019 22:59:13: 21000000 INFO @ Sat, 24 Aug 2019 22:59:13: 17000000 INFO @ Sat, 24 Aug 2019 22:59:17: 20000000 INFO @ Sat, 24 Aug 2019 22:59:21: 22000000 INFO @ Sat, 24 Aug 2019 22:59:22: 18000000 INFO @ Sat, 24 Aug 2019 22:59:24: 21000000 INFO @ Sat, 24 Aug 2019 22:59:29: 23000000 INFO @ Sat, 24 Aug 2019 22:59:30: 22000000 INFO @ Sat, 24 Aug 2019 22:59:30: 19000000 INFO @ Sat, 24 Aug 2019 22:59:36: 23000000 INFO @ Sat, 24 Aug 2019 22:59:37: 24000000 INFO @ Sat, 24 Aug 2019 22:59:39: 20000000 INFO @ Sat, 24 Aug 2019 22:59:42: 24000000 INFO @ Sat, 24 Aug 2019 22:59:45: 25000000 INFO @ Sat, 24 Aug 2019 22:59:47: 21000000 INFO @ Sat, 24 Aug 2019 22:59:48: 25000000 INFO @ Sat, 24 Aug 2019 22:59:54: 26000000 INFO @ Sat, 24 Aug 2019 22:59:55: 26000000 INFO @ Sat, 24 Aug 2019 22:59:56: 22000000 INFO @ Sat, 24 Aug 2019 23:00:01: 27000000 INFO @ Sat, 24 Aug 2019 23:00:03: 27000000 INFO @ Sat, 24 Aug 2019 23:00:04: 23000000 INFO @ Sat, 24 Aug 2019 23:00:08: 28000000 INFO @ Sat, 24 Aug 2019 23:00:11: 28000000 INFO @ Sat, 24 Aug 2019 23:00:12: 24000000 INFO @ Sat, 24 Aug 2019 23:00:14: 29000000 INFO @ Sat, 24 Aug 2019 23:00:20: 29000000 INFO @ Sat, 24 Aug 2019 23:00:20: 30000000 INFO @ Sat, 24 Aug 2019 23:00:21: 25000000 INFO @ Sat, 24 Aug 2019 23:00:26: 31000000 INFO @ Sat, 24 Aug 2019 23:00:29: 30000000 INFO @ Sat, 24 Aug 2019 23:00:30: 26000000 INFO @ Sat, 24 Aug 2019 23:00:33: 32000000 INFO @ Sat, 24 Aug 2019 23:00:37: 31000000 INFO @ Sat, 24 Aug 2019 23:00:38: 27000000 INFO @ Sat, 24 Aug 2019 23:00:39: 33000000 INFO @ Sat, 24 Aug 2019 23:00:45: 34000000 INFO @ Sat, 24 Aug 2019 23:00:46: 32000000 INFO @ Sat, 24 Aug 2019 23:00:47: 28000000 INFO @ Sat, 24 Aug 2019 23:00:52: 35000000 INFO @ Sat, 24 Aug 2019 23:00:55: 33000000 INFO @ Sat, 24 Aug 2019 23:00:56: 29000000 INFO @ Sat, 24 Aug 2019 23:00:58: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 23:01:03: 34000000 INFO @ Sat, 24 Aug 2019 23:01:04: 37000000 INFO @ Sat, 24 Aug 2019 23:01:04: 30000000 INFO @ Sat, 24 Aug 2019 23:01:10: 38000000 INFO @ Sat, 24 Aug 2019 23:01:11: 35000000 INFO @ Sat, 24 Aug 2019 23:01:13: 31000000 INFO @ Sat, 24 Aug 2019 23:01:16: 39000000 INFO @ Sat, 24 Aug 2019 23:01:20: 36000000 INFO @ Sat, 24 Aug 2019 23:01:21: 32000000 INFO @ Sat, 24 Aug 2019 23:01:23: 40000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 23:01:29: 37000000 INFO @ Sat, 24 Aug 2019 23:01:29: 41000000 INFO @ Sat, 24 Aug 2019 23:01:30: 33000000 INFO @ Sat, 24 Aug 2019 23:01:35: 42000000 INFO @ Sat, 24 Aug 2019 23:01:37: 38000000 INFO @ Sat, 24 Aug 2019 23:01:39: 34000000 INFO @ Sat, 24 Aug 2019 23:01:42: 43000000 INFO @ Sat, 24 Aug 2019 23:01:45: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 23:01:45: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 23:01:45: #1 total tags in treatment: 19652019 INFO @ Sat, 24 Aug 2019 23:01:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 23:01:45: #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 23:01:45: 39000000 INFO @ Sat, 24 Aug 2019 23:01:45: #1 tags after filtering in treatment: 12176606 INFO @ Sat, 24 Aug 2019 23:01:45: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 24 Aug 2019 23:01:45: #1 finished! INFO @ Sat, 24 Aug 2019 23:01:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 23:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 23:01:46: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 23:01:46: 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, 24 Aug 2019 23:01:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.20_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/SRX6403226/SRX6403226.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 23:01:47: 35000000 INFO @ Sat, 24 Aug 2019 23:01:53: 40000000 INFO @ Sat, 24 Aug 2019 23:01:55: 36000000 INFO @ Sat, 24 Aug 2019 23:02:01: 41000000 INFO @ Sat, 24 Aug 2019 23:02:04: 37000000 INFO @ Sat, 24 Aug 2019 23:02:10: 42000000 INFO @ Sat, 24 Aug 2019 23:02:12: 38000000 INFO @ Sat, 24 Aug 2019 23:02:18: 43000000 INFO @ Sat, 24 Aug 2019 23:02:20: 39000000 INFO @ Sat, 24 Aug 2019 23:02:22: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 23:02:22: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 23:02:22: #1 total tags in treatment: 19652019 INFO @ Sat, 24 Aug 2019 23:02:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 23:02:22: #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 23:02:22: #1 tags after filtering in treatment: 12176606 INFO @ Sat, 24 Aug 2019 23:02:22: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 24 Aug 2019 23:02:22: #1 finished! INFO @ Sat, 24 Aug 2019 23:02:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 23:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 23:02:23: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 23:02:23: 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 23:02:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.05_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/SRX6403226/SRX6403226.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 23:02:27: 40000000 INFO @ Sat, 24 Aug 2019 23:02:34: 41000000 INFO @ Sat, 24 Aug 2019 23:02:41: 42000000 INFO @ Sat, 24 Aug 2019 23:02:48: 43000000 INFO @ Sat, 24 Aug 2019 23:02:51: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 23:02:51: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 23:02:51: #1 total tags in treatment: 19652019 INFO @ Sat, 24 Aug 2019 23:02:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 23:02:51: #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 23:02:52: #1 tags after filtering in treatment: 12176606 INFO @ Sat, 24 Aug 2019 23:02:52: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 24 Aug 2019 23:02:52: #1 finished! INFO @ Sat, 24 Aug 2019 23:02:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 23:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 23:02:53: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 23:02:53: 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 23:02:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.10_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/SRX6403226/SRX6403226.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403226/SRX6403226.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling