Job ID = 2011684 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:12:49 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 ) 2019-07-05T17:23:13 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 ) 2019-07-05T17:23:57 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 : 23,426,783 reads read : 46,853,566 reads written : 46,853,566 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: 00:40:22 23426783 reads; of these: 23426783 (100.00%) were paired; of these: 4409446 (18.82%) aligned concordantly 0 times 16111680 (68.77%) aligned concordantly exactly 1 time 2905657 (12.40%) aligned concordantly >1 times ---- 4409446 pairs aligned concordantly 0 times; of these: 2212938 (50.19%) aligned discordantly 1 time ---- 2196508 pairs aligned 0 times concordantly or discordantly; of these: 4393016 mates make up the pairs; of these: 3150903 (71.73%) aligned 0 times 379143 (8.63%) aligned exactly 1 time 862970 (19.64%) aligned >1 times 93.27% overall alignment rate Time searching: 00:40:22 Overall time: 00:40:22 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 28 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] 701269 / 21087648 = 0.0333 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 03:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.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 03:53:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:53:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.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 03:53:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:53:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.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 03:53:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:53:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:53:16: 1000000 INFO @ Sat, 06 Jul 2019 03:53:16: 1000000 INFO @ Sat, 06 Jul 2019 03:53:19: 1000000 INFO @ Sat, 06 Jul 2019 03:53:25: 2000000 INFO @ Sat, 06 Jul 2019 03:53:27: 2000000 INFO @ Sat, 06 Jul 2019 03:53:34: 2000000 INFO @ Sat, 06 Jul 2019 03:53:34: 3000000 INFO @ Sat, 06 Jul 2019 03:53:37: 3000000 INFO @ Sat, 06 Jul 2019 03:53:43: 4000000 INFO @ Sat, 06 Jul 2019 03:53:48: 4000000 INFO @ Sat, 06 Jul 2019 03:53:48: 3000000 INFO @ Sat, 06 Jul 2019 03:53:53: 5000000 INFO @ Sat, 06 Jul 2019 03:53:58: 5000000 INFO @ Sat, 06 Jul 2019 03:54:02: 6000000 INFO @ Sat, 06 Jul 2019 03:54:03: 4000000 INFO @ Sat, 06 Jul 2019 03:54:09: 6000000 INFO @ Sat, 06 Jul 2019 03:54:11: 7000000 INFO @ Sat, 06 Jul 2019 03:54:17: 5000000 INFO @ Sat, 06 Jul 2019 03:54:19: 7000000 INFO @ Sat, 06 Jul 2019 03:54:20: 8000000 INFO @ Sat, 06 Jul 2019 03:54:29: 9000000 INFO @ Sat, 06 Jul 2019 03:54:29: 8000000 INFO @ Sat, 06 Jul 2019 03:54:32: 6000000 INFO @ Sat, 06 Jul 2019 03:54:37: 10000000 INFO @ Sat, 06 Jul 2019 03:54:40: 9000000 INFO @ Sat, 06 Jul 2019 03:54:46: 7000000 INFO @ Sat, 06 Jul 2019 03:54:46: 11000000 INFO @ Sat, 06 Jul 2019 03:54:50: 10000000 INFO @ Sat, 06 Jul 2019 03:54:55: 12000000 INFO @ Sat, 06 Jul 2019 03:55:00: 11000000 INFO @ Sat, 06 Jul 2019 03:55:00: 8000000 INFO @ Sat, 06 Jul 2019 03:55:04: 13000000 INFO @ Sat, 06 Jul 2019 03:55:10: 12000000 INFO @ Sat, 06 Jul 2019 03:55:13: 14000000 INFO @ Sat, 06 Jul 2019 03:55:14: 9000000 INFO @ Sat, 06 Jul 2019 03:55:21: 13000000 INFO @ Sat, 06 Jul 2019 03:55:22: 15000000 INFO @ Sat, 06 Jul 2019 03:55:28: 10000000 INFO @ Sat, 06 Jul 2019 03:55:31: 14000000 INFO @ Sat, 06 Jul 2019 03:55:31: 16000000 INFO @ Sat, 06 Jul 2019 03:55:40: 17000000 INFO @ Sat, 06 Jul 2019 03:55:41: 15000000 INFO @ Sat, 06 Jul 2019 03:55:42: 11000000 INFO @ Sat, 06 Jul 2019 03:55:49: 18000000 INFO @ Sat, 06 Jul 2019 03:55:51: 16000000 INFO @ Sat, 06 Jul 2019 03:55:57: 12000000 INFO @ Sat, 06 Jul 2019 03:55:58: 19000000 INFO @ Sat, 06 Jul 2019 03:56:01: 17000000 INFO @ Sat, 06 Jul 2019 03:56:07: 20000000 INFO @ Sat, 06 Jul 2019 03:56:11: 13000000 INFO @ Sat, 06 Jul 2019 03:56:12: 18000000 INFO @ Sat, 06 Jul 2019 03:56:16: 21000000 INFO @ Sat, 06 Jul 2019 03:56:22: 19000000 INFO @ Sat, 06 Jul 2019 03:56:25: 14000000 INFO @ Sat, 06 Jul 2019 03:56:25: 22000000 INFO @ Sat, 06 Jul 2019 03:56:32: 20000000 INFO @ Sat, 06 Jul 2019 03:56:34: 23000000 INFO @ Sat, 06 Jul 2019 03:56:38: 15000000 INFO @ Sat, 06 Jul 2019 03:56:42: 21000000 INFO @ Sat, 06 Jul 2019 03:56:42: 24000000 INFO @ Sat, 06 Jul 2019 03:56:51: 25000000 INFO @ Sat, 06 Jul 2019 03:56:52: 16000000 INFO @ Sat, 06 Jul 2019 03:56:52: 22000000 INFO @ Sat, 06 Jul 2019 03:57:00: 26000000 INFO @ Sat, 06 Jul 2019 03:57:02: 23000000 INFO @ Sat, 06 Jul 2019 03:57:04: 17000000 INFO @ Sat, 06 Jul 2019 03:57:09: 27000000 INFO @ Sat, 06 Jul 2019 03:57:12: 24000000 INFO @ Sat, 06 Jul 2019 03:57:15: 18000000 INFO @ Sat, 06 Jul 2019 03:57:18: 28000000 INFO @ Sat, 06 Jul 2019 03:57:22: 25000000 INFO @ Sat, 06 Jul 2019 03:57:27: 29000000 INFO @ Sat, 06 Jul 2019 03:57:27: 19000000 INFO @ Sat, 06 Jul 2019 03:57:32: 26000000 INFO @ Sat, 06 Jul 2019 03:57:35: 30000000 INFO @ Sat, 06 Jul 2019 03:57:39: 20000000 INFO @ Sat, 06 Jul 2019 03:57:42: 27000000 INFO @ Sat, 06 Jul 2019 03:57:44: 31000000 INFO @ Sat, 06 Jul 2019 03:57:51: 21000000 INFO @ Sat, 06 Jul 2019 03:57:52: 28000000 INFO @ Sat, 06 Jul 2019 03:57:53: 32000000 INFO @ Sat, 06 Jul 2019 03:58:01: 29000000 INFO @ Sat, 06 Jul 2019 03:58:02: 33000000 INFO @ Sat, 06 Jul 2019 03:58:03: 22000000 INFO @ Sat, 06 Jul 2019 03:58:11: 34000000 INFO @ Sat, 06 Jul 2019 03:58:11: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:58:14: 23000000 INFO @ Sat, 06 Jul 2019 03:58:19: 35000000 INFO @ Sat, 06 Jul 2019 03:58:21: 31000000 INFO @ Sat, 06 Jul 2019 03:58:26: 24000000 INFO @ Sat, 06 Jul 2019 03:58:28: 36000000 INFO @ Sat, 06 Jul 2019 03:58:31: 32000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:58:37: 37000000 INFO @ Sat, 06 Jul 2019 03:58:38: 25000000 INFO @ Sat, 06 Jul 2019 03:58:41: 33000000 INFO @ Sat, 06 Jul 2019 03:58:46: 38000000 INFO @ Sat, 06 Jul 2019 03:58:50: 26000000 INFO @ Sat, 06 Jul 2019 03:58:51: 34000000 INFO @ Sat, 06 Jul 2019 03:58:54: 39000000 INFO @ Sat, 06 Jul 2019 03:59:01: 35000000 INFO @ Sat, 06 Jul 2019 03:59:03: 27000000 INFO @ Sat, 06 Jul 2019 03:59:03: 40000000 INFO @ Sat, 06 Jul 2019 03:59:11: 36000000 INFO @ Sat, 06 Jul 2019 03:59:12: 41000000 INFO @ Sat, 06 Jul 2019 03:59:15: 28000000 INFO @ Sat, 06 Jul 2019 03:59:20: 37000000 INFO @ Sat, 06 Jul 2019 03:59:21: 42000000 INFO @ Sat, 06 Jul 2019 03:59:24: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:59:24: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:59:24: #1 total tags in treatment: 18368229 INFO @ Sat, 06 Jul 2019 03:59:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:59:24: #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 03:59:24: #1 tags after filtering in treatment: 11512080 INFO @ Sat, 06 Jul 2019 03:59:24: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:59:24: #1 finished! INFO @ Sat, 06 Jul 2019 03:59:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:59:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:59:25: 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 03:59:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.20_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/SRX4560565/SRX4560565.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:59:27: 29000000 INFO @ Sat, 06 Jul 2019 03:59:30: 38000000 INFO @ Sat, 06 Jul 2019 03:59:39: 30000000 INFO @ Sat, 06 Jul 2019 03:59:40: 39000000 INFO @ Sat, 06 Jul 2019 03:59:50: 40000000 INFO @ Sat, 06 Jul 2019 03:59:50: 31000000 INFO @ Sat, 06 Jul 2019 03:59:59: 41000000 INFO @ Sat, 06 Jul 2019 04:00:02: 32000000 INFO @ Sat, 06 Jul 2019 04:00:09: 42000000 INFO @ Sat, 06 Jul 2019 04:00:12: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 04:00:12: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 04:00:12: #1 total tags in treatment: 18368229 INFO @ Sat, 06 Jul 2019 04:00:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:00:12: #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 04:00:13: #1 tags after filtering in treatment: 11512080 INFO @ Sat, 06 Jul 2019 04:00:13: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 04:00:13: #1 finished! INFO @ Sat, 06 Jul 2019 04:00:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:00:14: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:00:14: 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 04:00:14: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 04:00:14: 33000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.10_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/SRX4560565/SRX4560565.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:00:25: 34000000 INFO @ Sat, 06 Jul 2019 04:00:37: 35000000 INFO @ Sat, 06 Jul 2019 04:00:48: 36000000 INFO @ Sat, 06 Jul 2019 04:01:00: 37000000 INFO @ Sat, 06 Jul 2019 04:01:11: 38000000 INFO @ Sat, 06 Jul 2019 04:01:23: 39000000 INFO @ Sat, 06 Jul 2019 04:01:34: 40000000 INFO @ Sat, 06 Jul 2019 04:01:45: 41000000 INFO @ Sat, 06 Jul 2019 04:01:57: 42000000 INFO @ Sat, 06 Jul 2019 04:02:01: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 04:02:01: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 04:02:01: #1 total tags in treatment: 18368229 INFO @ Sat, 06 Jul 2019 04:02:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:02:01: #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 04:02:01: #1 tags after filtering in treatment: 11512080 INFO @ Sat, 06 Jul 2019 04:02:01: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 04:02:01: #1 finished! INFO @ Sat, 06 Jul 2019 04:02:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:02:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:02:02: 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 04:02:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.05_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/SRX4560565/SRX4560565.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560565/SRX4560565.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling