Job ID = 2011862 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:57:46 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 : 24,381,890 reads read : 48,763,780 reads written : 48,763,780 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: 00:18:54 24381890 reads; of these: 24381890 (100.00%) were paired; of these: 2027836 (8.32%) aligned concordantly 0 times 18473777 (75.77%) aligned concordantly exactly 1 time 3880277 (15.91%) aligned concordantly >1 times ---- 2027836 pairs aligned concordantly 0 times; of these: 755562 (37.26%) aligned discordantly 1 time ---- 1272274 pairs aligned 0 times concordantly or discordantly; of these: 2544548 mates make up the pairs; of these: 1336399 (52.52%) aligned 0 times 703965 (27.67%) aligned exactly 1 time 504184 (19.81%) aligned >1 times 97.26% overall alignment rate Time searching: 00:18:54 Overall time: 00:18:54 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] 1376658 / 22446889 = 0.0613 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 03:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.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 03:38:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:38:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.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 03:38:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:38:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:38:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.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 03:38:57: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:38:57: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:01: 1000000 INFO @ Sat, 06 Jul 2019 03:39:05: 1000000 INFO @ Sat, 06 Jul 2019 03:39:05: 1000000 INFO @ Sat, 06 Jul 2019 03:39:07: 2000000 INFO @ Sat, 06 Jul 2019 03:39:12: 2000000 INFO @ Sat, 06 Jul 2019 03:39:14: 3000000 INFO @ Sat, 06 Jul 2019 03:39:14: 2000000 INFO @ Sat, 06 Jul 2019 03:39:19: 3000000 INFO @ Sat, 06 Jul 2019 03:39:20: 4000000 INFO @ Sat, 06 Jul 2019 03:39:23: 3000000 INFO @ Sat, 06 Jul 2019 03:39:26: 4000000 INFO @ Sat, 06 Jul 2019 03:39:27: 5000000 INFO @ Sat, 06 Jul 2019 03:39:32: 4000000 INFO @ Sat, 06 Jul 2019 03:39:33: 6000000 INFO @ Sat, 06 Jul 2019 03:39:34: 5000000 INFO @ Sat, 06 Jul 2019 03:39:39: 7000000 INFO @ Sat, 06 Jul 2019 03:39:41: 6000000 INFO @ Sat, 06 Jul 2019 03:39:42: 5000000 INFO @ Sat, 06 Jul 2019 03:39:46: 8000000 INFO @ Sat, 06 Jul 2019 03:39:48: 7000000 INFO @ Sat, 06 Jul 2019 03:39:52: 9000000 INFO @ Sat, 06 Jul 2019 03:39:53: 6000000 INFO @ Sat, 06 Jul 2019 03:39:56: 8000000 INFO @ Sat, 06 Jul 2019 03:39:58: 10000000 INFO @ Sat, 06 Jul 2019 03:40:03: 9000000 INFO @ Sat, 06 Jul 2019 03:40:03: 7000000 INFO @ Sat, 06 Jul 2019 03:40:04: 11000000 INFO @ Sat, 06 Jul 2019 03:40:10: 10000000 INFO @ Sat, 06 Jul 2019 03:40:11: 12000000 INFO @ Sat, 06 Jul 2019 03:40:14: 8000000 INFO @ Sat, 06 Jul 2019 03:40:17: 13000000 INFO @ Sat, 06 Jul 2019 03:40:17: 11000000 INFO @ Sat, 06 Jul 2019 03:40:23: 14000000 INFO @ Sat, 06 Jul 2019 03:40:24: 9000000 INFO @ Sat, 06 Jul 2019 03:40:25: 12000000 INFO @ Sat, 06 Jul 2019 03:40:30: 15000000 INFO @ Sat, 06 Jul 2019 03:40:32: 13000000 INFO @ Sat, 06 Jul 2019 03:40:35: 10000000 INFO @ Sat, 06 Jul 2019 03:40:36: 16000000 INFO @ Sat, 06 Jul 2019 03:40:39: 14000000 INFO @ Sat, 06 Jul 2019 03:40:42: 17000000 INFO @ Sat, 06 Jul 2019 03:40:45: 11000000 INFO @ Sat, 06 Jul 2019 03:40:46: 15000000 INFO @ Sat, 06 Jul 2019 03:40:49: 18000000 INFO @ Sat, 06 Jul 2019 03:40:54: 16000000 INFO @ Sat, 06 Jul 2019 03:40:55: 19000000 INFO @ Sat, 06 Jul 2019 03:40:56: 12000000 INFO @ Sat, 06 Jul 2019 03:41:01: 17000000 INFO @ Sat, 06 Jul 2019 03:41:01: 20000000 INFO @ Sat, 06 Jul 2019 03:41:07: 13000000 INFO @ Sat, 06 Jul 2019 03:41:07: 21000000 INFO @ Sat, 06 Jul 2019 03:41:08: 18000000 INFO @ Sat, 06 Jul 2019 03:41:13: 22000000 INFO @ Sat, 06 Jul 2019 03:41:15: 19000000 INFO @ Sat, 06 Jul 2019 03:41:17: 14000000 INFO @ Sat, 06 Jul 2019 03:41:20: 23000000 INFO @ Sat, 06 Jul 2019 03:41:22: 20000000 INFO @ Sat, 06 Jul 2019 03:41:26: 24000000 INFO @ Sat, 06 Jul 2019 03:41:28: 15000000 INFO @ Sat, 06 Jul 2019 03:41:30: 21000000 INFO @ Sat, 06 Jul 2019 03:41:32: 25000000 INFO @ Sat, 06 Jul 2019 03:41:37: 22000000 INFO @ Sat, 06 Jul 2019 03:41:38: 26000000 INFO @ Sat, 06 Jul 2019 03:41:39: 16000000 INFO @ Sat, 06 Jul 2019 03:41:44: 23000000 INFO @ Sat, 06 Jul 2019 03:41:45: 27000000 INFO @ Sat, 06 Jul 2019 03:41:49: 17000000 INFO @ Sat, 06 Jul 2019 03:41:51: 28000000 INFO @ Sat, 06 Jul 2019 03:41:51: 24000000 INFO @ Sat, 06 Jul 2019 03:41:57: 29000000 INFO @ Sat, 06 Jul 2019 03:41:58: 25000000 INFO @ Sat, 06 Jul 2019 03:42:00: 18000000 INFO @ Sat, 06 Jul 2019 03:42:03: 30000000 INFO @ Sat, 06 Jul 2019 03:42:05: 26000000 INFO @ Sat, 06 Jul 2019 03:42:09: 31000000 INFO @ Sat, 06 Jul 2019 03:42:11: 19000000 INFO @ Sat, 06 Jul 2019 03:42:12: 27000000 INFO @ Sat, 06 Jul 2019 03:42:16: 32000000 INFO @ Sat, 06 Jul 2019 03:42:19: 28000000 INFO @ Sat, 06 Jul 2019 03:42:21: 20000000 INFO @ Sat, 06 Jul 2019 03:42:22: 33000000 INFO @ Sat, 06 Jul 2019 03:42:27: 29000000 INFO @ Sat, 06 Jul 2019 03:42:28: 34000000 INFO @ Sat, 06 Jul 2019 03:42:32: 21000000 INFO @ Sat, 06 Jul 2019 03:42:34: 30000000 INFO @ Sat, 06 Jul 2019 03:42:34: 35000000 INFO @ Sat, 06 Jul 2019 03:42:41: 36000000 INFO @ Sat, 06 Jul 2019 03:42:41: 31000000 INFO @ Sat, 06 Jul 2019 03:42:43: 22000000 INFO @ Sat, 06 Jul 2019 03:42:47: 37000000 INFO @ Sat, 06 Jul 2019 03:42:48: 32000000 INFO @ Sat, 06 Jul 2019 03:42:53: 38000000 INFO @ Sat, 06 Jul 2019 03:42:53: 23000000 INFO @ Sat, 06 Jul 2019 03:42:55: 33000000 INFO @ Sat, 06 Jul 2019 03:42:59: 39000000 INFO @ Sat, 06 Jul 2019 03:43:02: 34000000 INFO @ Sat, 06 Jul 2019 03:43:04: 24000000 INFO @ Sat, 06 Jul 2019 03:43:05: 40000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:43:10: 35000000 INFO @ Sat, 06 Jul 2019 03:43:12: 41000000 INFO @ Sat, 06 Jul 2019 03:43:14: 25000000 INFO @ Sat, 06 Jul 2019 03:43:17: 36000000 INFO @ Sat, 06 Jul 2019 03:43:18: 42000000 INFO @ Sat, 06 Jul 2019 03:43:24: 43000000 INFO @ Sat, 06 Jul 2019 03:43:25: 26000000 INFO @ Sat, 06 Jul 2019 03:43:25: 37000000 INFO @ Sat, 06 Jul 2019 03:43:30: 44000000 INFO @ Sat, 06 Jul 2019 03:43:32: 38000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:43:34: 27000000 INFO @ Sat, 06 Jul 2019 03:43:35: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:43:35: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:43:35: #1 total tags in treatment: 20978716 INFO @ Sat, 06 Jul 2019 03:43:35: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:43:35: #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 03:43:35: #1 tags after filtering in treatment: 12168813 INFO @ Sat, 06 Jul 2019 03:43:35: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:43:35: #1 finished! INFO @ Sat, 06 Jul 2019 03:43:35: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:43:36: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:43:36: 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 03:43:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.05_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/SRX5170659/SRX5170659.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:43:39: 39000000 INFO @ Sat, 06 Jul 2019 03:43:44: 28000000 INFO @ Sat, 06 Jul 2019 03:43:46: 40000000 INFO @ Sat, 06 Jul 2019 03:43:52: 41000000 INFO @ Sat, 06 Jul 2019 03:43:53: 29000000 INFO @ Sat, 06 Jul 2019 03:43:59: 42000000 INFO @ Sat, 06 Jul 2019 03:44:03: 30000000 INFO @ Sat, 06 Jul 2019 03:44:06: 43000000 INFO @ Sat, 06 Jul 2019 03:44:12: 31000000 INFO @ Sat, 06 Jul 2019 03:44:13: 44000000 INFO @ Sat, 06 Jul 2019 03:44:18: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:44:18: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:44:18: #1 total tags in treatment: 20978716 INFO @ Sat, 06 Jul 2019 03:44:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:44:18: #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 03:44:19: #1 tags after filtering in treatment: 12168813 INFO @ Sat, 06 Jul 2019 03:44:19: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:44:19: #1 finished! INFO @ Sat, 06 Jul 2019 03:44:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:44:20: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:44:20: 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 03:44:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.20_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/SRX5170659/SRX5170659.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:44:21: 32000000 INFO @ Sat, 06 Jul 2019 03:44:30: 33000000 INFO @ Sat, 06 Jul 2019 03:44:39: 34000000 INFO @ Sat, 06 Jul 2019 03:44:48: 35000000 INFO @ Sat, 06 Jul 2019 03:44:57: 36000000 INFO @ Sat, 06 Jul 2019 03:45:06: 37000000 INFO @ Sat, 06 Jul 2019 03:45:15: 38000000 INFO @ Sat, 06 Jul 2019 03:45:24: 39000000 INFO @ Sat, 06 Jul 2019 03:45:33: 40000000 INFO @ Sat, 06 Jul 2019 03:45:42: 41000000 INFO @ Sat, 06 Jul 2019 03:45:51: 42000000 INFO @ Sat, 06 Jul 2019 03:46:00: 43000000 INFO @ Sat, 06 Jul 2019 03:46:09: 44000000 INFO @ Sat, 06 Jul 2019 03:46:15: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:46:15: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:46:15: #1 total tags in treatment: 20978716 INFO @ Sat, 06 Jul 2019 03:46:15: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:46:15: #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 03:46:15: #1 tags after filtering in treatment: 12168813 INFO @ Sat, 06 Jul 2019 03:46:15: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:46:15: #1 finished! INFO @ Sat, 06 Jul 2019 03:46:15: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:46:16: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:46:16: 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 03:46:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.10_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/SRX5170659/SRX5170659.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170659/SRX5170659.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling