Job ID = 2011688 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:21:46 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 ) 2019-07-05T17:21:47 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 ) 2019-07-05T17:21:47 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 ) 2019-07-05T17:21:47 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 ) 2019-07-05T17:26:38 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 : 20,745,348 reads read : 41,490,696 reads written : 41,490,696 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: 00:30:47 20745348 reads; of these: 20745348 (100.00%) were paired; of these: 3630488 (17.50%) aligned concordantly 0 times 14196357 (68.43%) aligned concordantly exactly 1 time 2918503 (14.07%) aligned concordantly >1 times ---- 3630488 pairs aligned concordantly 0 times; of these: 1807713 (49.79%) aligned discordantly 1 time ---- 1822775 pairs aligned 0 times concordantly or discordantly; of these: 3645550 mates make up the pairs; of these: 2537153 (69.60%) aligned 0 times 299759 (8.22%) aligned exactly 1 time 808638 (22.18%) aligned >1 times 93.89% overall alignment rate Time searching: 00:30:47 Overall time: 00:30:47 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 24 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] 741094 / 18804926 = 0.0394 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 03:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.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 03:36:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:36:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:36:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.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 03:36:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:36:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.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 03:36:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:36:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:36:46: 1000000 INFO @ Sat, 06 Jul 2019 03:36:47: 1000000 INFO @ Sat, 06 Jul 2019 03:36:52: 1000000 INFO @ Sat, 06 Jul 2019 03:36:55: 2000000 INFO @ Sat, 06 Jul 2019 03:36:56: 2000000 INFO @ Sat, 06 Jul 2019 03:37:04: 3000000 INFO @ Sat, 06 Jul 2019 03:37:05: 2000000 INFO @ Sat, 06 Jul 2019 03:37:06: 3000000 INFO @ Sat, 06 Jul 2019 03:37:13: 4000000 INFO @ Sat, 06 Jul 2019 03:37:15: 4000000 INFO @ Sat, 06 Jul 2019 03:37:18: 3000000 INFO @ Sat, 06 Jul 2019 03:37:23: 5000000 INFO @ Sat, 06 Jul 2019 03:37:25: 5000000 INFO @ Sat, 06 Jul 2019 03:37:31: 4000000 INFO @ Sat, 06 Jul 2019 03:37:32: 6000000 INFO @ Sat, 06 Jul 2019 03:37:34: 6000000 INFO @ Sat, 06 Jul 2019 03:37:41: 7000000 INFO @ Sat, 06 Jul 2019 03:37:44: 7000000 INFO @ Sat, 06 Jul 2019 03:37:45: 5000000 INFO @ Sat, 06 Jul 2019 03:37:50: 8000000 INFO @ Sat, 06 Jul 2019 03:37:53: 8000000 INFO @ Sat, 06 Jul 2019 03:37:58: 6000000 INFO @ Sat, 06 Jul 2019 03:38:00: 9000000 INFO @ Sat, 06 Jul 2019 03:38:03: 9000000 INFO @ Sat, 06 Jul 2019 03:38:09: 10000000 INFO @ Sat, 06 Jul 2019 03:38:11: 7000000 INFO @ Sat, 06 Jul 2019 03:38:12: 10000000 INFO @ Sat, 06 Jul 2019 03:38:18: 11000000 INFO @ Sat, 06 Jul 2019 03:38:22: 11000000 INFO @ Sat, 06 Jul 2019 03:38:24: 8000000 INFO @ Sat, 06 Jul 2019 03:38:27: 12000000 INFO @ Sat, 06 Jul 2019 03:38:31: 12000000 INFO @ Sat, 06 Jul 2019 03:38:36: 13000000 INFO @ Sat, 06 Jul 2019 03:38:38: 9000000 INFO @ Sat, 06 Jul 2019 03:38:41: 13000000 INFO @ Sat, 06 Jul 2019 03:38:46: 14000000 INFO @ Sat, 06 Jul 2019 03:38:50: 14000000 INFO @ Sat, 06 Jul 2019 03:38:51: 10000000 INFO @ Sat, 06 Jul 2019 03:38:55: 15000000 INFO @ Sat, 06 Jul 2019 03:38:59: 15000000 INFO @ Sat, 06 Jul 2019 03:39:04: 16000000 INFO @ Sat, 06 Jul 2019 03:39:05: 11000000 INFO @ Sat, 06 Jul 2019 03:39:08: 16000000 INFO @ Sat, 06 Jul 2019 03:39:13: 17000000 INFO @ Sat, 06 Jul 2019 03:39:18: 17000000 INFO @ Sat, 06 Jul 2019 03:39:18: 12000000 INFO @ Sat, 06 Jul 2019 03:39:22: 18000000 INFO @ Sat, 06 Jul 2019 03:39:27: 18000000 INFO @ Sat, 06 Jul 2019 03:39:31: 13000000 INFO @ Sat, 06 Jul 2019 03:39:31: 19000000 INFO @ Sat, 06 Jul 2019 03:39:36: 19000000 INFO @ Sat, 06 Jul 2019 03:39:40: 20000000 INFO @ Sat, 06 Jul 2019 03:39:44: 14000000 INFO @ Sat, 06 Jul 2019 03:39:45: 20000000 INFO @ Sat, 06 Jul 2019 03:39:49: 21000000 INFO @ Sat, 06 Jul 2019 03:39:55: 21000000 INFO @ Sat, 06 Jul 2019 03:39:57: 15000000 INFO @ Sat, 06 Jul 2019 03:39:59: 22000000 INFO @ Sat, 06 Jul 2019 03:40:04: 22000000 INFO @ Sat, 06 Jul 2019 03:40:08: 23000000 INFO @ Sat, 06 Jul 2019 03:40:11: 16000000 INFO @ Sat, 06 Jul 2019 03:40:14: 23000000 INFO @ Sat, 06 Jul 2019 03:40:17: 24000000 INFO @ Sat, 06 Jul 2019 03:40:23: 24000000 INFO @ Sat, 06 Jul 2019 03:40:24: 17000000 INFO @ Sat, 06 Jul 2019 03:40:26: 25000000 INFO @ Sat, 06 Jul 2019 03:40:32: 25000000 INFO @ Sat, 06 Jul 2019 03:40:35: 26000000 INFO @ Sat, 06 Jul 2019 03:40:37: 18000000 INFO @ Sat, 06 Jul 2019 03:40:41: 26000000 INFO @ Sat, 06 Jul 2019 03:40:44: 27000000 INFO @ Sat, 06 Jul 2019 03:40:50: 27000000 INFO @ Sat, 06 Jul 2019 03:40:51: 19000000 INFO @ Sat, 06 Jul 2019 03:40:53: 28000000 INFO @ Sat, 06 Jul 2019 03:41:00: 28000000 INFO @ Sat, 06 Jul 2019 03:41:02: 29000000 INFO @ Sat, 06 Jul 2019 03:41:04: 20000000 INFO @ Sat, 06 Jul 2019 03:41:09: 29000000 INFO @ Sat, 06 Jul 2019 03:41:12: 30000000 INFO @ Sat, 06 Jul 2019 03:41:17: 21000000 INFO @ Sat, 06 Jul 2019 03:41:18: 30000000 INFO @ Sat, 06 Jul 2019 03:41:21: 31000000 INFO @ Sat, 06 Jul 2019 03:41:27: 31000000 INFO @ Sat, 06 Jul 2019 03:41:30: 32000000 INFO @ Sat, 06 Jul 2019 03:41:31: 22000000 INFO @ Sat, 06 Jul 2019 03:41:37: 32000000 INFO @ Sat, 06 Jul 2019 03:41:39: 33000000 INFO @ Sat, 06 Jul 2019 03:41:44: 23000000 INFO @ Sat, 06 Jul 2019 03:41:46: 33000000 INFO @ Sat, 06 Jul 2019 03:41:48: 34000000 INFO @ Sat, 06 Jul 2019 03:41:55: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:41:57: 35000000 INFO @ Sat, 06 Jul 2019 03:41:57: 24000000 INFO @ Sat, 06 Jul 2019 03:42:04: 35000000 INFO @ Sat, 06 Jul 2019 03:42:06: 36000000 INFO @ Sat, 06 Jul 2019 03:42:11: 25000000 INFO @ Sat, 06 Jul 2019 03:42:13: 36000000 INFO @ Sat, 06 Jul 2019 03:42:15: 37000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:42:20: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:42:20: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:42:20: #1 total tags in treatment: 16411491 INFO @ Sat, 06 Jul 2019 03:42:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:42:20: #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 03:42:20: #1 tags after filtering in treatment: 10748914 INFO @ Sat, 06 Jul 2019 03:42:20: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:42:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:42:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:42:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:42:21: 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 03:42:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.05_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/SRX4560569/SRX4560569.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:42:22: 37000000 INFO @ Sat, 06 Jul 2019 03:42:24: 26000000 INFO @ Sat, 06 Jul 2019 03:42:27: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:42:27: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:42:27: #1 total tags in treatment: 16411491 INFO @ Sat, 06 Jul 2019 03:42:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:42:27: #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 03:42:27: #1 tags after filtering in treatment: 10748914 INFO @ Sat, 06 Jul 2019 03:42:27: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:42:27: #1 finished! INFO @ Sat, 06 Jul 2019 03:42:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:42:28: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:42:28: 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 03:42:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.10_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/SRX4560569/SRX4560569.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:42:37: 27000000 INFO @ Sat, 06 Jul 2019 03:42:49: 28000000 INFO @ Sat, 06 Jul 2019 03:43:02: 29000000 INFO @ Sat, 06 Jul 2019 03:43:15: 30000000 INFO @ Sat, 06 Jul 2019 03:43:27: 31000000 INFO @ Sat, 06 Jul 2019 03:43:40: 32000000 INFO @ Sat, 06 Jul 2019 03:43:53: 33000000 INFO @ Sat, 06 Jul 2019 03:44:05: 34000000 INFO @ Sat, 06 Jul 2019 03:44:18: 35000000 INFO @ Sat, 06 Jul 2019 03:44:31: 36000000 INFO @ Sat, 06 Jul 2019 03:44:43: 37000000 INFO @ Sat, 06 Jul 2019 03:44:49: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:44:49: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:44:49: #1 total tags in treatment: 16411491 INFO @ Sat, 06 Jul 2019 03:44:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:44:49: #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 03:44:49: #1 tags after filtering in treatment: 10748914 INFO @ Sat, 06 Jul 2019 03:44:49: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:44:49: #1 finished! INFO @ Sat, 06 Jul 2019 03:44:49: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:44:50: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:44:50: 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 03:44:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.20_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/SRX4560569/SRX4560569.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560569/SRX4560569.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling