Job ID = 2010688 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:55:01 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 ) 2019-07-05T14:58:02 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 ) 2019-07-05T14:58:02 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 ) 2019-07-05T14:58:02 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 ) 2019-07-05T14:58:02 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 ) 2019-07-05T14:58:08 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 ) 2019-07-05T14:59:22 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 ) 2019-07-05T14:59:22 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 ) 2019-07-05T14:59:22 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 ) 2019-07-05T14:59:22 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 : 12,891,913 reads read : 25,783,826 reads written : 25,783,826 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: 00:07:42 12891913 reads; of these: 12891913 (100.00%) were paired; of these: 4882459 (37.87%) aligned concordantly 0 times 6875334 (53.33%) aligned concordantly exactly 1 time 1134120 (8.80%) aligned concordantly >1 times ---- 4882459 pairs aligned concordantly 0 times; of these: 30160 (0.62%) aligned discordantly 1 time ---- 4852299 pairs aligned 0 times concordantly or discordantly; of these: 9704598 mates make up the pairs; of these: 6143703 (63.31%) aligned 0 times 3010449 (31.02%) aligned exactly 1 time 550446 (5.67%) aligned >1 times 76.17% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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 8 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] 595675 / 8037440 = 0.0741 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 00:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.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 00:13:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:13:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.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 00:13:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:13:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.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 00:13:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:13:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:13:13: 1000000 INFO @ Sat, 06 Jul 2019 00:13:16: 1000000 INFO @ Sat, 06 Jul 2019 00:13:17: 1000000 INFO @ Sat, 06 Jul 2019 00:13:20: 2000000 INFO @ Sat, 06 Jul 2019 00:13:26: 3000000 INFO @ Sat, 06 Jul 2019 00:13:27: 2000000 INFO @ Sat, 06 Jul 2019 00:13:29: 2000000 INFO @ Sat, 06 Jul 2019 00:13:33: 4000000 INFO @ Sat, 06 Jul 2019 00:13:38: 3000000 INFO @ Sat, 06 Jul 2019 00:13:40: 5000000 INFO @ Sat, 06 Jul 2019 00:13:41: 3000000 INFO @ Sat, 06 Jul 2019 00:13:46: 6000000 INFO @ Sat, 06 Jul 2019 00:13:49: 4000000 INFO @ Sat, 06 Jul 2019 00:13:52: 4000000 INFO @ Sat, 06 Jul 2019 00:13:53: 7000000 INFO @ Sat, 06 Jul 2019 00:13:59: 5000000 INFO @ Sat, 06 Jul 2019 00:14:00: 8000000 INFO @ Sat, 06 Jul 2019 00:14:04: 5000000 INFO @ Sat, 06 Jul 2019 00:14:07: 9000000 INFO @ Sat, 06 Jul 2019 00:14:10: 6000000 INFO @ Sat, 06 Jul 2019 00:14:14: 10000000 INFO @ Sat, 06 Jul 2019 00:14:15: 6000000 INFO @ Sat, 06 Jul 2019 00:14:20: 7000000 INFO @ Sat, 06 Jul 2019 00:14:21: 11000000 INFO @ Sat, 06 Jul 2019 00:14:26: 7000000 INFO @ Sat, 06 Jul 2019 00:14:27: 12000000 INFO @ Sat, 06 Jul 2019 00:14:30: 8000000 INFO @ Sat, 06 Jul 2019 00:14:34: 13000000 INFO @ Sat, 06 Jul 2019 00:14:38: 8000000 INFO @ Sat, 06 Jul 2019 00:14:40: 14000000 INFO @ Sat, 06 Jul 2019 00:14:40: 9000000 INFO @ Sat, 06 Jul 2019 00:14:47: 15000000 INFO @ Sat, 06 Jul 2019 00:14:49: 9000000 INFO @ Sat, 06 Jul 2019 00:14:51: 10000000 INFO @ Sat, 06 Jul 2019 00:14:53: 16000000 INFO @ Sat, 06 Jul 2019 00:15:00: 10000000 INFO @ Sat, 06 Jul 2019 00:15:00: 17000000 INFO @ Sat, 06 Jul 2019 00:15:01: 11000000 INFO @ Sat, 06 Jul 2019 00:15:07: 18000000 INFO @ Sat, 06 Jul 2019 00:15:10: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:15:10: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:15:10: #1 total tags in treatment: 7414162 INFO @ Sat, 06 Jul 2019 00:15:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:15:10: #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 00:15:10: #1 tags after filtering in treatment: 4125520 INFO @ Sat, 06 Jul 2019 00:15:10: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 00:15:10: #1 finished! INFO @ Sat, 06 Jul 2019 00:15:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:15:10: #2 number of paired peaks: 3 WARNING @ Sat, 06 Jul 2019 00:15:10: Too few paired peaks (3) 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 00:15:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.20_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/SRX3865916/SRX3865916.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:15:11: 11000000 INFO @ Sat, 06 Jul 2019 00:15:12: 12000000 INFO @ Sat, 06 Jul 2019 00:15:22: 13000000 INFO @ Sat, 06 Jul 2019 00:15:23: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:15:33: 14000000 INFO @ Sat, 06 Jul 2019 00:15:35: 13000000 INFO @ Sat, 06 Jul 2019 00:15:43: 15000000 INFO @ Sat, 06 Jul 2019 00:15:47: 14000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:15:54: 16000000 INFO @ Sat, 06 Jul 2019 00:15:58: 15000000 INFO @ Sat, 06 Jul 2019 00:16:05: 17000000 INFO @ Sat, 06 Jul 2019 00:16:08: 16000000 INFO @ Sat, 06 Jul 2019 00:16:16: 18000000 INFO @ Sat, 06 Jul 2019 00:16:17: 17000000 INFO @ Sat, 06 Jul 2019 00:16:19: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:16:19: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:16:19: #1 total tags in treatment: 7414162 INFO @ Sat, 06 Jul 2019 00:16:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:16:19: #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 00:16:19: #1 tags after filtering in treatment: 4125520 INFO @ Sat, 06 Jul 2019 00:16:19: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 00:16:19: #1 finished! INFO @ Sat, 06 Jul 2019 00:16:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:16:20: #2 number of paired peaks: 3 WARNING @ Sat, 06 Jul 2019 00:16:20: Too few paired peaks (3) 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 00:16:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.10_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/SRX3865916/SRX3865916.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:16:27: 18000000 INFO @ Sat, 06 Jul 2019 00:16:31: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:16:31: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:16:31: #1 total tags in treatment: 7414162 INFO @ Sat, 06 Jul 2019 00:16:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:16:31: #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 00:16:31: #1 tags after filtering in treatment: 4125520 INFO @ Sat, 06 Jul 2019 00:16:31: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 06 Jul 2019 00:16:31: #1 finished! INFO @ Sat, 06 Jul 2019 00:16:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:16:32: #2 number of paired peaks: 3 WARNING @ Sat, 06 Jul 2019 00:16:32: Too few paired peaks (3) 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 00:16:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.05_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/SRX3865916/SRX3865916.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865916/SRX3865916.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling