Job ID = 2010690 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:52:51 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 ) 2019-07-05T14:52:51 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 ) 2019-07-05T14:52:51 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 ) 2019-07-05T14:52:51 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 ) 2019-07-05T14:58:07 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 ) 2019-07-05T14:58:07 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 : 14,002,230 reads read : 28,004,460 reads written : 28,004,460 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: 00:07:30 14002230 reads; of these: 14002230 (100.00%) were paired; of these: 4823988 (34.45%) aligned concordantly 0 times 8634184 (61.66%) aligned concordantly exactly 1 time 544058 (3.89%) aligned concordantly >1 times ---- 4823988 pairs aligned concordantly 0 times; of these: 14142 (0.29%) aligned discordantly 1 time ---- 4809846 pairs aligned 0 times concordantly or discordantly; of these: 9619692 mates make up the pairs; of these: 5912667 (61.46%) aligned 0 times 3463145 (36.00%) aligned exactly 1 time 243880 (2.54%) aligned >1 times 78.89% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 502115 / 9191178 = 0.0546 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 00:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.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 00:14:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:14:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.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 00:14:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:14:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:14:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.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 00:14:33: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:14:33: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:14:39: 1000000 INFO @ Sat, 06 Jul 2019 00:14:40: 1000000 INFO @ Sat, 06 Jul 2019 00:14:41: 1000000 INFO @ Sat, 06 Jul 2019 00:14:47: 2000000 INFO @ Sat, 06 Jul 2019 00:14:48: 2000000 INFO @ Sat, 06 Jul 2019 00:14:49: 2000000 INFO @ Sat, 06 Jul 2019 00:14:55: 3000000 INFO @ Sat, 06 Jul 2019 00:14:56: 3000000 INFO @ Sat, 06 Jul 2019 00:14:57: 3000000 INFO @ Sat, 06 Jul 2019 00:15:03: 4000000 INFO @ Sat, 06 Jul 2019 00:15:05: 4000000 INFO @ Sat, 06 Jul 2019 00:15:05: 4000000 INFO @ Sat, 06 Jul 2019 00:15:11: 5000000 INFO @ Sat, 06 Jul 2019 00:15:13: 5000000 INFO @ Sat, 06 Jul 2019 00:15:14: 5000000 INFO @ Sat, 06 Jul 2019 00:15:20: 6000000 INFO @ Sat, 06 Jul 2019 00:15:21: 6000000 INFO @ Sat, 06 Jul 2019 00:15:22: 6000000 INFO @ Sat, 06 Jul 2019 00:15:28: 7000000 INFO @ Sat, 06 Jul 2019 00:15:29: 7000000 INFO @ Sat, 06 Jul 2019 00:15:30: 7000000 INFO @ Sat, 06 Jul 2019 00:15:36: 8000000 INFO @ Sat, 06 Jul 2019 00:15:38: 8000000 INFO @ Sat, 06 Jul 2019 00:15:38: 8000000 INFO @ Sat, 06 Jul 2019 00:15:44: 9000000 INFO @ Sat, 06 Jul 2019 00:15:46: 9000000 INFO @ Sat, 06 Jul 2019 00:15:46: 9000000 INFO @ Sat, 06 Jul 2019 00:15:52: 10000000 INFO @ Sat, 06 Jul 2019 00:15:54: 10000000 INFO @ Sat, 06 Jul 2019 00:15:55: 10000000 INFO @ Sat, 06 Jul 2019 00:16:00: 11000000 INFO @ Sat, 06 Jul 2019 00:16:02: 11000000 INFO @ Sat, 06 Jul 2019 00:16:03: 11000000 INFO @ Sat, 06 Jul 2019 00:16:08: 12000000 INFO @ Sat, 06 Jul 2019 00:16:10: 12000000 INFO @ Sat, 06 Jul 2019 00:16:11: 12000000 INFO @ Sat, 06 Jul 2019 00:16:16: 13000000 INFO @ Sat, 06 Jul 2019 00:16:18: 13000000 INFO @ Sat, 06 Jul 2019 00:16:19: 13000000 INFO @ Sat, 06 Jul 2019 00:16:24: 14000000 INFO @ Sat, 06 Jul 2019 00:16:27: 14000000 INFO @ Sat, 06 Jul 2019 00:16:27: 14000000 INFO @ Sat, 06 Jul 2019 00:16:32: 15000000 INFO @ Sat, 06 Jul 2019 00:16:35: 15000000 INFO @ Sat, 06 Jul 2019 00:16:36: 15000000 INFO @ Sat, 06 Jul 2019 00:16:40: 16000000 INFO @ Sat, 06 Jul 2019 00:16:43: 16000000 INFO @ Sat, 06 Jul 2019 00:16:44: 16000000 INFO @ Sat, 06 Jul 2019 00:16:48: 17000000 INFO @ Sat, 06 Jul 2019 00:16:51: 17000000 INFO @ Sat, 06 Jul 2019 00:16:52: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:16:56: 18000000 INFO @ Sat, 06 Jul 2019 00:16:59: 18000000 INFO @ Sat, 06 Jul 2019 00:17:00: 18000000 INFO @ Sat, 06 Jul 2019 00:17:04: 19000000 INFO @ Sat, 06 Jul 2019 00:17:08: 19000000 INFO @ Sat, 06 Jul 2019 00:17:08: 19000000 INFO @ Sat, 06 Jul 2019 00:17:12: 20000000 INFO @ Sat, 06 Jul 2019 00:17:16: 20000000 INFO @ Sat, 06 Jul 2019 00:17:17: 20000000 INFO @ Sat, 06 Jul 2019 00:17:20: 21000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:17:21: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:17:21: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:17:21: #1 total tags in treatment: 8676260 INFO @ Sat, 06 Jul 2019 00:17:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:17:21: #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 00:17:21: #1 tags after filtering in treatment: 4377515 INFO @ Sat, 06 Jul 2019 00:17:21: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 06 Jul 2019 00:17:21: #1 finished! INFO @ Sat, 06 Jul 2019 00:17:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:17:22: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:17:22: 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 00:17:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.05_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/SRX3865917/SRX3865917.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:17:24: 21000000 INFO @ Sat, 06 Jul 2019 00:17:25: 21000000 INFO @ Sat, 06 Jul 2019 00:17:25: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:17:25: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:17:25: #1 total tags in treatment: 8676260 INFO @ Sat, 06 Jul 2019 00:17:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:17:25: #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 00:17:25: #1 tags after filtering in treatment: 4377515 INFO @ Sat, 06 Jul 2019 00:17:25: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 06 Jul 2019 00:17:25: #1 finished! INFO @ Sat, 06 Jul 2019 00:17:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:17:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:17:25: 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 00:17:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.10_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 00:17:25: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:17:25: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:17:25: #1 total tags in treatment: 8676260 INFO @ Sat, 06 Jul 2019 00:17:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:17:25: #1 tags after filtering in treatment: 4377515 INFO @ Sat, 06 Jul 2019 00:17:25: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 06 Jul 2019 00:17:25: #1 finished! INFO @ Sat, 06 Jul 2019 00:17:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:17:26: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:17:26: 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 00:17:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.20_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/SRX3865917/SRX3865917.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865917/SRX3865917.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling