Job ID = 2010661 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:48:05 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 ) 2019-07-05T14:48:39 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 ) 2019-07-05T14:48:39 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 ) 2019-07-05T14:50:22 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 ) 2019-07-05T14:50:22 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 ) 2019-07-05T14:50:22 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 ) 2019-07-05T14:52:28 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 : 5,665,123 reads read : 11,330,246 reads written : 11,330,246 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: 00:04:01 5665123 reads; of these: 5665123 (100.00%) were paired; of these: 399848 (7.06%) aligned concordantly 0 times 5025202 (88.70%) aligned concordantly exactly 1 time 240073 (4.24%) aligned concordantly >1 times ---- 399848 pairs aligned concordantly 0 times; of these: 178460 (44.63%) aligned discordantly 1 time ---- 221388 pairs aligned 0 times concordantly or discordantly; of these: 442776 mates make up the pairs; of these: 339961 (76.78%) aligned 0 times 76141 (17.20%) aligned exactly 1 time 26674 (6.02%) aligned >1 times 97.00% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 258295 / 5432926 = 0.0475 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 00:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.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 00:01:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:01:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.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 00:01:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:01:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.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 00:01:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:01:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:01:47: 1000000 INFO @ Sat, 06 Jul 2019 00:01:49: 1000000 INFO @ Sat, 06 Jul 2019 00:01:50: 1000000 INFO @ Sat, 06 Jul 2019 00:01:55: 2000000 INFO @ Sat, 06 Jul 2019 00:01:57: 2000000 INFO @ Sat, 06 Jul 2019 00:01:58: 2000000 INFO @ Sat, 06 Jul 2019 00:02:02: 3000000 INFO @ Sat, 06 Jul 2019 00:02:05: 3000000 INFO @ Sat, 06 Jul 2019 00:02:06: 3000000 INFO @ Sat, 06 Jul 2019 00:02:09: 4000000 INFO @ Sat, 06 Jul 2019 00:02:13: 4000000 INFO @ Sat, 06 Jul 2019 00:02:14: 4000000 INFO @ Sat, 06 Jul 2019 00:02:16: 5000000 INFO @ Sat, 06 Jul 2019 00:02:21: 5000000 INFO @ Sat, 06 Jul 2019 00:02:22: 5000000 INFO @ Sat, 06 Jul 2019 00:02:23: 6000000 INFO @ Sat, 06 Jul 2019 00:02:29: 6000000 INFO @ Sat, 06 Jul 2019 00:02:30: 6000000 INFO @ Sat, 06 Jul 2019 00:02:30: 7000000 INFO @ Sat, 06 Jul 2019 00:02:37: 8000000 INFO @ Sat, 06 Jul 2019 00:02:37: 7000000 INFO @ Sat, 06 Jul 2019 00:02:38: 7000000 INFO @ Sat, 06 Jul 2019 00:02:44: 9000000 INFO @ Sat, 06 Jul 2019 00:02:45: 8000000 INFO @ Sat, 06 Jul 2019 00:02:46: 8000000 INFO @ Sat, 06 Jul 2019 00:02:51: 10000000 INFO @ Sat, 06 Jul 2019 00:02:53: 9000000 INFO @ Sat, 06 Jul 2019 00:02:53: 9000000 INFO @ Sat, 06 Jul 2019 00:02:54: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:02:54: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:02:54: #1 total tags in treatment: 5009746 INFO @ Sat, 06 Jul 2019 00:02:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:02:54: #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 00:02:54: #1 tags after filtering in treatment: 3289445 INFO @ Sat, 06 Jul 2019 00:02:54: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 00:02:54: #1 finished! INFO @ Sat, 06 Jul 2019 00:02:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:02:55: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:02:55: 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 00:02:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.05_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/SRX3865858/SRX3865858.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:03:01: 10000000 INFO @ Sat, 06 Jul 2019 00:03:01: 10000000 INFO @ Sat, 06 Jul 2019 00:03:05: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:03:05: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:03:05: #1 total tags in treatment: 5009746 INFO @ Sat, 06 Jul 2019 00:03:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:03:05: #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 00:03:05: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:03:05: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:03:05: #1 total tags in treatment: 5009746 INFO @ Sat, 06 Jul 2019 00:03:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:03:05: #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 00:03:05: #1 tags after filtering in treatment: 3289445 INFO @ Sat, 06 Jul 2019 00:03:05: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 00:03:05: #1 finished! INFO @ Sat, 06 Jul 2019 00:03:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:03:05: #1 tags after filtering in treatment: 3289445 INFO @ Sat, 06 Jul 2019 00:03:05: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 00:03:05: #1 finished! INFO @ Sat, 06 Jul 2019 00:03:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:03:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:03:05: 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 00:03:05: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:03:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:03:05: 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 00:03:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.10_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/SRX3865858/SRX3865858.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.20_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/SRX3865858/SRX3865858.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865858/SRX3865858.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。