Job ID = 2010705 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:06:44 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 ) 2019-07-05T15:06:44 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 ) 2019-07-05T15:06:44 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 : 9,701,572 reads read : 19,403,144 reads written : 19,403,144 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: 00:09:39 9701572 reads; of these: 9701572 (100.00%) were paired; of these: 1278290 (13.18%) aligned concordantly 0 times 7778758 (80.18%) aligned concordantly exactly 1 time 644524 (6.64%) aligned concordantly >1 times ---- 1278290 pairs aligned concordantly 0 times; of these: 121840 (9.53%) aligned discordantly 1 time ---- 1156450 pairs aligned 0 times concordantly or discordantly; of these: 2312900 mates make up the pairs; of these: 2011266 (86.96%) aligned 0 times 227689 (9.84%) aligned exactly 1 time 73945 (3.20%) aligned >1 times 89.63% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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] 104095 / 8518900 = 0.0122 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 00:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.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 00:33:26: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:33:26: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.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 00:33:27: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:33:27: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:33:36: 1000000 INFO @ Sat, 06 Jul 2019 00:33:36: 1000000 INFO @ Sat, 06 Jul 2019 00:33:45: 2000000 INFO @ Sat, 06 Jul 2019 00:33:45: 2000000 INFO @ Sat, 06 Jul 2019 00:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.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 00:33:52: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:33:52: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:33:54: 3000000 INFO @ Sat, 06 Jul 2019 00:33:54: 3000000 INFO @ Sat, 06 Jul 2019 00:34:03: 1000000 INFO @ Sat, 06 Jul 2019 00:34:03: 4000000 INFO @ Sat, 06 Jul 2019 00:34:03: 4000000 INFO @ Sat, 06 Jul 2019 00:34:13: 5000000 INFO @ Sat, 06 Jul 2019 00:34:13: 5000000 INFO @ Sat, 06 Jul 2019 00:34:14: 2000000 INFO @ Sat, 06 Jul 2019 00:34:22: 6000000 INFO @ Sat, 06 Jul 2019 00:34:23: 6000000 INFO @ Sat, 06 Jul 2019 00:34:24: 3000000 INFO @ Sat, 06 Jul 2019 00:34:32: 7000000 INFO @ Sat, 06 Jul 2019 00:34:32: 7000000 INFO @ Sat, 06 Jul 2019 00:34:35: 4000000 INFO @ Sat, 06 Jul 2019 00:34:41: 8000000 INFO @ Sat, 06 Jul 2019 00:34:42: 8000000 INFO @ Sat, 06 Jul 2019 00:34:46: 5000000 INFO @ Sat, 06 Jul 2019 00:34:51: 9000000 INFO @ Sat, 06 Jul 2019 00:34:51: 9000000 INFO @ Sat, 06 Jul 2019 00:34:57: 6000000 INFO @ Sat, 06 Jul 2019 00:35:00: 10000000 INFO @ Sat, 06 Jul 2019 00:35:00: 10000000 INFO @ Sat, 06 Jul 2019 00:35:08: 7000000 INFO @ Sat, 06 Jul 2019 00:35:10: 11000000 INFO @ Sat, 06 Jul 2019 00:35:10: 11000000 INFO @ Sat, 06 Jul 2019 00:35:18: 12000000 INFO @ Sat, 06 Jul 2019 00:35:18: 12000000 INFO @ Sat, 06 Jul 2019 00:35:18: 8000000 INFO @ Sat, 06 Jul 2019 00:35:26: 13000000 INFO @ Sat, 06 Jul 2019 00:35:27: 13000000 INFO @ Sat, 06 Jul 2019 00:35:29: 9000000 INFO @ Sat, 06 Jul 2019 00:35:35: 14000000 INFO @ Sat, 06 Jul 2019 00:35:35: 14000000 INFO @ Sat, 06 Jul 2019 00:35:40: 10000000 INFO @ Sat, 06 Jul 2019 00:35:43: 15000000 INFO @ Sat, 06 Jul 2019 00:35:43: 15000000 INFO @ Sat, 06 Jul 2019 00:35:50: 11000000 INFO @ Sat, 06 Jul 2019 00:35:51: 16000000 INFO @ Sat, 06 Jul 2019 00:35:52: 16000000 INFO @ Sat, 06 Jul 2019 00:35:59: 17000000 INFO @ Sat, 06 Jul 2019 00:36:00: 17000000 INFO @ Sat, 06 Jul 2019 00:36:01: 12000000 INFO @ Sat, 06 Jul 2019 00:36:01: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:36:01: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:36:01: #1 total tags in treatment: 8320063 INFO @ Sat, 06 Jul 2019 00:36:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:36:01: #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 00:36:01: #1 tags after filtering in treatment: 6245255 INFO @ Sat, 06 Jul 2019 00:36:01: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 00:36:01: #1 finished! INFO @ Sat, 06 Jul 2019 00:36:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:36:02: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:36:02: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:36:02: #1 total tags in treatment: 8320063 INFO @ Sat, 06 Jul 2019 00:36:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:36:02: #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 00:36:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:36:02: 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 00:36:02: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:36:02: #1 tags after filtering in treatment: 6245255 INFO @ Sat, 06 Jul 2019 00:36:02: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 00:36:02: #1 finished! INFO @ Sat, 06 Jul 2019 00:36:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:36:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:36:02: 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 00:36:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis rm: needLargeMem: trying to allocate 0 bytes (limit: 17179869184)cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.05_model.r’ : No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:36:11: 13000000 INFO @ Sat, 06 Jul 2019 00:36:21: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:36:32: 15000000 INFO @ Sat, 06 Jul 2019 00:36:43: 16000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:36:53: 17000000 INFO @ Sat, 06 Jul 2019 00:36:55: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:36:55: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:36:55: #1 total tags in treatment: 8320063 INFO @ Sat, 06 Jul 2019 00:36:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:36:55: #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 00:36:55: #1 tags after filtering in treatment: 6245255 INFO @ Sat, 06 Jul 2019 00:36:55: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 00:36:55: #1 finished! INFO @ Sat, 06 Jul 2019 00:36:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:36:55: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:36:55: 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 00:36:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.20_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/SRX386886/SRX386886.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386886/SRX386886.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling