Job ID = 2010655 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:46:44 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 ) 2019-07-05T14:46:44 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 ) 2019-07-05T14:47:56 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 ) 2019-07-05T14:48:39 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 ) spots read : 7,305,699 reads read : 14,611,398 reads written : 14,611,398 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: 00:05:06 7305699 reads; of these: 7305699 (100.00%) were paired; of these: 533607 (7.30%) aligned concordantly 0 times 6433317 (88.06%) aligned concordantly exactly 1 time 338775 (4.64%) aligned concordantly >1 times ---- 533607 pairs aligned concordantly 0 times; of these: 151787 (28.45%) aligned discordantly 1 time ---- 381820 pairs aligned 0 times concordantly or discordantly; of these: 763640 mates make up the pairs; of these: 640503 (83.87%) aligned 0 times 96816 (12.68%) aligned exactly 1 time 26321 (3.45%) aligned >1 times 95.62% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 277259 / 6876419 = 0.0403 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 00:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.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 00:04:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.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 00:04:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.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 00:04:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:26: 1000000 INFO @ Sat, 06 Jul 2019 00:04:27: 1000000 INFO @ Sat, 06 Jul 2019 00:04:27: 1000000 INFO @ Sat, 06 Jul 2019 00:04:32: 2000000 INFO @ Sat, 06 Jul 2019 00:04:34: 2000000 INFO @ Sat, 06 Jul 2019 00:04:36: 2000000 INFO @ Sat, 06 Jul 2019 00:04:39: 3000000 INFO @ Sat, 06 Jul 2019 00:04:41: 3000000 INFO @ Sat, 06 Jul 2019 00:04:45: 4000000 INFO @ Sat, 06 Jul 2019 00:04:46: 3000000 INFO @ Sat, 06 Jul 2019 00:04:49: 4000000 INFO @ Sat, 06 Jul 2019 00:04:52: 5000000 INFO @ Sat, 06 Jul 2019 00:04:55: 4000000 INFO @ Sat, 06 Jul 2019 00:04:56: 5000000 INFO @ Sat, 06 Jul 2019 00:04:59: 6000000 INFO @ Sat, 06 Jul 2019 00:05:03: 6000000 INFO @ Sat, 06 Jul 2019 00:05:04: 5000000 INFO @ Sat, 06 Jul 2019 00:05:05: 7000000 INFO @ Sat, 06 Jul 2019 00:05:11: 7000000 INFO @ Sat, 06 Jul 2019 00:05:11: 8000000 INFO @ Sat, 06 Jul 2019 00:05:13: 6000000 INFO @ Sat, 06 Jul 2019 00:05:18: 8000000 INFO @ Sat, 06 Jul 2019 00:05:18: 9000000 INFO @ Sat, 06 Jul 2019 00:05:22: 7000000 INFO @ Sat, 06 Jul 2019 00:05:24: 10000000 INFO @ Sat, 06 Jul 2019 00:05:25: 9000000 INFO @ Sat, 06 Jul 2019 00:05:31: 11000000 INFO @ Sat, 06 Jul 2019 00:05:31: 8000000 INFO @ Sat, 06 Jul 2019 00:05:32: 10000000 INFO @ Sat, 06 Jul 2019 00:05:38: 12000000 INFO @ Sat, 06 Jul 2019 00:05:39: 11000000 INFO @ Sat, 06 Jul 2019 00:05:41: 9000000 INFO @ Sat, 06 Jul 2019 00:05:44: 13000000 INFO @ Sat, 06 Jul 2019 00:05:46: 12000000 INFO @ Sat, 06 Jul 2019 00:05:47: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:05:47: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:05:47: #1 total tags in treatment: 6495187 INFO @ Sat, 06 Jul 2019 00:05:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:47: #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 00:05:47: #1 tags after filtering in treatment: 4089826 INFO @ Sat, 06 Jul 2019 00:05:47: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 00:05:47: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:05:47: 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 00:05:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.10_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/SRX3865847/SRX3865847.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:05:50: 10000000 INFO @ Sat, 06 Jul 2019 00:05:53: 13000000 INFO @ Sat, 06 Jul 2019 00:05:56: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:05:56: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:05:56: #1 total tags in treatment: 6495187 INFO @ Sat, 06 Jul 2019 00:05:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:56: #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 00:05:56: #1 tags after filtering in treatment: 4089826 INFO @ Sat, 06 Jul 2019 00:05:56: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 00:05:56: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:05:57: 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 00:05:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.20_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/SRX3865847/SRX3865847.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:05:58: 11000000 INFO @ Sat, 06 Jul 2019 00:06:05: 12000000 INFO @ Sat, 06 Jul 2019 00:06:12: 13000000 INFO @ Sat, 06 Jul 2019 00:06:15: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:06:15: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:06:15: #1 total tags in treatment: 6495187 INFO @ Sat, 06 Jul 2019 00:06:15: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:06:15: #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 00:06:15: #1 tags after filtering in treatment: 4089826 INFO @ Sat, 06 Jul 2019 00:06:15: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 00:06:15: #1 finished! INFO @ Sat, 06 Jul 2019 00:06:15: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:06:16: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:06:16: 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 00:06:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.05_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/SRX3865847/SRX3865847.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865847/SRX3865847.05_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。