Job ID = 2008182 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:35:43 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 ) 2019-07-05T08:35:43 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 ) 2019-07-05T08:35:43 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 ) 2019-07-05T08:35:43 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 : 14,101,055 reads read : 28,202,110 reads written : 28,202,110 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629058.sra.cache’: 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: 00:13:30 14101055 reads; of these: 14101055 (100.00%) were paired; of these: 4167295 (29.55%) aligned concordantly 0 times 9155623 (64.93%) aligned concordantly exactly 1 time 778137 (5.52%) aligned concordantly >1 times ---- 4167295 pairs aligned concordantly 0 times; of these: 162467 (3.90%) aligned discordantly 1 time ---- 4004828 pairs aligned 0 times concordantly or discordantly; of these: 8009656 mates make up the pairs; of these: 7901039 (98.64%) aligned 0 times 75536 (0.94%) aligned exactly 1 time 33081 (0.41%) aligned >1 times 71.98% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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 12 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] 5029997 / 10065967 = 0.4997 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 @ Fri, 05 Jul 2019 17:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.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 @ Fri, 05 Jul 2019 17:59:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:59:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.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 @ Fri, 05 Jul 2019 17:59:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:59:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:59:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.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 @ Fri, 05 Jul 2019 17:59:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:59:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:00:00: 1000000 INFO @ Fri, 05 Jul 2019 18:00:00: 1000000 INFO @ Fri, 05 Jul 2019 18:00:00: 1000000 INFO @ Fri, 05 Jul 2019 18:00:09: 2000000 INFO @ Fri, 05 Jul 2019 18:00:12: 2000000 INFO @ Fri, 05 Jul 2019 18:00:12: 2000000 INFO @ Fri, 05 Jul 2019 18:00:23: 3000000 INFO @ Fri, 05 Jul 2019 18:00:28: 3000000 INFO @ Fri, 05 Jul 2019 18:00:30: 3000000 INFO @ Fri, 05 Jul 2019 18:00:34: 4000000 INFO @ Fri, 05 Jul 2019 18:00:38: 4000000 INFO @ Fri, 05 Jul 2019 18:00:42: 4000000 INFO @ Fri, 05 Jul 2019 18:00:44: 5000000 INFO @ Fri, 05 Jul 2019 18:00:50: 5000000 INFO @ Fri, 05 Jul 2019 18:00:53: 6000000 INFO @ Fri, 05 Jul 2019 18:00:53: 5000000 INFO @ Fri, 05 Jul 2019 18:01:00: 6000000 INFO @ Fri, 05 Jul 2019 18:01:04: 7000000 INFO @ Fri, 05 Jul 2019 18:01:06: 6000000 INFO @ Fri, 05 Jul 2019 18:01:11: 7000000 INFO @ Fri, 05 Jul 2019 18:01:13: 8000000 INFO @ Fri, 05 Jul 2019 18:01:18: 7000000 INFO @ Fri, 05 Jul 2019 18:01:19: 8000000 INFO @ Fri, 05 Jul 2019 18:01:23: 9000000 INFO @ Fri, 05 Jul 2019 18:01:27: 9000000 INFO @ Fri, 05 Jul 2019 18:01:29: 8000000 INFO @ Fri, 05 Jul 2019 18:01:32: 10000000 INFO @ Fri, 05 Jul 2019 18:01:36: 10000000 INFO @ Fri, 05 Jul 2019 18:01:39: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:01:39: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:01:39: #1 total tags in treatment: 4945284 INFO @ Fri, 05 Jul 2019 18:01:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:01:39: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:01:39: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:01:39: #1 total tags in treatment: 4945284 INFO @ Fri, 05 Jul 2019 18:01:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:01:39: #1 tags after filtering in treatment: 2953352 INFO @ Fri, 05 Jul 2019 18:01:39: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 18:01:39: #1 finished! INFO @ Fri, 05 Jul 2019 18:01:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:01:39: #1 tags after filtering in treatment: 2953352 INFO @ Fri, 05 Jul 2019 18:01:39: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 18:01:39: #1 finished! INFO @ Fri, 05 Jul 2019 18:01:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:01:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:01:39: 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 @ Fri, 05 Jul 2019 18:01:39: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:01:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:01:39: 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 @ Fri, 05 Jul 2019 18:01:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.05_model.r’: No such file or directoryrm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:01:41: 9000000 INFO @ Fri, 05 Jul 2019 18:01:52: 10000000 INFO @ Fri, 05 Jul 2019 18:01:55: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:01:55: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:01:55: #1 total tags in treatment: 4945284 INFO @ Fri, 05 Jul 2019 18:01:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:01:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:01:55: #1 tags after filtering in treatment: 2953352 INFO @ Fri, 05 Jul 2019 18:01:55: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 18:01:55: #1 finished! INFO @ Fri, 05 Jul 2019 18:01:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:01:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:01:55: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:01:55: 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 @ Fri, 05 Jul 2019 18:01:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.10_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/ERX585717/ERX585717.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585717/ERX585717.10_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。