Job ID = 2009847 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T11:10:16 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 : 16,000,000 reads read : 32,000,000 reads written : 32,000,000 2019-07-05T11:13:31 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 ) 2019-07-05T11:13:31 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 : 2,858,665 reads read : 5,717,330 reads written : 5,717,330 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR583969.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR583970.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: 00:24:33 18858665 reads; of these: 18858665 (100.00%) were paired; of these: 5943920 (31.52%) aligned concordantly 0 times 12062243 (63.96%) aligned concordantly exactly 1 time 852502 (4.52%) aligned concordantly >1 times ---- 5943920 pairs aligned concordantly 0 times; of these: 2477099 (41.67%) aligned discordantly 1 time ---- 3466821 pairs aligned 0 times concordantly or discordantly; of these: 6933642 mates make up the pairs; of these: 4866972 (70.19%) aligned 0 times 1660552 (23.95%) aligned exactly 1 time 406118 (5.86%) aligned >1 times 87.10% overall alignment rate Time searching: 00:24:33 Overall time: 00:24:33 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 16 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] 3381035 / 15091710 = 0.2240 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 21:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.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 21:03:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.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 21:03:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.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 21:03:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:27: 1000000 INFO @ Fri, 05 Jul 2019 21:03:28: 1000000 INFO @ Fri, 05 Jul 2019 21:03:28: 1000000 INFO @ Fri, 05 Jul 2019 21:03:37: 2000000 INFO @ Fri, 05 Jul 2019 21:03:37: 2000000 INFO @ Fri, 05 Jul 2019 21:03:39: 2000000 INFO @ Fri, 05 Jul 2019 21:03:47: 3000000 INFO @ Fri, 05 Jul 2019 21:03:47: 3000000 INFO @ Fri, 05 Jul 2019 21:03:50: 3000000 INFO @ Fri, 05 Jul 2019 21:03:56: 4000000 INFO @ Fri, 05 Jul 2019 21:03:56: 4000000 INFO @ Fri, 05 Jul 2019 21:04:01: 4000000 INFO @ Fri, 05 Jul 2019 21:04:05: 5000000 INFO @ Fri, 05 Jul 2019 21:04:06: 5000000 INFO @ Fri, 05 Jul 2019 21:04:11: 5000000 INFO @ Fri, 05 Jul 2019 21:04:14: 6000000 INFO @ Fri, 05 Jul 2019 21:04:15: 6000000 INFO @ Fri, 05 Jul 2019 21:04:22: 6000000 INFO @ Fri, 05 Jul 2019 21:04:23: 7000000 INFO @ Fri, 05 Jul 2019 21:04:24: 7000000 INFO @ Fri, 05 Jul 2019 21:04:32: 8000000 INFO @ Fri, 05 Jul 2019 21:04:33: 7000000 INFO @ Fri, 05 Jul 2019 21:04:34: 8000000 INFO @ Fri, 05 Jul 2019 21:04:42: 9000000 INFO @ Fri, 05 Jul 2019 21:04:43: 9000000 INFO @ Fri, 05 Jul 2019 21:04:43: 8000000 INFO @ Fri, 05 Jul 2019 21:04:51: 10000000 INFO @ Fri, 05 Jul 2019 21:04:52: 10000000 INFO @ Fri, 05 Jul 2019 21:04:54: 9000000 INFO @ Fri, 05 Jul 2019 21:05:00: 11000000 INFO @ Fri, 05 Jul 2019 21:05:01: 11000000 INFO @ Fri, 05 Jul 2019 21:05:05: 10000000 INFO @ Fri, 05 Jul 2019 21:05:09: 12000000 INFO @ Fri, 05 Jul 2019 21:05:11: 12000000 INFO @ Fri, 05 Jul 2019 21:05:16: 11000000 INFO @ Fri, 05 Jul 2019 21:05:18: 13000000 INFO @ Fri, 05 Jul 2019 21:05:20: 13000000 INFO @ Fri, 05 Jul 2019 21:05:27: 12000000 INFO @ Fri, 05 Jul 2019 21:05:27: 14000000 INFO @ Fri, 05 Jul 2019 21:05:29: 14000000 INFO @ Fri, 05 Jul 2019 21:05:36: 15000000 INFO @ Fri, 05 Jul 2019 21:05:37: 13000000 INFO @ Fri, 05 Jul 2019 21:05:38: 15000000 INFO @ Fri, 05 Jul 2019 21:05:46: 16000000 INFO @ Fri, 05 Jul 2019 21:05:48: 16000000 INFO @ Fri, 05 Jul 2019 21:05:48: 14000000 INFO @ Fri, 05 Jul 2019 21:05:55: 17000000 INFO @ Fri, 05 Jul 2019 21:05:57: 17000000 INFO @ Fri, 05 Jul 2019 21:05:59: 15000000 INFO @ Fri, 05 Jul 2019 21:06:04: 18000000 INFO @ Fri, 05 Jul 2019 21:06:06: 18000000 INFO @ Fri, 05 Jul 2019 21:06:10: 16000000 INFO @ Fri, 05 Jul 2019 21:06:13: 19000000 INFO @ Fri, 05 Jul 2019 21:06:15: 19000000 INFO @ Fri, 05 Jul 2019 21:06:21: 17000000 INFO @ Fri, 05 Jul 2019 21:06:21: 20000000 INFO @ Fri, 05 Jul 2019 21:06:23: 20000000 INFO @ Fri, 05 Jul 2019 21:06:30: 21000000 INFO @ Fri, 05 Jul 2019 21:06:32: 18000000 INFO @ Fri, 05 Jul 2019 21:06:32: 21000000 INFO @ Fri, 05 Jul 2019 21:06:39: 22000000 INFO @ Fri, 05 Jul 2019 21:06:41: 22000000 INFO @ Fri, 05 Jul 2019 21:06:42: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:06:47: 23000000 INFO @ Fri, 05 Jul 2019 21:06:50: 23000000 INFO @ Fri, 05 Jul 2019 21:06:52: 20000000 INFO @ Fri, 05 Jul 2019 21:06:56: 24000000 INFO @ Fri, 05 Jul 2019 21:06:58: 24000000 INFO @ Fri, 05 Jul 2019 21:07:03: 21000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:07:04: 25000000 INFO @ Fri, 05 Jul 2019 21:07:07: 25000000 INFO @ Fri, 05 Jul 2019 21:07:13: 22000000 INFO @ Fri, 05 Jul 2019 21:07:13: 26000000 INFO @ Fri, 05 Jul 2019 21:07:14: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:07:14: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:07:14: #1 total tags in treatment: 9976260 INFO @ Fri, 05 Jul 2019 21:07:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:07:14: #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 21:07:15: #1 tags after filtering in treatment: 4494615 INFO @ Fri, 05 Jul 2019 21:07:15: #1 Redundant rate of treatment: 0.55 INFO @ Fri, 05 Jul 2019 21:07:15: #1 finished! INFO @ Fri, 05 Jul 2019 21:07:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:07:15: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:07:15: 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 21:07:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.20_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/SRX193164/SRX193164.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:07:16: 26000000 INFO @ Fri, 05 Jul 2019 21:07:17: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:07:17: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:07:17: #1 total tags in treatment: 9976260 INFO @ Fri, 05 Jul 2019 21:07:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:07:17: #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 21:07:17: #1 tags after filtering in treatment: 4494615 INFO @ Fri, 05 Jul 2019 21:07:17: #1 Redundant rate of treatment: 0.55 INFO @ Fri, 05 Jul 2019 21:07:17: #1 finished! INFO @ Fri, 05 Jul 2019 21:07:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:07:17: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:07:17: 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 21:07:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.10_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/SRX193164/SRX193164.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:07:23: 23000000 INFO @ Fri, 05 Jul 2019 21:07:33: 24000000 INFO @ Fri, 05 Jul 2019 21:07:42: 25000000 INFO @ Fri, 05 Jul 2019 21:07:53: 26000000 INFO @ Fri, 05 Jul 2019 21:07:54: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:07:54: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:07:54: #1 total tags in treatment: 9976260 INFO @ Fri, 05 Jul 2019 21:07:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:07:54: #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 21:07:54: #1 tags after filtering in treatment: 4494615 INFO @ Fri, 05 Jul 2019 21:07:54: #1 Redundant rate of treatment: 0.55 INFO @ Fri, 05 Jul 2019 21:07:54: #1 finished! INFO @ Fri, 05 Jul 2019 21:07:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:07:54: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:07:54: 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 21:07:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 383 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193164/SRX193164.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling