Job ID = 2010694 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:52:30 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:52:30 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.55' 2019-07-05T14:52:30 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.24) from '172.19.7.55' 2019-07-05T14:52:30 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/006756/SRR6918480' 2019-07-05T14:52:30 fasterq-dump.2.9.6 err: invalid accession 'SRR6918480' spots read : 4,008,995 reads read : 8,017,990 reads written : 8,017,990 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: 00:02:08 4008995 reads; of these: 4008995 (100.00%) were paired; of these: 2301993 (57.42%) aligned concordantly 0 times 1371064 (34.20%) aligned concordantly exactly 1 time 335938 (8.38%) aligned concordantly >1 times ---- 2301993 pairs aligned concordantly 0 times; of these: 64628 (2.81%) aligned discordantly 1 time ---- 2237365 pairs aligned 0 times concordantly or discordantly; of these: 4474730 mates make up the pairs; of these: 2915471 (65.15%) aligned 0 times 1240404 (27.72%) aligned exactly 1 time 318855 (7.13%) aligned >1 times 63.64% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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_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] 248867 / 1771001 = 0.1405 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 23:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.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 23:59:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.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 23:59:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.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 23:59:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:00:01: 1000000 INFO @ Sat, 06 Jul 2019 00:00:04: 1000000 INFO @ Sat, 06 Jul 2019 00:00:05: 1000000 INFO @ Sat, 06 Jul 2019 00:00:07: 2000000 INFO @ Sat, 06 Jul 2019 00:00:11: 2000000 INFO @ Sat, 06 Jul 2019 00:00:13: 3000000 INFO @ Sat, 06 Jul 2019 00:00:14: 2000000 INFO @ Sat, 06 Jul 2019 00:00:19: 3000000 INFO @ Sat, 06 Jul 2019 00:00:20: 4000000 INFO @ Sat, 06 Jul 2019 00:00:22: 3000000 INFO @ Sat, 06 Jul 2019 00:00:23: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:23: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:23: #1 total tags in treatment: 1464222 INFO @ Sat, 06 Jul 2019 00:00:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:23: #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 00:00:23: #1 tags after filtering in treatment: 1112785 INFO @ Sat, 06 Jul 2019 00:00:23: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:00:23: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:24: #2 number of paired peaks: 34 WARNING @ Sat, 06 Jul 2019 00:00:24: Too few paired peaks (34) 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 00:00:24: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:00:26: 4000000 INFO @ Sat, 06 Jul 2019 00:00:30: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:30: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:30: #1 total tags in treatment: 1464222 INFO @ Sat, 06 Jul 2019 00:00:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:30: #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 00:00:30: #1 tags after filtering in treatment: 1112785 INFO @ Sat, 06 Jul 2019 00:00:30: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:00:30: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:30: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis INFO @ Sat, 06 Jul 2019 00:00:30: #2 number of paired peaks: 34 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) WARNING @ Sat, 06 Jul 2019 00:00:30: Too few paired peaks (34) 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 00:00:30: Process for pairing-model is terminated! rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.20_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/SRX3865926/SRX3865926.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:31: 4000000 INFO @ Sat, 06 Jul 2019 00:00:36: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:36: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:36: #1 total tags in treatment: 1464222 INFO @ Sat, 06 Jul 2019 00:00:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:36: #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 00:00:36: #1 tags after filtering in treatment: 1112785 INFO @ Sat, 06 Jul 2019 00:00:36: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:00:36: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:36: #2 number of paired peaks: 34 WARNING @ Sat, 06 Jul 2019 00:00:36: Too few paired peaks (34) 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 00:00:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.10_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/SRX3865926/SRX3865926.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865926/SRX3865926.10_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。