Job ID = 2640982 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:09:06 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 ) 2019-08-24T11:09:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.43' 2019-08-24T11:09:06 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' (130.14.250.26) from '172.19.7.43' 2019-08-24T11:09:06 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/sra72/SRR/007919/SRR8109512' 2019-08-24T11:09:06 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 ) 2019-08-24T11:09:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.43' 2019-08-24T11:09:06 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' (130.14.250.26) from '172.19.7.43' 2019-08-24T11:09:06 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/sra72/SRR/007919/SRR8109512' 2019-08-24T11:09:19 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8109512' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-08-24T11:09:19 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-08-24T11:09:19 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8109512' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-08-24T11:09:19 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 9,904,401 reads read : 19,808,802 reads written : 19,808,802 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: 00:12:14 9904401 reads; of these: 9904401 (100.00%) were paired; of these: 1080483 (10.91%) aligned concordantly 0 times 8084992 (81.63%) aligned concordantly exactly 1 time 738926 (7.46%) aligned concordantly >1 times ---- 1080483 pairs aligned concordantly 0 times; of these: 172095 (15.93%) aligned discordantly 1 time ---- 908388 pairs aligned 0 times concordantly or discordantly; of these: 1816776 mates make up the pairs; of these: 1740907 (95.82%) aligned 0 times 36762 (2.02%) aligned exactly 1 time 39107 (2.15%) aligned >1 times 91.21% overall alignment rate Time searching: 00:12:14 Overall time: 00:12:14 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] 90280 / 8993700 = 0.0100 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.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, 24 Aug 2019 21:11:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:11:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:11:43: 1000000 INFO @ Sat, 24 Aug 2019 21:11:51: 2000000 INFO @ Sat, 24 Aug 2019 21:11:58: 3000000 INFO @ Sat, 24 Aug 2019 21:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.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, 24 Aug 2019 21:12:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:12:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:12:06: 4000000 INFO @ Sat, 24 Aug 2019 21:12:14: 5000000 INFO @ Sat, 24 Aug 2019 21:12:15: 1000000 INFO @ Sat, 24 Aug 2019 21:12:22: 6000000 INFO @ Sat, 24 Aug 2019 21:12:24: 2000000 INFO @ Sat, 24 Aug 2019 21:12:29: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:12:33: 3000000 INFO @ Sat, 24 Aug 2019 21:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.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, 24 Aug 2019 21:12:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:12:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:12:37: 8000000 INFO @ Sat, 24 Aug 2019 21:12:43: 4000000 INFO @ Sat, 24 Aug 2019 21:12:45: 9000000 INFO @ Sat, 24 Aug 2019 21:12:47: 1000000 INFO @ Sat, 24 Aug 2019 21:12:52: 5000000 INFO @ Sat, 24 Aug 2019 21:12:53: 10000000 INFO @ Sat, 24 Aug 2019 21:12:58: 2000000 INFO @ Sat, 24 Aug 2019 21:13:01: 11000000 INFO @ Sat, 24 Aug 2019 21:13:01: 6000000 INFO @ Sat, 24 Aug 2019 21:13:09: 12000000 INFO @ Sat, 24 Aug 2019 21:13:09: 3000000 INFO @ Sat, 24 Aug 2019 21:13:10: 7000000 INFO @ Sat, 24 Aug 2019 21:13:16: 13000000 INFO @ Sat, 24 Aug 2019 21:13:19: 8000000 INFO @ Sat, 24 Aug 2019 21:13:20: 4000000 INFO @ Sat, 24 Aug 2019 21:13:24: 14000000 INFO @ Sat, 24 Aug 2019 21:13:28: 9000000 INFO @ Sat, 24 Aug 2019 21:13:31: 5000000 INFO @ Sat, 24 Aug 2019 21:13:32: 15000000 INFO @ Sat, 24 Aug 2019 21:13:37: 10000000 INFO @ Sat, 24 Aug 2019 21:13:40: 16000000 INFO @ Sat, 24 Aug 2019 21:13:41: 6000000 INFO @ Sat, 24 Aug 2019 21:13:45: 11000000 INFO @ Sat, 24 Aug 2019 21:13:48: 17000000 INFO @ Sat, 24 Aug 2019 21:13:51: 7000000 INFO @ Sat, 24 Aug 2019 21:13:54: 12000000 INFO @ Sat, 24 Aug 2019 21:13:55: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:13:55: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:13:55: #1 total tags in treatment: 8735226 INFO @ Sat, 24 Aug 2019 21:13:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:13:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:13:55: #1 tags after filtering in treatment: 6935631 INFO @ Sat, 24 Aug 2019 21:13:55: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 21:13:55: #1 finished! INFO @ Sat, 24 Aug 2019 21:13:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:13:56: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:13:56: 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, 24 Aug 2019 21:13:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.05_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/SRX4936088/SRX4936088.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:14:02: 8000000 INFO @ Sat, 24 Aug 2019 21:14:03: 13000000 INFO @ Sat, 24 Aug 2019 21:14:12: 14000000 INFO @ Sat, 24 Aug 2019 21:14:12: 9000000 INFO @ Sat, 24 Aug 2019 21:14:21: 15000000 INFO @ Sat, 24 Aug 2019 21:14:22: 10000000 INFO @ Sat, 24 Aug 2019 21:14:29: 16000000 INFO @ Sat, 24 Aug 2019 21:14:33: 11000000 INFO @ Sat, 24 Aug 2019 21:14:38: 17000000 INFO @ Sat, 24 Aug 2019 21:14:43: 12000000 INFO @ Sat, 24 Aug 2019 21:14:46: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:14:46: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:14:46: #1 total tags in treatment: 8735226 INFO @ Sat, 24 Aug 2019 21:14:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:14:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:14:46: #1 tags after filtering in treatment: 6935631 INFO @ Sat, 24 Aug 2019 21:14:46: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 21:14:46: #1 finished! INFO @ Sat, 24 Aug 2019 21:14:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:14:47: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:14:47: 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, 24 Aug 2019 21:14:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.10_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/SRX4936088/SRX4936088.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:14:55: 13000000 INFO @ Sat, 24 Aug 2019 21:15:05: 14000000 INFO @ Sat, 24 Aug 2019 21:15:16: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:15:27: 16000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:15:38: 17000000 INFO @ Sat, 24 Aug 2019 21:15:47: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:15:47: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:15:47: #1 total tags in treatment: 8735226 INFO @ Sat, 24 Aug 2019 21:15:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:15:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:15:47: #1 tags after filtering in treatment: 6935631 INFO @ Sat, 24 Aug 2019 21:15:47: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 21:15:47: #1 finished! INFO @ Sat, 24 Aug 2019 21:15:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:15:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:15:48: 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, 24 Aug 2019 21:15:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.20_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/SRX4936088/SRX4936088.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936088/SRX4936088.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling