Job ID = 2010693 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:52:31 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 ) 2019-07-05T14:52:31 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' 2019-07-05T14:52:31 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' 2019-07-05T14:52:31 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/SRR6918473' 2019-07-05T14:52:31 fasterq-dump.2.9.6 err: invalid accession 'SRR6918473' 2019-07-05T14:57:55 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 : 12,621,573 reads read : 25,243,146 reads written : 25,243,146 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: 00:08:20 12621573 reads; of these: 12621573 (100.00%) were paired; of these: 4090725 (32.41%) aligned concordantly 0 times 7421756 (58.80%) aligned concordantly exactly 1 time 1109092 (8.79%) aligned concordantly >1 times ---- 4090725 pairs aligned concordantly 0 times; of these: 21081 (0.52%) aligned discordantly 1 time ---- 4069644 pairs aligned 0 times concordantly or discordantly; of these: 8139288 mates make up the pairs; of these: 4828563 (59.32%) aligned 0 times 2849051 (35.00%) aligned exactly 1 time 461674 (5.67%) aligned >1 times 80.87% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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] 427436 / 8550201 = 0.0500 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 00:16:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.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 00:16:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:16:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.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 00:16:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:16:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:16:47: 1000000 INFO @ Sat, 06 Jul 2019 00:16:49: 1000000 INFO @ Sat, 06 Jul 2019 00:16:53: 2000000 INFO @ Sat, 06 Jul 2019 00:16:56: 2000000 INFO @ Sat, 06 Jul 2019 00:16:59: 3000000 INFO @ Sat, 06 Jul 2019 00:17:03: 3000000 INFO @ Sat, 06 Jul 2019 00:17:06: 4000000 INFO @ Sat, 06 Jul 2019 00:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.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 00:17:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:17:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:17:11: 4000000 INFO @ Sat, 06 Jul 2019 00:17:12: 5000000 INFO @ Sat, 06 Jul 2019 00:17:18: 5000000 INFO @ Sat, 06 Jul 2019 00:17:18: 6000000 INFO @ Sat, 06 Jul 2019 00:17:19: 1000000 INFO @ Sat, 06 Jul 2019 00:17:25: 7000000 INFO @ Sat, 06 Jul 2019 00:17:25: 6000000 INFO @ Sat, 06 Jul 2019 00:17:29: 2000000 INFO @ Sat, 06 Jul 2019 00:17:31: 8000000 INFO @ Sat, 06 Jul 2019 00:17:33: 7000000 INFO @ Sat, 06 Jul 2019 00:17:38: 9000000 INFO @ Sat, 06 Jul 2019 00:17:39: 3000000 INFO @ Sat, 06 Jul 2019 00:17:40: 8000000 INFO @ Sat, 06 Jul 2019 00:17:44: 10000000 INFO @ Sat, 06 Jul 2019 00:17:48: 9000000 INFO @ Sat, 06 Jul 2019 00:17:49: 4000000 INFO @ Sat, 06 Jul 2019 00:17:51: 11000000 INFO @ Sat, 06 Jul 2019 00:17:55: 10000000 INFO @ Sat, 06 Jul 2019 00:17:57: 12000000 INFO @ Sat, 06 Jul 2019 00:17:58: 5000000 INFO @ Sat, 06 Jul 2019 00:18:02: 11000000 INFO @ Sat, 06 Jul 2019 00:18:03: 13000000 INFO @ Sat, 06 Jul 2019 00:18:08: 6000000 INFO @ Sat, 06 Jul 2019 00:18:10: 12000000 INFO @ Sat, 06 Jul 2019 00:18:10: 14000000 INFO @ Sat, 06 Jul 2019 00:18:16: 15000000 INFO @ Sat, 06 Jul 2019 00:18:17: 13000000 INFO @ Sat, 06 Jul 2019 00:18:18: 7000000 INFO @ Sat, 06 Jul 2019 00:18:23: 16000000 INFO @ Sat, 06 Jul 2019 00:18:24: 14000000 INFO @ Sat, 06 Jul 2019 00:18:28: 8000000 INFO @ Sat, 06 Jul 2019 00:18:29: 17000000 INFO @ Sat, 06 Jul 2019 00:18:31: 15000000 INFO @ Sat, 06 Jul 2019 00:18:35: 18000000 INFO @ Sat, 06 Jul 2019 00:18:38: 9000000 INFO @ Sat, 06 Jul 2019 00:18:39: 16000000 INFO @ Sat, 06 Jul 2019 00:18:42: 19000000 INFO @ Sat, 06 Jul 2019 00:18:45: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:18:45: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:18:45: #1 total tags in treatment: 8103571 INFO @ Sat, 06 Jul 2019 00:18:45: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:18:45: #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 00:18:46: #1 tags after filtering in treatment: 4606140 INFO @ Sat, 06 Jul 2019 00:18:46: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 06 Jul 2019 00:18:46: #1 finished! INFO @ Sat, 06 Jul 2019 00:18:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:18:46: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:18:46: 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 00:18:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 00:18:46: 17000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:18:48: 10000000 INFO @ Sat, 06 Jul 2019 00:18:53: 18000000 INFO @ Sat, 06 Jul 2019 00:18:56: 11000000 INFO @ Sat, 06 Jul 2019 00:19:01: 19000000 INFO @ Sat, 06 Jul 2019 00:19:04: 12000000 INFO @ Sat, 06 Jul 2019 00:19:05: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:19:05: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:19:05: #1 total tags in treatment: 8103571 INFO @ Sat, 06 Jul 2019 00:19:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:19:05: #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 00:19:05: #1 tags after filtering in treatment: 4606140 INFO @ Sat, 06 Jul 2019 00:19:05: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 06 Jul 2019 00:19:05: #1 finished! INFO @ Sat, 06 Jul 2019 00:19:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:19:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:19:05: 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 00:19:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.10_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/SRX3865919/SRX3865919.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:19:12: 13000000 INFO @ Sat, 06 Jul 2019 00:19:21: 14000000 INFO @ Sat, 06 Jul 2019 00:19:29: 15000000 INFO @ Sat, 06 Jul 2019 00:19:38: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:19:46: 17000000 INFO @ Sat, 06 Jul 2019 00:19:55: 18000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:20:03: 19000000 INFO @ Sat, 06 Jul 2019 00:20:08: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:20:08: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:20:08: #1 total tags in treatment: 8103571 INFO @ Sat, 06 Jul 2019 00:20:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:20:08: #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 00:20:08: #1 tags after filtering in treatment: 4606140 INFO @ Sat, 06 Jul 2019 00:20:08: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 06 Jul 2019 00:20:08: #1 finished! INFO @ Sat, 06 Jul 2019 00:20:08: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:20:09: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:20:09: 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 00:20:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.20_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/SRX3865919/SRX3865919.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865919/SRX3865919.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling