Job ID = 5791632 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:41:57 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 ) 2020-04-22T00:41:57 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.231' from '172.19.7.191' 2020-04-22T00:41:57 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' (165.112.9.231) from '172.19.7.191' 2020-04-22T00:41:57 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/sra23/SRR/010482/SRR10733590' 2020-04-22T00:41:57 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR10733590' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:41:57 fasterq-dump.2.9.6 err: invalid accession 'SRR10733590' spots read : 35,809,708 reads read : 71,619,416 reads written : 71,619,416 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: 00:20:12 35809708 reads; of these: 35809708 (100.00%) were paired; of these: 1252982 (3.50%) aligned concordantly 0 times 31324610 (87.48%) aligned concordantly exactly 1 time 3232116 (9.03%) aligned concordantly >1 times ---- 1252982 pairs aligned concordantly 0 times; of these: 97766 (7.80%) aligned discordantly 1 time ---- 1155216 pairs aligned 0 times concordantly or discordantly; of these: 2310432 mates make up the pairs; of these: 2037024 (88.17%) aligned 0 times 215467 (9.33%) aligned exactly 1 time 57941 (2.51%) aligned >1 times 97.16% overall alignment rate Time searching: 00:20:12 Overall time: 00:20:12 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 32 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] 14952607 / 34567108 = 0.4326 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.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 @ Wed, 22 Apr 2020 10:37:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:37:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:37:58: 1000000 INFO @ Wed, 22 Apr 2020 10:38:02: 2000000 INFO @ Wed, 22 Apr 2020 10:38:07: 3000000 INFO @ Wed, 22 Apr 2020 10:38:11: 4000000 INFO @ Wed, 22 Apr 2020 10:38:15: 5000000 INFO @ Wed, 22 Apr 2020 10:38:20: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.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 @ Wed, 22 Apr 2020 10:38:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:38:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:38:24: 7000000 INFO @ Wed, 22 Apr 2020 10:38:27: 1000000 INFO @ Wed, 22 Apr 2020 10:38:29: 8000000 INFO @ Wed, 22 Apr 2020 10:38:32: 2000000 INFO @ Wed, 22 Apr 2020 10:38:33: 9000000 INFO @ Wed, 22 Apr 2020 10:38:36: 3000000 INFO @ Wed, 22 Apr 2020 10:38:38: 10000000 INFO @ Wed, 22 Apr 2020 10:38:41: 4000000 INFO @ Wed, 22 Apr 2020 10:38:42: 11000000 INFO @ Wed, 22 Apr 2020 10:38:46: 5000000 INFO @ Wed, 22 Apr 2020 10:38:47: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:38:51: 6000000 INFO @ Wed, 22 Apr 2020 10:38:52: 13000000 INFO @ Wed, 22 Apr 2020 10:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.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 @ Wed, 22 Apr 2020 10:38:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:38:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:38:56: 14000000 INFO @ Wed, 22 Apr 2020 10:38:57: 7000000 INFO @ Wed, 22 Apr 2020 10:38:58: 1000000 INFO @ Wed, 22 Apr 2020 10:39:01: 15000000 INFO @ Wed, 22 Apr 2020 10:39:02: 8000000 INFO @ Wed, 22 Apr 2020 10:39:04: 2000000 INFO @ Wed, 22 Apr 2020 10:39:06: 16000000 INFO @ Wed, 22 Apr 2020 10:39:07: 9000000 INFO @ Wed, 22 Apr 2020 10:39:09: 3000000 INFO @ Wed, 22 Apr 2020 10:39:11: 17000000 INFO @ Wed, 22 Apr 2020 10:39:11: 10000000 INFO @ Wed, 22 Apr 2020 10:39:15: 4000000 INFO @ Wed, 22 Apr 2020 10:39:16: 11000000 INFO @ Wed, 22 Apr 2020 10:39:17: 18000000 INFO @ Wed, 22 Apr 2020 10:39:20: 5000000 INFO @ Wed, 22 Apr 2020 10:39:21: 12000000 INFO @ Wed, 22 Apr 2020 10:39:22: 19000000 INFO @ Wed, 22 Apr 2020 10:39:25: 6000000 INFO @ Wed, 22 Apr 2020 10:39:26: 13000000 INFO @ Wed, 22 Apr 2020 10:39:27: 20000000 INFO @ Wed, 22 Apr 2020 10:39:31: 14000000 INFO @ Wed, 22 Apr 2020 10:39:31: 7000000 INFO @ Wed, 22 Apr 2020 10:39:33: 21000000 INFO @ Wed, 22 Apr 2020 10:39:36: 15000000 INFO @ Wed, 22 Apr 2020 10:39:36: 8000000 INFO @ Wed, 22 Apr 2020 10:39:38: 22000000 INFO @ Wed, 22 Apr 2020 10:39:40: 16000000 INFO @ Wed, 22 Apr 2020 10:39:42: 9000000 INFO @ Wed, 22 Apr 2020 10:39:43: 23000000 INFO @ Wed, 22 Apr 2020 10:39:45: 17000000 INFO @ Wed, 22 Apr 2020 10:39:47: 10000000 INFO @ Wed, 22 Apr 2020 10:39:49: 24000000 INFO @ Wed, 22 Apr 2020 10:39:50: 18000000 INFO @ Wed, 22 Apr 2020 10:39:52: 11000000 INFO @ Wed, 22 Apr 2020 10:39:54: 25000000 INFO @ Wed, 22 Apr 2020 10:39:55: 19000000 INFO @ Wed, 22 Apr 2020 10:39:57: 12000000 INFO @ Wed, 22 Apr 2020 10:39:59: 20000000 INFO @ Wed, 22 Apr 2020 10:40:00: 26000000 INFO @ Wed, 22 Apr 2020 10:40:03: 13000000 INFO @ Wed, 22 Apr 2020 10:40:04: 21000000 INFO @ Wed, 22 Apr 2020 10:40:05: 27000000 INFO @ Wed, 22 Apr 2020 10:40:08: 14000000 INFO @ Wed, 22 Apr 2020 10:40:09: 22000000 INFO @ Wed, 22 Apr 2020 10:40:10: 28000000 INFO @ Wed, 22 Apr 2020 10:40:13: 15000000 INFO @ Wed, 22 Apr 2020 10:40:14: 23000000 INFO @ Wed, 22 Apr 2020 10:40:16: 29000000 INFO @ Wed, 22 Apr 2020 10:40:18: 24000000 INFO @ Wed, 22 Apr 2020 10:40:19: 16000000 INFO @ Wed, 22 Apr 2020 10:40:21: 30000000 INFO @ Wed, 22 Apr 2020 10:40:23: 25000000 INFO @ Wed, 22 Apr 2020 10:40:24: 17000000 INFO @ Wed, 22 Apr 2020 10:40:27: 31000000 INFO @ Wed, 22 Apr 2020 10:40:28: 26000000 INFO @ Wed, 22 Apr 2020 10:40:30: 18000000 INFO @ Wed, 22 Apr 2020 10:40:32: 32000000 INFO @ Wed, 22 Apr 2020 10:40:32: 27000000 INFO @ Wed, 22 Apr 2020 10:40:35: 19000000 INFO @ Wed, 22 Apr 2020 10:40:37: 28000000 INFO @ Wed, 22 Apr 2020 10:40:37: 33000000 INFO @ Wed, 22 Apr 2020 10:40:40: 20000000 INFO @ Wed, 22 Apr 2020 10:40:41: 29000000 INFO @ Wed, 22 Apr 2020 10:40:43: 34000000 INFO @ Wed, 22 Apr 2020 10:40:46: 21000000 INFO @ Wed, 22 Apr 2020 10:40:46: 30000000 INFO @ Wed, 22 Apr 2020 10:40:48: 35000000 INFO @ Wed, 22 Apr 2020 10:40:51: 31000000 INFO @ Wed, 22 Apr 2020 10:40:51: 22000000 INFO @ Wed, 22 Apr 2020 10:40:54: 36000000 INFO @ Wed, 22 Apr 2020 10:40:55: 32000000 INFO @ Wed, 22 Apr 2020 10:40:56: 23000000 INFO @ Wed, 22 Apr 2020 10:40:59: 37000000 INFO @ Wed, 22 Apr 2020 10:41:00: 33000000 INFO @ Wed, 22 Apr 2020 10:41:02: 24000000 INFO @ Wed, 22 Apr 2020 10:41:05: 38000000 INFO @ Wed, 22 Apr 2020 10:41:05: 34000000 INFO @ Wed, 22 Apr 2020 10:41:07: 25000000 INFO @ Wed, 22 Apr 2020 10:41:09: 35000000 INFO @ Wed, 22 Apr 2020 10:41:10: 39000000 INFO @ Wed, 22 Apr 2020 10:41:13: 26000000 INFO @ Wed, 22 Apr 2020 10:41:14: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:41:14: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:41:14: #1 total tags in treatment: 19608194 INFO @ Wed, 22 Apr 2020 10:41:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:41:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:41:14: 36000000 INFO @ Wed, 22 Apr 2020 10:41:14: #1 tags after filtering in treatment: 10529399 INFO @ Wed, 22 Apr 2020 10:41:14: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 10:41:14: #1 finished! INFO @ Wed, 22 Apr 2020 10:41:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:41:15: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:41:15: 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 @ Wed, 22 Apr 2020 10:41:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.05_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/SRX7409600/SRX7409600.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:41:18: 27000000 INFO @ Wed, 22 Apr 2020 10:41:19: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:41:23: 28000000 INFO @ Wed, 22 Apr 2020 10:41:24: 38000000 INFO @ Wed, 22 Apr 2020 10:41:28: 29000000 INFO @ Wed, 22 Apr 2020 10:41:28: 39000000 INFO @ Wed, 22 Apr 2020 10:41:32: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:41:32: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:41:32: #1 total tags in treatment: 19608194 INFO @ Wed, 22 Apr 2020 10:41:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:41:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:41:32: #1 tags after filtering in treatment: 10529399 INFO @ Wed, 22 Apr 2020 10:41:32: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 10:41:32: #1 finished! INFO @ Wed, 22 Apr 2020 10:41:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:41:33: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:41:33: 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 @ Wed, 22 Apr 2020 10:41:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:41:33: 30000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:41:39: 31000000 INFO @ Wed, 22 Apr 2020 10:41:43: 32000000 INFO @ Wed, 22 Apr 2020 10:41:49: 33000000 INFO @ Wed, 22 Apr 2020 10:41:54: 34000000 INFO @ Wed, 22 Apr 2020 10:41:59: 35000000 INFO @ Wed, 22 Apr 2020 10:42:04: 36000000 INFO @ Wed, 22 Apr 2020 10:42:09: 37000000 INFO @ Wed, 22 Apr 2020 10:42:14: 38000000 INFO @ Wed, 22 Apr 2020 10:42:19: 39000000 INFO @ Wed, 22 Apr 2020 10:42:22: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:42:22: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:42:22: #1 total tags in treatment: 19608194 INFO @ Wed, 22 Apr 2020 10:42:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:42:22: #1 tags after filtering in treatment: 10529399 INFO @ Wed, 22 Apr 2020 10:42:22: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 10:42:22: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:23: 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 @ Wed, 22 Apr 2020 10:42:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.20_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/SRX7409600/SRX7409600.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409600/SRX7409600.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling