Job ID = 5791283 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:19:54 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 ) 2020-04-22T00:19:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.238' from '172.19.7.212' 2020-04-22T00:19:54 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' (165.112.9.238) from '172.19.7.212' 2020-04-22T00:19:54 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/sra66/SRR/010481/SRR10733532' 2020-04-22T00:19:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR10733532' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:19:54 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:19:54 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 ) 2020-04-22T00:19:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.238' from '172.19.7.212' 2020-04-22T00:19:54 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' (165.112.9.238) from '172.19.7.212' 2020-04-22T00:19:54 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/sra66/SRR/010481/SRR10733532' 2020-04-22T00:19:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR10733532' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:19:54 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:19:54 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 ) 2020-04-22T00:19:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.238' from '172.19.7.212' 2020-04-22T00:19:54 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' (165.112.9.238) from '172.19.7.212' 2020-04-22T00:19:54 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/sra66/SRR/010481/SRR10733532' 2020-04-22T00:19:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR10733532' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:19:54 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T00:22:31 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 ) 2020-04-22T00:33:54 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 ) 2020-04-22T00:48:39 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 ) 2020-04-22T00:49:47 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 : 28,427,192 reads read : 56,854,384 reads written : 56,854,384 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: 00:09:33 28427192 reads; of these: 28427192 (100.00%) were paired; of these: 10724029 (37.72%) aligned concordantly 0 times 15872170 (55.83%) aligned concordantly exactly 1 time 1830993 (6.44%) aligned concordantly >1 times ---- 10724029 pairs aligned concordantly 0 times; of these: 41803 (0.39%) aligned discordantly 1 time ---- 10682226 pairs aligned 0 times concordantly or discordantly; of these: 21364452 mates make up the pairs; of these: 20937355 (98.00%) aligned 0 times 370149 (1.73%) aligned exactly 1 time 56948 (0.27%) aligned >1 times 63.17% overall alignment rate Time searching: 00:09:33 Overall time: 00:09:33 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] 8860230 / 17712854 = 0.5002 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 10:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.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 10:16:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:16:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:17:01: 1000000 INFO @ Wed, 22 Apr 2020 10:17:06: 2000000 INFO @ Wed, 22 Apr 2020 10:17:11: 3000000 INFO @ Wed, 22 Apr 2020 10:17:15: 4000000 INFO @ Wed, 22 Apr 2020 10:17:20: 5000000 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 10:17:25: 6000000 INFO @ Wed, 22 Apr 2020 10:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.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 10:17:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:17:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:17:30: 7000000 INFO @ Wed, 22 Apr 2020 10:17:32: 1000000 INFO @ Wed, 22 Apr 2020 10:17:35: 8000000 INFO @ Wed, 22 Apr 2020 10:17:37: 2000000 INFO @ Wed, 22 Apr 2020 10:17:41: 9000000 INFO @ Wed, 22 Apr 2020 10:17:43: 3000000 INFO @ Wed, 22 Apr 2020 10:17:46: 10000000 INFO @ Wed, 22 Apr 2020 10:17:48: 4000000 INFO @ Wed, 22 Apr 2020 10:17:51: 11000000 INFO @ Wed, 22 Apr 2020 10:17:53: 5000000 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 10:17:56: 12000000 INFO @ Wed, 22 Apr 2020 10:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.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 10:17:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:17:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:17:59: 6000000 INFO @ Wed, 22 Apr 2020 10:18:02: 13000000 INFO @ Wed, 22 Apr 2020 10:18:03: 1000000 INFO @ Wed, 22 Apr 2020 10:18:05: 7000000 INFO @ Wed, 22 Apr 2020 10:18:08: 14000000 INFO @ Wed, 22 Apr 2020 10:18:09: 2000000 INFO @ Wed, 22 Apr 2020 10:18:10: 8000000 INFO @ Wed, 22 Apr 2020 10:18:13: 15000000 INFO @ Wed, 22 Apr 2020 10:18:16: 3000000 INFO @ Wed, 22 Apr 2020 10:18:16: 9000000 INFO @ Wed, 22 Apr 2020 10:18:19: 16000000 INFO @ Wed, 22 Apr 2020 10:18:22: 4000000 INFO @ Wed, 22 Apr 2020 10:18:22: 10000000 INFO @ Wed, 22 Apr 2020 10:18:25: 17000000 INFO @ Wed, 22 Apr 2020 10:18:28: 11000000 INFO @ Wed, 22 Apr 2020 10:18:28: 5000000 INFO @ Wed, 22 Apr 2020 10:18:30: 18000000 INFO @ Wed, 22 Apr 2020 10:18:32: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:18:32: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:18:32: #1 total tags in treatment: 8845663 INFO @ Wed, 22 Apr 2020 10:18:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:18:32: #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 10:18:32: #1 tags after filtering in treatment: 6946443 INFO @ Wed, 22 Apr 2020 10:18:32: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:18:32: #1 finished! INFO @ Wed, 22 Apr 2020 10:18:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:18:32: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:18:32: 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 10:18:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.05_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/SRX7409542/SRX7409542.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:18:33: 12000000 INFO @ Wed, 22 Apr 2020 10:18:34: 6000000 INFO @ Wed, 22 Apr 2020 10:18:39: 13000000 INFO @ Wed, 22 Apr 2020 10:18:41: 7000000 INFO @ Wed, 22 Apr 2020 10:18:45: 14000000 INFO @ Wed, 22 Apr 2020 10:18:47: 8000000 INFO @ Wed, 22 Apr 2020 10:18:50: 15000000 INFO @ Wed, 22 Apr 2020 10:18:53: 9000000 INFO @ Wed, 22 Apr 2020 10:18:56: 16000000 INFO @ Wed, 22 Apr 2020 10:19:00: 10000000 INFO @ Wed, 22 Apr 2020 10:19:02: 17000000 INFO @ Wed, 22 Apr 2020 10:19:06: 11000000 INFO @ Wed, 22 Apr 2020 10:19:07: 18000000 INFO @ Wed, 22 Apr 2020 10:19:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:09: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:09: #1 total tags in treatment: 8845663 INFO @ Wed, 22 Apr 2020 10:19:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:09: #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 10:19:09: #1 tags after filtering in treatment: 6946443 INFO @ Wed, 22 Apr 2020 10:19:09: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:19:09: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:19:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:19:09: 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 @ Wed, 22 Apr 2020 10:19:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.10_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/SRX7409542/SRX7409542.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:19:12: 12000000 INFO @ Wed, 22 Apr 2020 10:19:18: 13000000 INFO @ Wed, 22 Apr 2020 10:19:24: 14000000 INFO @ Wed, 22 Apr 2020 10:19:30: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:19:35: 16000000 INFO @ Wed, 22 Apr 2020 10:19:41: 17000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:19:47: 18000000 INFO @ Wed, 22 Apr 2020 10:19:48: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:48: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:48: #1 total tags in treatment: 8845663 INFO @ Wed, 22 Apr 2020 10:19:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:48: #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 10:19:48: #1 tags after filtering in treatment: 6946443 INFO @ Wed, 22 Apr 2020 10:19:48: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 10:19:48: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:19:49: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:19:49: 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 10:19:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.20_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/SRX7409542/SRX7409542.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409542/SRX7409542.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling