Job ID = 5791631 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 '172.19.7.208' 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 '172.19.7.208' 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/sra47/SRR/010482/SRR10733589' 2020-04-22T00:41:57 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR10733589' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-22T01:12:54 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 ) 2020-04-22T01:16:09 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 ) 2020-04-22T01:21:43 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 ) 2020-04-22T01:21:43 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 : 79,045,059 reads read : 158,090,118 reads written : 158,090,118 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: 00:08:09 79045059 reads; of these: 79045059 (100.00%) were paired; of these: 70356819 (89.01%) aligned concordantly 0 times 7776912 (9.84%) aligned concordantly exactly 1 time 911328 (1.15%) aligned concordantly >1 times ---- 70356819 pairs aligned concordantly 0 times; of these: 24195 (0.03%) aligned discordantly 1 time ---- 70332624 pairs aligned 0 times concordantly or discordantly; of these: 140665248 mates make up the pairs; of these: 140383811 (99.80%) aligned 0 times 243853 (0.17%) aligned exactly 1 time 37584 (0.03%) aligned >1 times 11.20% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 4762084 / 8702521 = 0.5472 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 10:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.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 10:42:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:23: 1000000 INFO @ Wed, 22 Apr 2020 10:42:28: 2000000 INFO @ Wed, 22 Apr 2020 10:42:33: 3000000 INFO @ Wed, 22 Apr 2020 10:42:39: 4000000 INFO @ Wed, 22 Apr 2020 10:42:44: 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 10:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.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 10:42:47: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:47: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:49: 6000000 INFO @ Wed, 22 Apr 2020 10:42:52: 1000000 INFO @ Wed, 22 Apr 2020 10:42:55: 7000000 INFO @ Wed, 22 Apr 2020 10:42:57: 2000000 INFO @ Wed, 22 Apr 2020 10:43:00: 8000000 INFO @ Wed, 22 Apr 2020 10:43:01: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:43:01: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:43:01: #1 total tags in treatment: 3939591 INFO @ Wed, 22 Apr 2020 10:43:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:43:01: #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 10:43:01: #1 tags after filtering in treatment: 3285539 INFO @ Wed, 22 Apr 2020 10:43:01: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:43:01: #1 finished! INFO @ Wed, 22 Apr 2020 10:43:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:43:02: 3000000 INFO @ Wed, 22 Apr 2020 10:43:02: #2 number of paired peaks: 84 WARNING @ Wed, 22 Apr 2020 10:43:02: Too few paired peaks (84) 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 10:43:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.05_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/SRX7409599/SRX7409599.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:43:06: 4000000 INFO @ Wed, 22 Apr 2020 10:43:11: 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 10:43:16: 6000000 INFO @ Wed, 22 Apr 2020 10:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.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 10:43:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:21: 7000000 INFO @ Wed, 22 Apr 2020 10:43:23: 1000000 INFO @ Wed, 22 Apr 2020 10:43:26: 8000000 INFO @ Wed, 22 Apr 2020 10:43:27: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:43:27: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:43:27: #1 total tags in treatment: 3939591 INFO @ Wed, 22 Apr 2020 10:43:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:43:27: #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 10:43:27: #1 tags after filtering in treatment: 3285539 INFO @ Wed, 22 Apr 2020 10:43:27: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:43:27: #1 finished! INFO @ Wed, 22 Apr 2020 10:43:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:43:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:43:27: #2 number of paired peaks: 84 WARNING @ Wed, 22 Apr 2020 10:43:27: Too few paired peaks (84) 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 10:43:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.10_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/SRX7409599/SRX7409599.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:43:28: 2000000 INFO @ Wed, 22 Apr 2020 10:43:33: 3000000 INFO @ Wed, 22 Apr 2020 10:43:38: 4000000 INFO @ Wed, 22 Apr 2020 10:43:43: 5000000 INFO @ Wed, 22 Apr 2020 10:43:47: 6000000 INFO @ Wed, 22 Apr 2020 10:43:52: 7000000 INFO @ Wed, 22 Apr 2020 10:43:57: 8000000 INFO @ Wed, 22 Apr 2020 10:43:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:43:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:43:57: #1 total tags in treatment: 3939591 INFO @ Wed, 22 Apr 2020 10:43:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:43:57: #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 10:43:57: #1 tags after filtering in treatment: 3285539 INFO @ Wed, 22 Apr 2020 10:43:57: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 10:43:57: #1 finished! INFO @ Wed, 22 Apr 2020 10:43:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:43:58: #2 number of paired peaks: 84 WARNING @ Wed, 22 Apr 2020 10:43:58: Too few paired peaks (84) 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 10:43:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.20_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/SRX7409599/SRX7409599.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409599/SRX7409599.20_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。