Job ID = 5791174 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:49:45 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 ) 2020-04-21T23:49:45 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 ) 2020-04-21T23:49:45 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 ) 2020-04-21T23:49:45 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 ) 2020-04-21T23:53:15 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 ) 2020-04-21T23:55:11 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 : 6,620,913 reads read : 13,241,826 reads written : 13,241,826 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: 00:03:41 6620913 reads; of these: 6620913 (100.00%) were paired; of these: 5642886 (85.23%) aligned concordantly 0 times 803043 (12.13%) aligned concordantly exactly 1 time 174984 (2.64%) aligned concordantly >1 times ---- 5642886 pairs aligned concordantly 0 times; of these: 596057 (10.56%) aligned discordantly 1 time ---- 5046829 pairs aligned 0 times concordantly or discordantly; of these: 10093658 mates make up the pairs; of these: 9831829 (97.41%) aligned 0 times 52071 (0.52%) aligned exactly 1 time 209758 (2.08%) aligned >1 times 25.75% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_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] 332638 / 1542683 = 0.2156 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 09:03:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.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 09:03:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:03:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:03:19: 1000000 INFO @ Wed, 22 Apr 2020 09:03:27: 2000000 INFO @ Wed, 22 Apr 2020 09:03:32: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:03:32: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:03:32: #1 total tags in treatment: 738618 INFO @ Wed, 22 Apr 2020 09:03:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:03:32: #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 09:03:32: #1 tags after filtering in treatment: 646106 INFO @ Wed, 22 Apr 2020 09:03:32: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 09:03:32: #1 finished! INFO @ Wed, 22 Apr 2020 09:03:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:03:32: #2 number of paired peaks: 96 WARNING @ Wed, 22 Apr 2020 09:03:32: Too few paired peaks (96) 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 09:03:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.05_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/SRX6614967/SRX6614967.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 09:03:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.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 09:03:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:03:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:03:50: 1000000 INFO @ Wed, 22 Apr 2020 09:03:59: 2000000 INFO @ Wed, 22 Apr 2020 09:04:07: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:04:07: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:04:07: #1 total tags in treatment: 738618 INFO @ Wed, 22 Apr 2020 09:04:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:04:07: #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 09:04:07: #1 tags after filtering in treatment: 646106 INFO @ Wed, 22 Apr 2020 09:04:07: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 09:04:07: #1 finished! INFO @ Wed, 22 Apr 2020 09:04:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:04:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:04:07: #2 number of paired peaks: 96 WARNING @ Wed, 22 Apr 2020 09:04:07: Too few paired peaks (96) 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 09:04:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.10_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/SRX6614967/SRX6614967.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 09:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.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 09:04:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:04:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:04:20: 1000000 INFO @ Wed, 22 Apr 2020 09:04:29: 2000000 INFO @ Wed, 22 Apr 2020 09:04:37: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:04:37: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:04:37: #1 total tags in treatment: 738618 INFO @ Wed, 22 Apr 2020 09:04:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:04:37: #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 09:04:37: #1 tags after filtering in treatment: 646106 INFO @ Wed, 22 Apr 2020 09:04:37: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 09:04:37: #1 finished! INFO @ Wed, 22 Apr 2020 09:04:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:04:37: #2 number of paired peaks: 96 WARNING @ Wed, 22 Apr 2020 09:04:37: Too few paired peaks (96) 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 09:04:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.20_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/SRX6614967/SRX6614967.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614967/SRX6614967.20_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。