Job ID = 5791623 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 ) 2020-04-22T00:48:39 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 ) 2020-04-22T00:52:06 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 ) 2020-04-22T00:52:06 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 : 28,056,637 reads read : 56,113,274 reads written : 56,113,274 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: 00:09:44 28056637 reads; of these: 28056637 (100.00%) were paired; of these: 10078031 (35.92%) aligned concordantly 0 times 16151814 (57.57%) aligned concordantly exactly 1 time 1826792 (6.51%) aligned concordantly >1 times ---- 10078031 pairs aligned concordantly 0 times; of these: 17412 (0.17%) aligned discordantly 1 time ---- 10060619 pairs aligned 0 times concordantly or discordantly; of these: 20121238 mates make up the pairs; of these: 19656285 (97.69%) aligned 0 times 410551 (2.04%) aligned exactly 1 time 54402 (0.27%) aligned >1 times 64.97% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 10988968 / 17984228 = 0.6110 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 10:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.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 10:11:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:11:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:11:41: 1000000 INFO @ Wed, 22 Apr 2020 10:11:45: 2000000 INFO @ Wed, 22 Apr 2020 10:11:50: 3000000 INFO @ Wed, 22 Apr 2020 10:11:54: 4000000 INFO @ Wed, 22 Apr 2020 10:11:59: 5000000 INFO @ Wed, 22 Apr 2020 10:12:03: 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 10:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.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 10:12:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:12:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:12:08: 7000000 INFO @ Wed, 22 Apr 2020 10:12:11: 1000000 INFO @ Wed, 22 Apr 2020 10:12:13: 8000000 INFO @ Wed, 22 Apr 2020 10:12:16: 2000000 INFO @ Wed, 22 Apr 2020 10:12:17: 9000000 INFO @ Wed, 22 Apr 2020 10:12:21: 3000000 INFO @ Wed, 22 Apr 2020 10:12:22: 10000000 INFO @ Wed, 22 Apr 2020 10:12:25: 4000000 INFO @ Wed, 22 Apr 2020 10:12:27: 11000000 INFO @ Wed, 22 Apr 2020 10:12:30: 5000000 INFO @ Wed, 22 Apr 2020 10:12:32: 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 10:12:35: 6000000 INFO @ Wed, 22 Apr 2020 10:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.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 10:12:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:12:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:12:37: 13000000 INFO @ Wed, 22 Apr 2020 10:12:40: 7000000 INFO @ Wed, 22 Apr 2020 10:12:42: 14000000 INFO @ Wed, 22 Apr 2020 10:12:42: 1000000 INFO @ Wed, 22 Apr 2020 10:12:44: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:12:44: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:12:44: #1 total tags in treatment: 6991198 INFO @ Wed, 22 Apr 2020 10:12:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:12:44: #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 10:12:44: #1 tags after filtering in treatment: 5710639 INFO @ Wed, 22 Apr 2020 10:12:44: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 10:12:44: #1 finished! INFO @ Wed, 22 Apr 2020 10:12:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:12:44: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:12:44: 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 10:12:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.05_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/SRX7409591/SRX7409591.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:12:45: 8000000 INFO @ Wed, 22 Apr 2020 10:12:48: 2000000 INFO @ Wed, 22 Apr 2020 10:12:50: 9000000 INFO @ Wed, 22 Apr 2020 10:12:54: 3000000 INFO @ Wed, 22 Apr 2020 10:12:55: 10000000 INFO @ Wed, 22 Apr 2020 10:12:59: 4000000 INFO @ Wed, 22 Apr 2020 10:13:00: 11000000 INFO @ Wed, 22 Apr 2020 10:13:05: 5000000 INFO @ Wed, 22 Apr 2020 10:13:05: 12000000 INFO @ Wed, 22 Apr 2020 10:13:10: 13000000 INFO @ Wed, 22 Apr 2020 10:13:11: 6000000 INFO @ Wed, 22 Apr 2020 10:13:15: 14000000 INFO @ Wed, 22 Apr 2020 10:13:17: 7000000 INFO @ Wed, 22 Apr 2020 10:13:18: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:13:18: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:13:18: #1 total tags in treatment: 6991198 INFO @ Wed, 22 Apr 2020 10:13:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:13:18: #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 10:13:18: #1 tags after filtering in treatment: 5710639 INFO @ Wed, 22 Apr 2020 10:13:18: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 10:13:18: #1 finished! INFO @ Wed, 22 Apr 2020 10:13:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:13:18: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:13:18: 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 10:13:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.10_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/SRX7409591/SRX7409591.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:13:22: 8000000 INFO @ Wed, 22 Apr 2020 10:13:28: 9000000 INFO @ Wed, 22 Apr 2020 10:13:33: 10000000 INFO @ Wed, 22 Apr 2020 10:13:37: 11000000 INFO @ Wed, 22 Apr 2020 10:13:42: 12000000 INFO @ Wed, 22 Apr 2020 10:13:47: 13000000 INFO @ Wed, 22 Apr 2020 10:13:52: 14000000 INFO @ Wed, 22 Apr 2020 10:13:54: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:13:54: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:13:54: #1 total tags in treatment: 6991198 INFO @ Wed, 22 Apr 2020 10:13:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:13:54: #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 10:13:54: #1 tags after filtering in treatment: 5710639 INFO @ Wed, 22 Apr 2020 10:13:54: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 10:13:54: #1 finished! INFO @ Wed, 22 Apr 2020 10:13:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:13:54: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:13:54: 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 10:13:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.20_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/SRX7409591/SRX7409591.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409591/SRX7409591.20_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。