Job ID = 5791625 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:41:21 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 ) 2020-04-22T00:41:21 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 ) 2020-04-22T00:41:21 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 ) 2020-04-22T00:53:19 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 ) 2020-04-22T00:56:19 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 ) 2020-04-22T00:57:30 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 : 31,879,734 reads read : 63,759,468 reads written : 63,759,468 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: 00:10:34 31879734 reads; of these: 31879734 (100.00%) were paired; of these: 13317419 (41.77%) aligned concordantly 0 times 16751023 (52.54%) aligned concordantly exactly 1 time 1811292 (5.68%) aligned concordantly >1 times ---- 13317419 pairs aligned concordantly 0 times; of these: 43039 (0.32%) aligned discordantly 1 time ---- 13274380 pairs aligned 0 times concordantly or discordantly; of these: 26548760 mates make up the pairs; of these: 26042920 (98.09%) aligned 0 times 441371 (1.66%) aligned exactly 1 time 64469 (0.24%) aligned >1 times 59.15% overall alignment rate Time searching: 00:10:34 Overall time: 00:10:34 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] 10402501 / 18571831 = 0.5601 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 10:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.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 10:17:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:17:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:18:03: 1000000 INFO @ Wed, 22 Apr 2020 10:18:07: 2000000 INFO @ Wed, 22 Apr 2020 10:18:12: 3000000 INFO @ Wed, 22 Apr 2020 10:18:17: 4000000 INFO @ Wed, 22 Apr 2020 10:18:21: 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 10:18:26: 6000000 INFO @ Wed, 22 Apr 2020 10:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.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 10:18:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:18:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:18:31: 7000000 INFO @ Wed, 22 Apr 2020 10:18:33: 1000000 INFO @ Wed, 22 Apr 2020 10:18:36: 8000000 INFO @ Wed, 22 Apr 2020 10:18:38: 2000000 INFO @ Wed, 22 Apr 2020 10:18:40: 9000000 INFO @ Wed, 22 Apr 2020 10:18:43: 3000000 INFO @ Wed, 22 Apr 2020 10:18:45: 10000000 INFO @ Wed, 22 Apr 2020 10:18:48: 4000000 INFO @ Wed, 22 Apr 2020 10:18:50: 11000000 INFO @ Wed, 22 Apr 2020 10:18:53: 5000000 INFO @ Wed, 22 Apr 2020 10:18:55: 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 10:18:58: 6000000 INFO @ Wed, 22 Apr 2020 10:18:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.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 10:18:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:18:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:18:59: 13000000 INFO @ Wed, 22 Apr 2020 10:19:03: 7000000 INFO @ Wed, 22 Apr 2020 10:19:03: 1000000 INFO @ Wed, 22 Apr 2020 10:19:04: 14000000 INFO @ Wed, 22 Apr 2020 10:19:08: 8000000 INFO @ Wed, 22 Apr 2020 10:19:08: 2000000 INFO @ Wed, 22 Apr 2020 10:19:09: 15000000 INFO @ Wed, 22 Apr 2020 10:19:13: 9000000 INFO @ Wed, 22 Apr 2020 10:19:14: 16000000 INFO @ Wed, 22 Apr 2020 10:19:14: 3000000 INFO @ Wed, 22 Apr 2020 10:19:17: 10000000 INFO @ Wed, 22 Apr 2020 10:19:19: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:19: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:19: #1 total tags in treatment: 8163795 INFO @ Wed, 22 Apr 2020 10:19:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:19: #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 10:19:19: #1 tags after filtering in treatment: 6533486 INFO @ Wed, 22 Apr 2020 10:19:19: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 10:19:19: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:19:19: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:19:19: 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 10:19:19: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:19:19: 4000000 INFO @ Wed, 22 Apr 2020 10:19:23: 11000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.05_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/SRX7409593/SRX7409593.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:19:25: 5000000 INFO @ Wed, 22 Apr 2020 10:19:27: 12000000 INFO @ Wed, 22 Apr 2020 10:19:30: 6000000 INFO @ Wed, 22 Apr 2020 10:19:32: 13000000 INFO @ Wed, 22 Apr 2020 10:19:35: 7000000 INFO @ Wed, 22 Apr 2020 10:19:37: 14000000 INFO @ Wed, 22 Apr 2020 10:19:40: 8000000 INFO @ Wed, 22 Apr 2020 10:19:42: 15000000 INFO @ Wed, 22 Apr 2020 10:19:45: 9000000 INFO @ Wed, 22 Apr 2020 10:19:47: 16000000 INFO @ Wed, 22 Apr 2020 10:19:50: 10000000 INFO @ Wed, 22 Apr 2020 10:19:52: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:52: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:52: #1 total tags in treatment: 8163795 INFO @ Wed, 22 Apr 2020 10:19:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:52: #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 10:19:52: #1 tags after filtering in treatment: 6533486 INFO @ Wed, 22 Apr 2020 10:19:52: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 10:19:52: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:19:52: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:19:52: 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 10:19:52: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:19:55: 11000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.10_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/SRX7409593/SRX7409593.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:20:00: 12000000 INFO @ Wed, 22 Apr 2020 10:20:05: 13000000 INFO @ Wed, 22 Apr 2020 10:20:10: 14000000 INFO @ Wed, 22 Apr 2020 10:20:15: 15000000 INFO @ Wed, 22 Apr 2020 10:20:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:20:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:20:24: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:20:24: #1 total tags in treatment: 8163795 INFO @ Wed, 22 Apr 2020 10:20:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:20:24: #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 10:20:24: #1 tags after filtering in treatment: 6533486 INFO @ Wed, 22 Apr 2020 10:20:24: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 10:20:24: #1 finished! INFO @ Wed, 22 Apr 2020 10:20:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:20:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:20:25: 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 10:20:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.20_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/SRX7409593/SRX7409593.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409593/SRX7409593.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。