Job ID = 5791095 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T23:28:03 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 ) 2020-04-21T23:28:04 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 ) 2020-04-21T23:28:04 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 ) 2020-04-21T23:28:04 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 ) 2020-04-21T23:30:01 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 : 11,404,373 reads read : 22,808,746 reads written : 11,404,373 reads 0-length : 11,404,373 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: 00:01:15 11404373 reads; of these: 11404373 (100.00%) were unpaired; of these: 919293 (8.06%) aligned 0 times 9008110 (78.99%) aligned exactly 1 time 1476970 (12.95%) aligned >1 times 91.94% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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_rmdupse_core] 3354504 / 10485080 = 0.3199 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 08:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.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 08:34:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:34:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:35:03: 1000000 INFO @ Wed, 22 Apr 2020 08:35:10: 2000000 INFO @ Wed, 22 Apr 2020 08:35:16: 3000000 INFO @ Wed, 22 Apr 2020 08:35:23: 4000000 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 08:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.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 08:35:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:35:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:35:30: 5000000 INFO @ Wed, 22 Apr 2020 08:35:32: 1000000 INFO @ Wed, 22 Apr 2020 08:35:37: 6000000 INFO @ Wed, 22 Apr 2020 08:35:39: 2000000 INFO @ Wed, 22 Apr 2020 08:35:44: 7000000 INFO @ Wed, 22 Apr 2020 08:35:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:35:45: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:35:45: #1 total tags in treatment: 7130576 INFO @ Wed, 22 Apr 2020 08:35:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:35:45: #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 08:35:45: #1 tags after filtering in treatment: 7130576 INFO @ Wed, 22 Apr 2020 08:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:35:45: #1 finished! INFO @ Wed, 22 Apr 2020 08:35:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:35:45: 3000000 INFO @ Wed, 22 Apr 2020 08:35:45: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:35:45: 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 08:35:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.05_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/SRX5936163/SRX5936163.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:35:51: 4000000 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 08:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.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 08:35:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:35:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:35:57: 5000000 INFO @ Wed, 22 Apr 2020 08:36:02: 1000000 INFO @ Wed, 22 Apr 2020 08:36:02: 6000000 INFO @ Wed, 22 Apr 2020 08:36:08: 2000000 INFO @ Wed, 22 Apr 2020 08:36:08: 7000000 INFO @ Wed, 22 Apr 2020 08:36:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:36:09: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:36:09: #1 total tags in treatment: 7130576 INFO @ Wed, 22 Apr 2020 08:36:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:36:09: #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 08:36:09: #1 tags after filtering in treatment: 7130576 INFO @ Wed, 22 Apr 2020 08:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:36:09: #1 finished! INFO @ Wed, 22 Apr 2020 08:36:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:36:10: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:36:10: 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 08:36:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.10_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/SRX5936163/SRX5936163.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:36:14: 3000000 INFO @ Wed, 22 Apr 2020 08:36:20: 4000000 INFO @ Wed, 22 Apr 2020 08:36:25: 5000000 INFO @ Wed, 22 Apr 2020 08:36:31: 6000000 INFO @ Wed, 22 Apr 2020 08:36:37: 7000000 INFO @ Wed, 22 Apr 2020 08:36:37: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:36:37: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:36:37: #1 total tags in treatment: 7130576 INFO @ Wed, 22 Apr 2020 08:36:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:36:37: #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 08:36:37: #1 tags after filtering in treatment: 7130576 INFO @ Wed, 22 Apr 2020 08:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:36:37: #1 finished! INFO @ Wed, 22 Apr 2020 08:36:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:36:38: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:36:38: 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 08:36:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.20_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/SRX5936163/SRX5936163.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936163/SRX5936163.20_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。