Job ID = 5791094 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 ) spots read : 6,973,046 reads read : 13,946,092 reads written : 6,973,046 reads 0-length : 6,973,046 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: 00:00:56 6973046 reads; of these: 6973046 (100.00%) were unpaired; of these: 700967 (10.05%) aligned 0 times 5547156 (79.55%) aligned exactly 1 time 724923 (10.40%) aligned >1 times 89.95% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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_rmdupse_core] 1701225 / 6272079 = 0.2712 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 08:33:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.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 08:33:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:33:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:33:13: 1000000 INFO @ Wed, 22 Apr 2020 08:33:19: 2000000 INFO @ Wed, 22 Apr 2020 08:33:26: 3000000 INFO @ Wed, 22 Apr 2020 08:33:32: 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 08:33:35: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:33:35: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:33:35: #1 total tags in treatment: 4570854 INFO @ Wed, 22 Apr 2020 08:33:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:33:35: #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 08:33:35: #1 tags after filtering in treatment: 4570854 INFO @ Wed, 22 Apr 2020 08:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:33:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:33:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:33:35: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 08:33:35: Too few paired peaks (26) 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 08:33:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.05_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/SRX5936162/SRX5936162.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.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 08:33:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:33:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:33:43: 1000000 INFO @ Wed, 22 Apr 2020 08:33:49: 2000000 INFO @ Wed, 22 Apr 2020 08:33:55: 3000000 INFO @ Wed, 22 Apr 2020 08:34:01: 4000000 INFO @ Wed, 22 Apr 2020 08:34:05: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:34:05: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:34:05: #1 total tags in treatment: 4570854 INFO @ Wed, 22 Apr 2020 08:34:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:34:05: #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 08:34:05: #1 tags after filtering in treatment: 4570854 INFO @ Wed, 22 Apr 2020 08:34:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:34:05: #1 finished! INFO @ Wed, 22 Apr 2020 08:34:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:34:05: #2 looking for paired plus/minus strand peaks... 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 08:34:05: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 08:34:05: Too few paired peaks (26) 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 08:34:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.10_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/SRX5936162/SRX5936162.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.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 08:34:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:34:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:34:13: 1000000 INFO @ Wed, 22 Apr 2020 08:34:19: 2000000 INFO @ Wed, 22 Apr 2020 08:34:26: 3000000 INFO @ Wed, 22 Apr 2020 08:34:32: 4000000 INFO @ Wed, 22 Apr 2020 08:34:35: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:34:35: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:34:35: #1 total tags in treatment: 4570854 INFO @ Wed, 22 Apr 2020 08:34:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:34:35: #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 08:34:35: #1 tags after filtering in treatment: 4570854 INFO @ Wed, 22 Apr 2020 08:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:34:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:34:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:34:35: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 08:34:35: Too few paired peaks (26) 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 08:34:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.20_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/SRX5936162/SRX5936162.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936162/SRX5936162.20_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。