Job ID = 5791691 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-22T01:27:59 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 ) 2020-04-22T01:27:59 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 : 12,740,460 reads read : 25,480,920 reads written : 12,740,460 reads 0-length : 12,740,460 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: 00:02:47 12740460 reads; of these: 12740460 (100.00%) were unpaired; of these: 922693 (7.24%) aligned 0 times 10245866 (80.42%) aligned exactly 1 time 1571901 (12.34%) aligned >1 times 92.76% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 3702101 / 11817767 = 0.3133 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 10:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.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 10:40:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:40:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:40:27: 1000000 INFO @ Wed, 22 Apr 2020 10:40:33: 2000000 INFO @ Wed, 22 Apr 2020 10:40:40: 3000000 INFO @ Wed, 22 Apr 2020 10:40:47: 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 10:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.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 10:40:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:40:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:40:55: 5000000 INFO @ Wed, 22 Apr 2020 10:40:59: 1000000 INFO @ Wed, 22 Apr 2020 10:41:03: 6000000 INFO @ Wed, 22 Apr 2020 10:41:07: 2000000 INFO @ Wed, 22 Apr 2020 10:41:12: 7000000 INFO @ Wed, 22 Apr 2020 10:41:16: 3000000 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 10:41:19: 8000000 INFO @ Wed, 22 Apr 2020 10:41:20: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 10:41:20: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 10:41:20: #1 total tags in treatment: 8115666 INFO @ Wed, 22 Apr 2020 10:41:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:41:20: #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 10:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.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 10:41:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:41:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:41:20: #1 tags after filtering in treatment: 8115666 INFO @ Wed, 22 Apr 2020 10:41:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:41:20: #1 finished! INFO @ Wed, 22 Apr 2020 10:41:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:41:20: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:41:20: 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 10:41:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.05_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/SRX7587251/SRX7587251.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:41:24: 4000000 INFO @ Wed, 22 Apr 2020 10:41:29: 1000000 INFO @ Wed, 22 Apr 2020 10:41:36: 5000000 INFO @ Wed, 22 Apr 2020 10:41:39: 2000000 INFO @ Wed, 22 Apr 2020 10:41:47: 6000000 INFO @ Wed, 22 Apr 2020 10:41:48: 3000000 INFO @ Wed, 22 Apr 2020 10:41:57: 4000000 INFO @ Wed, 22 Apr 2020 10:41:59: 7000000 INFO @ Wed, 22 Apr 2020 10:42:06: 5000000 INFO @ Wed, 22 Apr 2020 10:42:10: 8000000 INFO @ Wed, 22 Apr 2020 10:42:11: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 10:42:11: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 10:42:11: #1 total tags in treatment: 8115666 INFO @ Wed, 22 Apr 2020 10:42:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:11: #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 10:42:11: #1 tags after filtering in treatment: 8115666 INFO @ Wed, 22 Apr 2020 10:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:42:11: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:12: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:12: 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 10:42:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.10_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/SRX7587251/SRX7587251.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:42:15: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:42:27: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:42:37: 8000000 INFO @ Wed, 22 Apr 2020 10:42:38: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 10:42:38: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 10:42:38: #1 total tags in treatment: 8115666 INFO @ Wed, 22 Apr 2020 10:42:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:38: #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 10:42:38: #1 tags after filtering in treatment: 8115666 INFO @ Wed, 22 Apr 2020 10:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:42:38: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:39: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:39: 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 10:42:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.20_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/SRX7587251/SRX7587251.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7587251/SRX7587251.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling