Job ID = 5791089 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T23:29:04 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 ) 2020-04-21T23:29:04 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 ) spots read : 11,447,823 reads read : 22,895,646 reads written : 11,447,823 reads 0-length : 11,447,823 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: 00:01:18 11447823 reads; of these: 11447823 (100.00%) were unpaired; of these: 934010 (8.16%) aligned 0 times 9204260 (80.40%) aligned exactly 1 time 1309553 (11.44%) aligned >1 times 91.84% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 3226997 / 10513813 = 0.3069 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 08:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.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 08:34:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:34:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:34:48: 1000000 INFO @ Wed, 22 Apr 2020 08:34:53: 2000000 INFO @ Wed, 22 Apr 2020 08:34:58: 3000000 INFO @ Wed, 22 Apr 2020 08:35:03: 4000000 INFO @ Wed, 22 Apr 2020 08:35:08: 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 08:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.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 08:35:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:35:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:35:13: 6000000 INFO @ Wed, 22 Apr 2020 08:35:18: 1000000 INFO @ Wed, 22 Apr 2020 08:35:18: 7000000 INFO @ Wed, 22 Apr 2020 08:35:20: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:35:20: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:35:20: #1 total tags in treatment: 7286816 INFO @ Wed, 22 Apr 2020 08:35:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:35:20: #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 08:35:20: #1 tags after filtering in treatment: 7286816 INFO @ Wed, 22 Apr 2020 08:35:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:35:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:35:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:35:20: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:35:20: 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 08:35:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.05_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/SRX5936157/SRX5936157.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:35:24: 2000000 INFO @ Wed, 22 Apr 2020 08:35:29: 3000000 INFO @ Wed, 22 Apr 2020 08:35:34: 4000000 INFO @ Wed, 22 Apr 2020 08:35:40: 5000000 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 08:35:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.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 08:35:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:35:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:35:45: 6000000 INFO @ Wed, 22 Apr 2020 08:35:49: 1000000 INFO @ Wed, 22 Apr 2020 08:35:51: 7000000 INFO @ Wed, 22 Apr 2020 08:35:52: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:35:52: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:35:52: #1 total tags in treatment: 7286816 INFO @ Wed, 22 Apr 2020 08:35:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:35:52: #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 08:35:53: #1 tags after filtering in treatment: 7286816 INFO @ Wed, 22 Apr 2020 08:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:35:53: #1 finished! INFO @ Wed, 22 Apr 2020 08:35:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:35:53: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:35:53: 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 08:35:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.10_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/SRX5936157/SRX5936157.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:35:54: 2000000 INFO @ Wed, 22 Apr 2020 08:36:00: 3000000 INFO @ Wed, 22 Apr 2020 08:36:05: 4000000 INFO @ Wed, 22 Apr 2020 08:36:11: 5000000 INFO @ Wed, 22 Apr 2020 08:36:16: 6000000 INFO @ Wed, 22 Apr 2020 08:36:21: 7000000 INFO @ Wed, 22 Apr 2020 08:36:23: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 08:36:23: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 08:36:23: #1 total tags in treatment: 7286816 INFO @ Wed, 22 Apr 2020 08:36:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:36:23: #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 08:36:23: #1 tags after filtering in treatment: 7286816 INFO @ Wed, 22 Apr 2020 08:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:36:23: #1 finished! INFO @ Wed, 22 Apr 2020 08:36:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:36:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:36:23: 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 08:36:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.20_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/SRX5936157/SRX5936157.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5936157/SRX5936157.20_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。