Job ID = 5791874 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-22T01:48:44 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 : NET - Reading information from the socket failed ) 2020-04-22T01:48:44 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 : NET - Reading information from the socket failed ) spots read : 16,723,137 reads read : 16,723,137 reads written : 16,723,137 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: 00:02:11 16723137 reads; of these: 16723137 (100.00%) were unpaired; of these: 1055987 (6.31%) aligned 0 times 13501541 (80.74%) aligned exactly 1 time 2165609 (12.95%) aligned >1 times 93.69% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 5114414 / 15667150 = 0.3264 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 10:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.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 10:55:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:55:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:56:00: 1000000 INFO @ Wed, 22 Apr 2020 10:56:06: 2000000 INFO @ Wed, 22 Apr 2020 10:56:11: 3000000 INFO @ Wed, 22 Apr 2020 10:56:17: 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 10:56:23: 5000000 INFO @ Wed, 22 Apr 2020 10:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.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 10:56:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:56:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:56:29: 6000000 INFO @ Wed, 22 Apr 2020 10:56:30: 1000000 INFO @ Wed, 22 Apr 2020 10:56:35: 7000000 INFO @ Wed, 22 Apr 2020 10:56:36: 2000000 INFO @ Wed, 22 Apr 2020 10:56:41: 8000000 INFO @ Wed, 22 Apr 2020 10:56:42: 3000000 INFO @ Wed, 22 Apr 2020 10:56:47: 9000000 INFO @ Wed, 22 Apr 2020 10:56:48: 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 10:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.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 10:56:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:56:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:56:53: 10000000 INFO @ Wed, 22 Apr 2020 10:56:54: 5000000 INFO @ Wed, 22 Apr 2020 10:56:56: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 10:56:56: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 10:56:56: #1 total tags in treatment: 10552736 INFO @ Wed, 22 Apr 2020 10:56:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:56:56: #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 10:56:56: #1 tags after filtering in treatment: 10552736 INFO @ Wed, 22 Apr 2020 10:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:56:56: #1 finished! INFO @ Wed, 22 Apr 2020 10:56:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:56:57: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:56:57: 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 10:56:57: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:56:59: 1000000 INFO @ Wed, 22 Apr 2020 10:57:00: 6000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.05_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/SRX7887004/SRX7887004.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:57:05: 2000000 INFO @ Wed, 22 Apr 2020 10:57:06: 7000000 INFO @ Wed, 22 Apr 2020 10:57:11: 3000000 INFO @ Wed, 22 Apr 2020 10:57:12: 8000000 INFO @ Wed, 22 Apr 2020 10:57:17: 4000000 INFO @ Wed, 22 Apr 2020 10:57:18: 9000000 INFO @ Wed, 22 Apr 2020 10:57:23: 5000000 INFO @ Wed, 22 Apr 2020 10:57:24: 10000000 INFO @ Wed, 22 Apr 2020 10:57:27: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 10:57:27: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 10:57:27: #1 total tags in treatment: 10552736 INFO @ Wed, 22 Apr 2020 10:57:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:57:27: #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 10:57:27: #1 tags after filtering in treatment: 10552736 INFO @ Wed, 22 Apr 2020 10:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:57:27: #1 finished! INFO @ Wed, 22 Apr 2020 10:57:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:57:28: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:57:28: 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 10:57:28: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:57:29: 6000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.10_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/SRX7887004/SRX7887004.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:57:34: 7000000 INFO @ Wed, 22 Apr 2020 10:57:40: 8000000 INFO @ Wed, 22 Apr 2020 10:57:46: 9000000 INFO @ Wed, 22 Apr 2020 10:57:52: 10000000 INFO @ Wed, 22 Apr 2020 10:57:55: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 10:57:55: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 10:57:55: #1 total tags in treatment: 10552736 INFO @ Wed, 22 Apr 2020 10:57:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:57:55: #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 10:57:55: #1 tags after filtering in treatment: 10552736 INFO @ Wed, 22 Apr 2020 10:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:57:55: #1 finished! INFO @ Wed, 22 Apr 2020 10:57:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:57:55: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:57:55: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:57:55: 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 10:57:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.20_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/SRX7887004/SRX7887004.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887004/SRX7887004.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。