Job ID = 5791722 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-22T01:38:23 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 ) 1900-01-00T00:00:00 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 ) 2020-04-22T01:47:49 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 ) 2020-04-22T01:51:15 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 : 28,661,946 reads read : 28,661,946 reads written : 28,661,946 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: 00:03:15 28661946 reads; of these: 28661946 (100.00%) were unpaired; of these: 1614895 (5.63%) aligned 0 times 17807388 (62.13%) aligned exactly 1 time 9239663 (32.24%) aligned >1 times 94.37% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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 12 files... [bam_rmdupse_core] 15282927 / 27047051 = 0.5650 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 11:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.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 11:01:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:01:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:01:11: 1000000 INFO @ Wed, 22 Apr 2020 11:01:16: 2000000 INFO @ Wed, 22 Apr 2020 11:01:22: 3000000 INFO @ Wed, 22 Apr 2020 11:01:27: 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 11:01:33: 5000000 INFO @ Wed, 22 Apr 2020 11:01:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.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 11:01:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:01:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:01:38: 6000000 INFO @ Wed, 22 Apr 2020 11:01:42: 1000000 INFO @ Wed, 22 Apr 2020 11:01:45: 7000000 INFO @ Wed, 22 Apr 2020 11:01:48: 2000000 INFO @ Wed, 22 Apr 2020 11:01:51: 8000000 INFO @ Wed, 22 Apr 2020 11:01:54: 3000000 INFO @ Wed, 22 Apr 2020 11:01:57: 9000000 INFO @ Wed, 22 Apr 2020 11:02:00: 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 11:02:03: 10000000 INFO @ Wed, 22 Apr 2020 11:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.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 11:02:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:02:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:02:06: 5000000 INFO @ Wed, 22 Apr 2020 11:02:09: 11000000 INFO @ Wed, 22 Apr 2020 11:02:12: 1000000 INFO @ Wed, 22 Apr 2020 11:02:12: 6000000 INFO @ Wed, 22 Apr 2020 11:02:14: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 11:02:14: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 11:02:14: #1 total tags in treatment: 11764124 INFO @ Wed, 22 Apr 2020 11:02:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:02:14: #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 11:02:14: #1 tags after filtering in treatment: 11764124 INFO @ Wed, 22 Apr 2020 11:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 11:02:14: #1 finished! INFO @ Wed, 22 Apr 2020 11:02:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:02:14: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:02:14: 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 11:02:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.05_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/SRX7700981/SRX7700981.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:02:18: 2000000 INFO @ Wed, 22 Apr 2020 11:02:18: 7000000 INFO @ Wed, 22 Apr 2020 11:02:24: 3000000 INFO @ Wed, 22 Apr 2020 11:02:24: 8000000 INFO @ Wed, 22 Apr 2020 11:02:30: 4000000 INFO @ Wed, 22 Apr 2020 11:02:30: 9000000 INFO @ Wed, 22 Apr 2020 11:02:36: 5000000 INFO @ Wed, 22 Apr 2020 11:02:36: 10000000 INFO @ Wed, 22 Apr 2020 11:02:42: 6000000 INFO @ Wed, 22 Apr 2020 11:02:42: 11000000 INFO @ Wed, 22 Apr 2020 11:02:47: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 11:02:47: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 11:02:47: #1 total tags in treatment: 11764124 INFO @ Wed, 22 Apr 2020 11:02:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:02:47: #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 11:02:47: #1 tags after filtering in treatment: 11764124 INFO @ Wed, 22 Apr 2020 11:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 11:02:47: #1 finished! INFO @ Wed, 22 Apr 2020 11:02:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:02:48: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:02:48: 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 11:02:48: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:02:48: 7000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.10_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/SRX7700981/SRX7700981.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:02:54: 8000000 INFO @ Wed, 22 Apr 2020 11:02:59: 9000000 INFO @ Wed, 22 Apr 2020 11:03:05: 10000000 INFO @ Wed, 22 Apr 2020 11:03:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:03:15: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 11:03:15: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 11:03:15: #1 total tags in treatment: 11764124 INFO @ Wed, 22 Apr 2020 11:03:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:03:15: #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 11:03:15: #1 tags after filtering in treatment: 11764124 INFO @ Wed, 22 Apr 2020 11:03:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 11:03:15: #1 finished! INFO @ Wed, 22 Apr 2020 11:03:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:03:16: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:03:16: 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 11:03:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.20_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/SRX7700981/SRX7700981.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7700981/SRX7700981.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。