Job ID = 5791218 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-22T00:02:09 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 ) 2020-04-22T00:02:09 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 : 7,191,316 reads read : 14,382,632 reads written : 7,191,316 reads 0-length : 7,191,316 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: 00:00:51 7191316 reads; of these: 7191316 (100.00%) were unpaired; of these: 573463 (7.97%) aligned 0 times 5769678 (80.23%) aligned exactly 1 time 848175 (11.79%) aligned >1 times 92.03% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 1958141 / 6617853 = 0.2959 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 09:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.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 09:06:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:06:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:06:46: 1000000 INFO @ Wed, 22 Apr 2020 09:06:50: 2000000 INFO @ Wed, 22 Apr 2020 09:06:55: 3000000 INFO @ Wed, 22 Apr 2020 09:06:59: 4000000 INFO @ Wed, 22 Apr 2020 09:07:02: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:07:02: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:07:02: #1 total tags in treatment: 4659712 INFO @ Wed, 22 Apr 2020 09:07:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:02: #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 09:07:02: #1 tags after filtering in treatment: 4659712 INFO @ Wed, 22 Apr 2020 09:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:07:02: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:03: #2 number of paired peaks: 23 WARNING @ Wed, 22 Apr 2020 09:07:03: Too few paired peaks (23) 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 09:07:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.05_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/SRX6879623/SRX6879623.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 09:07:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.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 09:07:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:07:16: 1000000 INFO @ Wed, 22 Apr 2020 09:07:22: 2000000 INFO @ Wed, 22 Apr 2020 09:07:27: 3000000 INFO @ Wed, 22 Apr 2020 09:07:32: 4000000 INFO @ Wed, 22 Apr 2020 09:07:36: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:07:36: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:07:36: #1 total tags in treatment: 4659712 INFO @ Wed, 22 Apr 2020 09:07:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:36: #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 09:07:36: #1 tags after filtering in treatment: 4659712 INFO @ Wed, 22 Apr 2020 09:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:07:36: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:36: #2 number of paired peaks: 23 WARNING @ Wed, 22 Apr 2020 09:07:36: Too few paired peaks (23) 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 09:07:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.10_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/SRX6879623/SRX6879623.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 09:07:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.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 09:07:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:07:46: 1000000 INFO @ Wed, 22 Apr 2020 09:07:51: 2000000 INFO @ Wed, 22 Apr 2020 09:07:57: 3000000 INFO @ Wed, 22 Apr 2020 09:08:02: 4000000 INFO @ Wed, 22 Apr 2020 09:08:05: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:08:05: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:08:05: #1 total tags in treatment: 4659712 INFO @ Wed, 22 Apr 2020 09:08:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:08:05: #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 09:08:05: #1 tags after filtering in treatment: 4659712 INFO @ Wed, 22 Apr 2020 09:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:08:05: #1 finished! INFO @ Wed, 22 Apr 2020 09:08:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:08:05: #2 number of paired peaks: 23 WARNING @ Wed, 22 Apr 2020 09:08:05: Too few paired peaks (23) 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 09:08:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.20_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/SRX6879623/SRX6879623.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6879623/SRX6879623.20_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。