Job ID = 5791825 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-22T01:42:58 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 ) 2020-04-22T01:48:44 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 ) 2020-04-22T01:49:51 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 : 19,190,458 reads read : 19,190,458 reads written : 19,190,458 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: 00:00:01 Multiseed full-index search: 00:02:51 19190458 reads; of these: 19190458 (100.00%) were unpaired; of these: 5872505 (30.60%) aligned 0 times 10972049 (57.17%) aligned exactly 1 time 2345904 (12.22%) aligned >1 times 69.40% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 4842080 / 13317953 = 0.3636 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 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 10:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.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 10:57:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:57:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.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 10:57:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:57:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:57:25: 1000000 INFO @ Wed, 22 Apr 2020 10:57:26: 1000000 INFO @ Wed, 22 Apr 2020 10:57:31: 2000000 INFO @ Wed, 22 Apr 2020 10:57:32: 2000000 INFO @ Wed, 22 Apr 2020 10:57:36: 3000000 INFO @ Wed, 22 Apr 2020 10:57:38: 3000000 INFO @ Wed, 22 Apr 2020 10:57:42: 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 10:57:45: 4000000 INFO @ Wed, 22 Apr 2020 10:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.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 10:57:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:57:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:57:48: 5000000 INFO @ Wed, 22 Apr 2020 10:57:51: 5000000 INFO @ Wed, 22 Apr 2020 10:57:53: 1000000 INFO @ Wed, 22 Apr 2020 10:57:53: 6000000 INFO @ Wed, 22 Apr 2020 10:57:58: 6000000 INFO @ Wed, 22 Apr 2020 10:57:59: 7000000 INFO @ Wed, 22 Apr 2020 10:58:00: 2000000 INFO @ Wed, 22 Apr 2020 10:58:04: 7000000 INFO @ Wed, 22 Apr 2020 10:58:05: 8000000 INFO @ Wed, 22 Apr 2020 10:58:06: 3000000 INFO @ Wed, 22 Apr 2020 10:58:07: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 10:58:07: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 10:58:07: #1 total tags in treatment: 8475873 INFO @ Wed, 22 Apr 2020 10:58:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:07: #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 10:58:07: #1 tags after filtering in treatment: 8475873 INFO @ Wed, 22 Apr 2020 10:58:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:58:07: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:58:08: 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 10:58:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:58:11: 8000000 INFO @ Wed, 22 Apr 2020 10:58:13: 4000000 INFO @ Wed, 22 Apr 2020 10:58:14: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 10:58:14: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 10:58:14: #1 total tags in treatment: 8475873 INFO @ Wed, 22 Apr 2020 10:58:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:14: #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 10:58:14: #1 tags after filtering in treatment: 8475873 INFO @ Wed, 22 Apr 2020 10:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:58:14: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:14: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:58:14: 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 10:58:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.10_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/SRX7887002/SRX7887002.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:58:20: 5000000 INFO @ Wed, 22 Apr 2020 10:58:26: 6000000 INFO @ Wed, 22 Apr 2020 10:58:32: 7000000 INFO @ Wed, 22 Apr 2020 10:58:39: 8000000 INFO @ Wed, 22 Apr 2020 10:58:42: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 10:58:42: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 10:58:42: #1 total tags in treatment: 8475873 INFO @ Wed, 22 Apr 2020 10:58:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:58:42: #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 10:58:42: #1 tags after filtering in treatment: 8475873 INFO @ Wed, 22 Apr 2020 10:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 10:58:42: #1 finished! INFO @ Wed, 22 Apr 2020 10:58:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:58:42: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:58:42: 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 10:58:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7887002/SRX7887002.20_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。