Job ID = 5790814 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T22:37:57 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 ) 2020-04-21T22:50:53 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 ) 2020-04-21T22:50:53 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 ) 2020-04-21T22:56:22 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 : 12,691,063 reads read : 25,382,126 reads written : 25,382,126 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: 00:10:17 12691063 reads; of these: 12691063 (100.00%) were paired; of these: 1046657 (8.25%) aligned concordantly 0 times 10110981 (79.67%) aligned concordantly exactly 1 time 1533425 (12.08%) aligned concordantly >1 times ---- 1046657 pairs aligned concordantly 0 times; of these: 488554 (46.68%) aligned discordantly 1 time ---- 558103 pairs aligned 0 times concordantly or discordantly; of these: 1116206 mates make up the pairs; of these: 873520 (78.26%) aligned 0 times 77252 (6.92%) aligned exactly 1 time 165434 (14.82%) aligned >1 times 96.56% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2126435 / 12098092 = 0.1758 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 08:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.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 08:18:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:18:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:18:42: 1000000 INFO @ Wed, 22 Apr 2020 08:18:48: 2000000 INFO @ Wed, 22 Apr 2020 08:18:54: 3000000 INFO @ Wed, 22 Apr 2020 08:19:00: 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 08:19:05: 5000000 INFO @ Wed, 22 Apr 2020 08:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.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 08:19:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:19:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:19:12: 6000000 INFO @ Wed, 22 Apr 2020 08:19:13: 1000000 INFO @ Wed, 22 Apr 2020 08:19:18: 7000000 INFO @ Wed, 22 Apr 2020 08:19:19: 2000000 INFO @ Wed, 22 Apr 2020 08:19:24: 8000000 INFO @ Wed, 22 Apr 2020 08:19:26: 3000000 INFO @ Wed, 22 Apr 2020 08:19:30: 9000000 INFO @ Wed, 22 Apr 2020 08:19:33: 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 08:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.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 08:19:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:19:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:19:36: 10000000 INFO @ Wed, 22 Apr 2020 08:19:40: 5000000 INFO @ Wed, 22 Apr 2020 08:19:43: 11000000 INFO @ Wed, 22 Apr 2020 08:19:43: 1000000 INFO @ Wed, 22 Apr 2020 08:19:47: 6000000 INFO @ Wed, 22 Apr 2020 08:19:49: 12000000 INFO @ Wed, 22 Apr 2020 08:19:50: 2000000 INFO @ Wed, 22 Apr 2020 08:19:54: 7000000 INFO @ Wed, 22 Apr 2020 08:19:56: 13000000 INFO @ Wed, 22 Apr 2020 08:19:56: 3000000 INFO @ Wed, 22 Apr 2020 08:20:00: 8000000 INFO @ Wed, 22 Apr 2020 08:20:02: 14000000 INFO @ Wed, 22 Apr 2020 08:20:03: 4000000 INFO @ Wed, 22 Apr 2020 08:20:07: 9000000 INFO @ Wed, 22 Apr 2020 08:20:09: 15000000 INFO @ Wed, 22 Apr 2020 08:20:10: 5000000 INFO @ Wed, 22 Apr 2020 08:20:14: 10000000 INFO @ Wed, 22 Apr 2020 08:20:15: 16000000 INFO @ Wed, 22 Apr 2020 08:20:16: 6000000 INFO @ Wed, 22 Apr 2020 08:20:21: 11000000 INFO @ Wed, 22 Apr 2020 08:20:22: 17000000 INFO @ Wed, 22 Apr 2020 08:20:23: 7000000 INFO @ Wed, 22 Apr 2020 08:20:28: 12000000 INFO @ Wed, 22 Apr 2020 08:20:28: 18000000 INFO @ Wed, 22 Apr 2020 08:20:30: 8000000 INFO @ Wed, 22 Apr 2020 08:20:35: 13000000 INFO @ Wed, 22 Apr 2020 08:20:35: 19000000 INFO @ Wed, 22 Apr 2020 08:20:37: 9000000 INFO @ Wed, 22 Apr 2020 08:20:41: 14000000 INFO @ Wed, 22 Apr 2020 08:20:42: 20000000 INFO @ Wed, 22 Apr 2020 08:20:43: 10000000 INFO @ Wed, 22 Apr 2020 08:20:44: #1 tag size is determined as 99 bps INFO @ Wed, 22 Apr 2020 08:20:44: #1 tag size = 99 INFO @ Wed, 22 Apr 2020 08:20:44: #1 total tags in treatment: 9569608 INFO @ Wed, 22 Apr 2020 08:20:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:20:44: #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 08:20:44: #1 tags after filtering in treatment: 7066654 INFO @ Wed, 22 Apr 2020 08:20:44: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Apr 2020 08:20:44: #1 finished! INFO @ Wed, 22 Apr 2020 08:20:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:20:44: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:20:44: 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 08:20:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.05_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/DRX137663/DRX137663.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:20:48: 15000000 INFO @ Wed, 22 Apr 2020 08:20:49: 11000000 INFO @ Wed, 22 Apr 2020 08:20:54: 16000000 INFO @ Wed, 22 Apr 2020 08:20:55: 12000000 INFO @ Wed, 22 Apr 2020 08:21:01: 17000000 INFO @ Wed, 22 Apr 2020 08:21:01: 13000000 INFO @ Wed, 22 Apr 2020 08:21:07: 14000000 INFO @ Wed, 22 Apr 2020 08:21:08: 18000000 INFO @ Wed, 22 Apr 2020 08:21:14: 15000000 INFO @ Wed, 22 Apr 2020 08:21:15: 19000000 INFO @ Wed, 22 Apr 2020 08:21:20: 16000000 INFO @ Wed, 22 Apr 2020 08:21:21: 20000000 INFO @ Wed, 22 Apr 2020 08:21:23: #1 tag size is determined as 99 bps INFO @ Wed, 22 Apr 2020 08:21:23: #1 tag size = 99 INFO @ Wed, 22 Apr 2020 08:21:23: #1 total tags in treatment: 9569608 INFO @ Wed, 22 Apr 2020 08:21:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:21:23: #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 08:21:23: #1 tags after filtering in treatment: 7066654 INFO @ Wed, 22 Apr 2020 08:21:23: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Apr 2020 08:21:23: #1 finished! INFO @ Wed, 22 Apr 2020 08:21:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:21:24: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:21:24: 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 08:21:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.10_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/DRX137663/DRX137663.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:21:25: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:21:31: 18000000 INFO @ Wed, 22 Apr 2020 08:21:37: 19000000 INFO @ Wed, 22 Apr 2020 08:21:42: 20000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:21:44: #1 tag size is determined as 99 bps INFO @ Wed, 22 Apr 2020 08:21:44: #1 tag size = 99 INFO @ Wed, 22 Apr 2020 08:21:44: #1 total tags in treatment: 9569608 INFO @ Wed, 22 Apr 2020 08:21:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:21:44: #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 08:21:44: #1 tags after filtering in treatment: 7066654 INFO @ Wed, 22 Apr 2020 08:21:44: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Apr 2020 08:21:44: #1 finished! INFO @ Wed, 22 Apr 2020 08:21:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:21:44: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:21:44: 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 08:21:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.20_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/DRX137663/DRX137663.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/DRX137663/DRX137663.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling