Job ID = 5791490 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:31:46 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 ) 2020-04-22T00:31:46 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 ) 2020-04-22T00:31:46 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 ) 2020-04-22T00:36:59 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 ) 2020-04-22T00:38:55 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 ) 2020-04-22T00:44:06 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 ) 2020-04-22T00:47:40 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 : 41,167,887 reads read : 82,335,774 reads written : 82,335,774 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: 00:13:25 41167887 reads; of these: 41167887 (100.00%) were paired; of these: 17879875 (43.43%) aligned concordantly 0 times 20884348 (50.73%) aligned concordantly exactly 1 time 2403664 (5.84%) aligned concordantly >1 times ---- 17879875 pairs aligned concordantly 0 times; of these: 43236 (0.24%) aligned discordantly 1 time ---- 17836639 pairs aligned 0 times concordantly or discordantly; of these: 35673278 mates make up the pairs; of these: 35178888 (98.61%) aligned 0 times 423979 (1.19%) aligned exactly 1 time 70411 (0.20%) aligned >1 times 57.27% overall alignment rate Time searching: 00:13:25 Overall time: 00:13:25 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 20 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] 7330431 / 23303819 = 0.3146 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 10:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.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 10:19:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:19:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:19:27: 1000000 INFO @ Wed, 22 Apr 2020 10:19:31: 2000000 INFO @ Wed, 22 Apr 2020 10:19:35: 3000000 INFO @ Wed, 22 Apr 2020 10:19:40: 4000000 INFO @ Wed, 22 Apr 2020 10:19:44: 5000000 INFO @ Wed, 22 Apr 2020 10:19:48: 6000000 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 10:19:52: 7000000 INFO @ Wed, 22 Apr 2020 10:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.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 10:19:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:19:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:19:57: 8000000 INFO @ Wed, 22 Apr 2020 10:19:57: 1000000 INFO @ Wed, 22 Apr 2020 10:20:01: 9000000 INFO @ Wed, 22 Apr 2020 10:20:01: 2000000 INFO @ Wed, 22 Apr 2020 10:20:06: 10000000 INFO @ Wed, 22 Apr 2020 10:20:06: 3000000 INFO @ Wed, 22 Apr 2020 10:20:10: 11000000 INFO @ Wed, 22 Apr 2020 10:20:10: 4000000 INFO @ Wed, 22 Apr 2020 10:20:14: 12000000 INFO @ Wed, 22 Apr 2020 10:20:14: 5000000 INFO @ Wed, 22 Apr 2020 10:20:19: 13000000 INFO @ Wed, 22 Apr 2020 10:20:19: 6000000 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 10:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.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 10:20:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:20:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:20:23: 14000000 INFO @ Wed, 22 Apr 2020 10:20:23: 7000000 INFO @ Wed, 22 Apr 2020 10:20:27: 1000000 INFO @ Wed, 22 Apr 2020 10:20:28: 15000000 INFO @ Wed, 22 Apr 2020 10:20:28: 8000000 INFO @ Wed, 22 Apr 2020 10:20:32: 2000000 INFO @ Wed, 22 Apr 2020 10:20:32: 16000000 INFO @ Wed, 22 Apr 2020 10:20:32: 9000000 INFO @ Wed, 22 Apr 2020 10:20:37: 17000000 INFO @ Wed, 22 Apr 2020 10:20:37: 10000000 INFO @ Wed, 22 Apr 2020 10:20:37: 3000000 INFO @ Wed, 22 Apr 2020 10:20:41: 18000000 INFO @ Wed, 22 Apr 2020 10:20:41: 11000000 INFO @ Wed, 22 Apr 2020 10:20:41: 4000000 INFO @ Wed, 22 Apr 2020 10:20:45: 12000000 INFO @ Wed, 22 Apr 2020 10:20:46: 19000000 INFO @ Wed, 22 Apr 2020 10:20:46: 5000000 INFO @ Wed, 22 Apr 2020 10:20:50: 13000000 INFO @ Wed, 22 Apr 2020 10:20:50: 20000000 INFO @ Wed, 22 Apr 2020 10:20:51: 6000000 INFO @ Wed, 22 Apr 2020 10:20:54: 14000000 INFO @ Wed, 22 Apr 2020 10:20:54: 21000000 INFO @ Wed, 22 Apr 2020 10:20:55: 7000000 INFO @ Wed, 22 Apr 2020 10:20:59: 15000000 INFO @ Wed, 22 Apr 2020 10:20:59: 22000000 INFO @ Wed, 22 Apr 2020 10:21:00: 8000000 INFO @ Wed, 22 Apr 2020 10:21:03: 16000000 INFO @ Wed, 22 Apr 2020 10:21:03: 23000000 INFO @ Wed, 22 Apr 2020 10:21:04: 9000000 INFO @ Wed, 22 Apr 2020 10:21:07: 17000000 INFO @ Wed, 22 Apr 2020 10:21:08: 24000000 INFO @ Wed, 22 Apr 2020 10:21:08: 10000000 INFO @ Wed, 22 Apr 2020 10:21:12: 18000000 INFO @ Wed, 22 Apr 2020 10:21:12: 25000000 INFO @ Wed, 22 Apr 2020 10:21:13: 11000000 INFO @ Wed, 22 Apr 2020 10:21:16: 19000000 INFO @ Wed, 22 Apr 2020 10:21:17: 26000000 INFO @ Wed, 22 Apr 2020 10:21:17: 12000000 INFO @ Wed, 22 Apr 2020 10:21:20: 20000000 INFO @ Wed, 22 Apr 2020 10:21:21: 27000000 INFO @ Wed, 22 Apr 2020 10:21:21: 13000000 INFO @ Wed, 22 Apr 2020 10:21:25: 21000000 INFO @ Wed, 22 Apr 2020 10:21:25: 28000000 INFO @ Wed, 22 Apr 2020 10:21:26: 14000000 INFO @ Wed, 22 Apr 2020 10:21:29: 22000000 INFO @ Wed, 22 Apr 2020 10:21:30: 29000000 INFO @ Wed, 22 Apr 2020 10:21:30: 15000000 INFO @ Wed, 22 Apr 2020 10:21:34: 23000000 INFO @ Wed, 22 Apr 2020 10:21:34: 30000000 INFO @ Wed, 22 Apr 2020 10:21:35: 16000000 INFO @ Wed, 22 Apr 2020 10:21:38: 24000000 INFO @ Wed, 22 Apr 2020 10:21:39: 31000000 INFO @ Wed, 22 Apr 2020 10:21:39: 17000000 INFO @ Wed, 22 Apr 2020 10:21:42: 25000000 INFO @ Wed, 22 Apr 2020 10:21:43: 32000000 INFO @ Wed, 22 Apr 2020 10:21:44: 18000000 INFO @ Wed, 22 Apr 2020 10:21:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:21:45: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:21:45: #1 total tags in treatment: 15964259 INFO @ Wed, 22 Apr 2020 10:21:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:21:45: #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 10:21:46: #1 tags after filtering in treatment: 10845179 INFO @ Wed, 22 Apr 2020 10:21:46: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Apr 2020 10:21:46: #1 finished! INFO @ Wed, 22 Apr 2020 10:21:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:21:46: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:21:46: 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 10:21:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.05_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/SRX7409576/SRX7409576.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:21:47: 26000000 INFO @ Wed, 22 Apr 2020 10:21:48: 19000000 INFO @ Wed, 22 Apr 2020 10:21:51: 27000000 INFO @ Wed, 22 Apr 2020 10:21:52: 20000000 INFO @ Wed, 22 Apr 2020 10:21:55: 28000000 INFO @ Wed, 22 Apr 2020 10:21:57: 21000000 INFO @ Wed, 22 Apr 2020 10:21:59: 29000000 INFO @ Wed, 22 Apr 2020 10:22:01: 22000000 INFO @ Wed, 22 Apr 2020 10:22:04: 30000000 INFO @ Wed, 22 Apr 2020 10:22:05: 23000000 INFO @ Wed, 22 Apr 2020 10:22:08: 31000000 INFO @ Wed, 22 Apr 2020 10:22:10: 24000000 INFO @ Wed, 22 Apr 2020 10:22:12: 32000000 INFO @ Wed, 22 Apr 2020 10:22:14: 25000000 INFO @ Wed, 22 Apr 2020 10:22:15: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:22:15: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:22:15: #1 total tags in treatment: 15964259 INFO @ Wed, 22 Apr 2020 10:22:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:22:15: #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 10:22:15: #1 tags after filtering in treatment: 10845179 INFO @ Wed, 22 Apr 2020 10:22:15: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Apr 2020 10:22:15: #1 finished! INFO @ Wed, 22 Apr 2020 10:22:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:22:15: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:22:15: 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 10:22:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.10_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/SRX7409576/SRX7409576.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:22:18: 26000000 INFO @ Wed, 22 Apr 2020 10:22:23: 27000000 INFO @ Wed, 22 Apr 2020 10:22:27: 28000000 INFO @ Wed, 22 Apr 2020 10:22:31: 29000000 INFO @ Wed, 22 Apr 2020 10:22:35: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:22:39: 31000000 INFO @ Wed, 22 Apr 2020 10:22:44: 32000000 INFO @ Wed, 22 Apr 2020 10:22:46: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:22:46: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:22:46: #1 total tags in treatment: 15964259 INFO @ Wed, 22 Apr 2020 10:22:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:22:46: #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 10:22:46: #1 tags after filtering in treatment: 10845179 INFO @ Wed, 22 Apr 2020 10:22:46: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Apr 2020 10:22:46: #1 finished! INFO @ Wed, 22 Apr 2020 10:22:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:22:47: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:22:47: 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 10:22:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.20_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/SRX7409576/SRX7409576.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409576/SRX7409576.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。