Job ID = 5791489 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 ) 2020-04-22T00:36:59 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 ) 2020-04-22T00:47:40 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 ) 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 ) 2020-04-22T00:50:48 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 : 28,719,202 reads read : 57,438,404 reads written : 57,438,404 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: 00:14:50 28719202 reads; of these: 28719202 (100.00%) were paired; of these: 391777 (1.36%) aligned concordantly 0 times 25280222 (88.03%) aligned concordantly exactly 1 time 3047203 (10.61%) aligned concordantly >1 times ---- 391777 pairs aligned concordantly 0 times; of these: 83072 (21.20%) aligned discordantly 1 time ---- 308705 pairs aligned 0 times concordantly or discordantly; of these: 617410 mates make up the pairs; of these: 392462 (63.57%) aligned 0 times 171024 (27.70%) aligned exactly 1 time 53924 (8.73%) aligned >1 times 99.32% overall alignment rate Time searching: 00:14:50 Overall time: 00:14:50 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 24 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] 5893114 / 28350537 = 0.2079 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 10:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.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 10:17:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:17:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:17:29: 1000000 INFO @ Wed, 22 Apr 2020 10:17:34: 2000000 INFO @ Wed, 22 Apr 2020 10:17:40: 3000000 INFO @ Wed, 22 Apr 2020 10:17:46: 4000000 INFO @ Wed, 22 Apr 2020 10:17:51: 5000000 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 10:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.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 10:17:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:17:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:17:57: 6000000 INFO @ Wed, 22 Apr 2020 10:17:59: 1000000 INFO @ Wed, 22 Apr 2020 10:18:03: 7000000 INFO @ Wed, 22 Apr 2020 10:18:05: 2000000 INFO @ Wed, 22 Apr 2020 10:18:09: 8000000 INFO @ Wed, 22 Apr 2020 10:18:10: 3000000 INFO @ Wed, 22 Apr 2020 10:18:16: 4000000 INFO @ Wed, 22 Apr 2020 10:18:16: 9000000 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 10:18:22: 5000000 INFO @ Wed, 22 Apr 2020 10:18:22: 10000000 INFO @ Wed, 22 Apr 2020 10:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.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 10:18:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:18:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:18:27: 6000000 INFO @ Wed, 22 Apr 2020 10:18:29: 11000000 INFO @ Wed, 22 Apr 2020 10:18:29: 1000000 INFO @ Wed, 22 Apr 2020 10:18:33: 7000000 INFO @ Wed, 22 Apr 2020 10:18:34: 2000000 INFO @ Wed, 22 Apr 2020 10:18:35: 12000000 INFO @ Wed, 22 Apr 2020 10:18:38: 8000000 INFO @ Wed, 22 Apr 2020 10:18:40: 3000000 INFO @ Wed, 22 Apr 2020 10:18:41: 13000000 INFO @ Wed, 22 Apr 2020 10:18:44: 9000000 INFO @ Wed, 22 Apr 2020 10:18:46: 4000000 INFO @ Wed, 22 Apr 2020 10:18:48: 14000000 INFO @ Wed, 22 Apr 2020 10:18:49: 10000000 INFO @ Wed, 22 Apr 2020 10:18:51: 5000000 INFO @ Wed, 22 Apr 2020 10:18:54: 15000000 INFO @ Wed, 22 Apr 2020 10:18:55: 11000000 INFO @ Wed, 22 Apr 2020 10:18:57: 6000000 INFO @ Wed, 22 Apr 2020 10:19:00: 16000000 INFO @ Wed, 22 Apr 2020 10:19:01: 12000000 INFO @ Wed, 22 Apr 2020 10:19:03: 7000000 INFO @ Wed, 22 Apr 2020 10:19:06: 13000000 INFO @ Wed, 22 Apr 2020 10:19:07: 17000000 INFO @ Wed, 22 Apr 2020 10:19:08: 8000000 INFO @ Wed, 22 Apr 2020 10:19:12: 14000000 INFO @ Wed, 22 Apr 2020 10:19:13: 18000000 INFO @ Wed, 22 Apr 2020 10:19:14: 9000000 INFO @ Wed, 22 Apr 2020 10:19:17: 15000000 INFO @ Wed, 22 Apr 2020 10:19:19: 19000000 INFO @ Wed, 22 Apr 2020 10:19:19: 10000000 INFO @ Wed, 22 Apr 2020 10:19:23: 16000000 INFO @ Wed, 22 Apr 2020 10:19:25: 11000000 INFO @ Wed, 22 Apr 2020 10:19:25: 20000000 INFO @ Wed, 22 Apr 2020 10:19:28: 17000000 INFO @ Wed, 22 Apr 2020 10:19:30: 12000000 INFO @ Wed, 22 Apr 2020 10:19:32: 21000000 INFO @ Wed, 22 Apr 2020 10:19:34: 18000000 INFO @ Wed, 22 Apr 2020 10:19:36: 13000000 INFO @ Wed, 22 Apr 2020 10:19:38: 22000000 INFO @ Wed, 22 Apr 2020 10:19:40: 19000000 INFO @ Wed, 22 Apr 2020 10:19:41: 14000000 INFO @ Wed, 22 Apr 2020 10:19:44: 23000000 INFO @ Wed, 22 Apr 2020 10:19:45: 20000000 INFO @ Wed, 22 Apr 2020 10:19:47: 15000000 INFO @ Wed, 22 Apr 2020 10:19:50: 24000000 INFO @ Wed, 22 Apr 2020 10:19:51: 21000000 INFO @ Wed, 22 Apr 2020 10:19:52: 16000000 INFO @ Wed, 22 Apr 2020 10:19:56: 22000000 INFO @ Wed, 22 Apr 2020 10:19:57: 25000000 INFO @ Wed, 22 Apr 2020 10:19:58: 17000000 INFO @ Wed, 22 Apr 2020 10:20:02: 23000000 INFO @ Wed, 22 Apr 2020 10:20:03: 26000000 INFO @ Wed, 22 Apr 2020 10:20:03: 18000000 INFO @ Wed, 22 Apr 2020 10:20:08: 24000000 INFO @ Wed, 22 Apr 2020 10:20:09: 19000000 INFO @ Wed, 22 Apr 2020 10:20:09: 27000000 INFO @ Wed, 22 Apr 2020 10:20:13: 25000000 INFO @ Wed, 22 Apr 2020 10:20:14: 20000000 INFO @ Wed, 22 Apr 2020 10:20:16: 28000000 INFO @ Wed, 22 Apr 2020 10:20:19: 26000000 INFO @ Wed, 22 Apr 2020 10:20:20: 21000000 INFO @ Wed, 22 Apr 2020 10:20:22: 29000000 INFO @ Wed, 22 Apr 2020 10:20:25: 27000000 INFO @ Wed, 22 Apr 2020 10:20:25: 22000000 INFO @ Wed, 22 Apr 2020 10:20:28: 30000000 INFO @ Wed, 22 Apr 2020 10:20:30: 28000000 INFO @ Wed, 22 Apr 2020 10:20:31: 23000000 INFO @ Wed, 22 Apr 2020 10:20:34: 31000000 INFO @ Wed, 22 Apr 2020 10:20:36: 29000000 INFO @ Wed, 22 Apr 2020 10:20:36: 24000000 INFO @ Wed, 22 Apr 2020 10:20:41: 32000000 INFO @ Wed, 22 Apr 2020 10:20:42: 25000000 INFO @ Wed, 22 Apr 2020 10:20:42: 30000000 INFO @ Wed, 22 Apr 2020 10:20:47: 33000000 INFO @ Wed, 22 Apr 2020 10:20:47: 26000000 INFO @ Wed, 22 Apr 2020 10:20:48: 31000000 INFO @ Wed, 22 Apr 2020 10:20:53: 27000000 INFO @ Wed, 22 Apr 2020 10:20:53: 34000000 INFO @ Wed, 22 Apr 2020 10:20:54: 32000000 INFO @ Wed, 22 Apr 2020 10:20:58: 28000000 INFO @ Wed, 22 Apr 2020 10:20:59: 33000000 INFO @ Wed, 22 Apr 2020 10:20:59: 35000000 INFO @ Wed, 22 Apr 2020 10:21:04: 29000000 INFO @ Wed, 22 Apr 2020 10:21:05: 34000000 INFO @ Wed, 22 Apr 2020 10:21:06: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:21:09: 30000000 INFO @ Wed, 22 Apr 2020 10:21:11: 35000000 INFO @ Wed, 22 Apr 2020 10:21:12: 37000000 INFO @ Wed, 22 Apr 2020 10:21:15: 31000000 INFO @ Wed, 22 Apr 2020 10:21:16: 36000000 INFO @ Wed, 22 Apr 2020 10:21:18: 38000000 INFO @ Wed, 22 Apr 2020 10:21:21: 32000000 INFO @ Wed, 22 Apr 2020 10:21:22: 37000000 INFO @ Wed, 22 Apr 2020 10:21:24: 39000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:21:26: 33000000 INFO @ Wed, 22 Apr 2020 10:21:28: 38000000 INFO @ Wed, 22 Apr 2020 10:21:31: 40000000 INFO @ Wed, 22 Apr 2020 10:21:32: 34000000 INFO @ Wed, 22 Apr 2020 10:21:33: 39000000 INFO @ Wed, 22 Apr 2020 10:21:37: 41000000 INFO @ Wed, 22 Apr 2020 10:21:37: 35000000 INFO @ Wed, 22 Apr 2020 10:21:39: 40000000 INFO @ Wed, 22 Apr 2020 10:21:43: 36000000 INFO @ Wed, 22 Apr 2020 10:21:43: 42000000 INFO @ Wed, 22 Apr 2020 10:21:44: 41000000 INFO @ Wed, 22 Apr 2020 10:21:48: 37000000 INFO @ Wed, 22 Apr 2020 10:21:50: 43000000 INFO @ Wed, 22 Apr 2020 10:21:50: 42000000 INFO @ Wed, 22 Apr 2020 10:21:54: 38000000 INFO @ Wed, 22 Apr 2020 10:21:56: 43000000 INFO @ Wed, 22 Apr 2020 10:21:56: 44000000 INFO @ Wed, 22 Apr 2020 10:21:59: 39000000 INFO @ Wed, 22 Apr 2020 10:22:01: 44000000 INFO @ Wed, 22 Apr 2020 10:22:02: 45000000 INFO @ Wed, 22 Apr 2020 10:22:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:22:04: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:22:04: #1 total tags in treatment: 22436624 INFO @ Wed, 22 Apr 2020 10:22:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:22:04: #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 10:22:04: #1 tags after filtering in treatment: 13519163 INFO @ Wed, 22 Apr 2020 10:22:04: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:22:04: #1 finished! INFO @ Wed, 22 Apr 2020 10:22:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:22:05: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:22:05: 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 10:22:05: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:22:05: 40000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.05_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/SRX7409575/SRX7409575.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:22:08: 45000000 INFO @ Wed, 22 Apr 2020 10:22:10: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:22:10: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:22:10: #1 total tags in treatment: 22436624 INFO @ Wed, 22 Apr 2020 10:22:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:22:10: #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 10:22:10: #1 tags after filtering in treatment: 13519163 INFO @ Wed, 22 Apr 2020 10:22:10: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:22:10: #1 finished! INFO @ Wed, 22 Apr 2020 10:22:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:22:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:22:10: 41000000 INFO @ Wed, 22 Apr 2020 10:22:11: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:22:11: 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 10:22:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.10_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/SRX7409575/SRX7409575.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:22:16: 42000000 INFO @ Wed, 22 Apr 2020 10:22:21: 43000000 INFO @ Wed, 22 Apr 2020 10:22:26: 44000000 INFO @ Wed, 22 Apr 2020 10:22:31: 45000000 INFO @ Wed, 22 Apr 2020 10:22:32: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:22:32: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:22:32: #1 total tags in treatment: 22436624 INFO @ Wed, 22 Apr 2020 10:22:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:22:32: #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 10:22:33: #1 tags after filtering in treatment: 13519163 INFO @ Wed, 22 Apr 2020 10:22:33: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:22:33: #1 finished! INFO @ Wed, 22 Apr 2020 10:22:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:22:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:22:34: 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 10:22:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.20_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/SRX7409575/SRX7409575.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409575/SRX7409575.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling