Job ID = 5791314 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:32:37 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 ) 2020-04-22T00:32:37 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 ) 2020-04-22T00:34:54 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 ) 2020-04-22T00:40:54 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 ) 2020-04-22T00:40:54 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 ) 2020-04-22T00:41:46 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 ) spots read : 26,971,702 reads read : 53,943,404 reads written : 53,943,404 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: 00:15:11 26971702 reads; of these: 26971702 (100.00%) were paired; of these: 701909 (2.60%) aligned concordantly 0 times 22425054 (83.14%) aligned concordantly exactly 1 time 3844739 (14.25%) aligned concordantly >1 times ---- 701909 pairs aligned concordantly 0 times; of these: 66277 (9.44%) aligned discordantly 1 time ---- 635632 pairs aligned 0 times concordantly or discordantly; of these: 1271264 mates make up the pairs; of these: 960920 (75.59%) aligned 0 times 238287 (18.74%) aligned exactly 1 time 72057 (5.67%) aligned >1 times 98.22% overall alignment rate Time searching: 00:15:11 Overall time: 00:15:11 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] 5603076 / 26279951 = 0.2132 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 10:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.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 10:16:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:16:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:16:10: 1000000 INFO @ Wed, 22 Apr 2020 10:16:15: 2000000 INFO @ Wed, 22 Apr 2020 10:16:20: 3000000 INFO @ Wed, 22 Apr 2020 10:16:25: 4000000 INFO @ Wed, 22 Apr 2020 10:16:30: 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 10:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.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 10:16:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:16:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:16:35: 6000000 INFO @ Wed, 22 Apr 2020 10:16:41: 7000000 INFO @ Wed, 22 Apr 2020 10:16:41: 1000000 INFO @ Wed, 22 Apr 2020 10:16:46: 8000000 INFO @ Wed, 22 Apr 2020 10:16:47: 2000000 INFO @ Wed, 22 Apr 2020 10:16:52: 9000000 INFO @ Wed, 22 Apr 2020 10:16:54: 3000000 INFO @ Wed, 22 Apr 2020 10:16:58: 10000000 INFO @ Wed, 22 Apr 2020 10:17:00: 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 10:17:03: 11000000 INFO @ Wed, 22 Apr 2020 10:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.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 10:17:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:17:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:17:06: 5000000 INFO @ Wed, 22 Apr 2020 10:17:09: 12000000 INFO @ Wed, 22 Apr 2020 10:17:11: 1000000 INFO @ Wed, 22 Apr 2020 10:17:13: 6000000 INFO @ Wed, 22 Apr 2020 10:17:15: 13000000 INFO @ Wed, 22 Apr 2020 10:17:18: 2000000 INFO @ Wed, 22 Apr 2020 10:17:19: 7000000 INFO @ Wed, 22 Apr 2020 10:17:21: 14000000 INFO @ Wed, 22 Apr 2020 10:17:24: 3000000 INFO @ Wed, 22 Apr 2020 10:17:25: 8000000 INFO @ Wed, 22 Apr 2020 10:17:26: 15000000 INFO @ Wed, 22 Apr 2020 10:17:30: 4000000 INFO @ Wed, 22 Apr 2020 10:17:32: 9000000 INFO @ Wed, 22 Apr 2020 10:17:32: 16000000 INFO @ Wed, 22 Apr 2020 10:17:37: 5000000 INFO @ Wed, 22 Apr 2020 10:17:38: 17000000 INFO @ Wed, 22 Apr 2020 10:17:38: 10000000 INFO @ Wed, 22 Apr 2020 10:17:43: 6000000 INFO @ Wed, 22 Apr 2020 10:17:44: 18000000 INFO @ Wed, 22 Apr 2020 10:17:45: 11000000 INFO @ Wed, 22 Apr 2020 10:17:49: 7000000 INFO @ Wed, 22 Apr 2020 10:17:50: 19000000 INFO @ Wed, 22 Apr 2020 10:17:51: 12000000 INFO @ Wed, 22 Apr 2020 10:17:55: 20000000 INFO @ Wed, 22 Apr 2020 10:17:56: 8000000 INFO @ Wed, 22 Apr 2020 10:17:58: 13000000 INFO @ Wed, 22 Apr 2020 10:18:01: 21000000 INFO @ Wed, 22 Apr 2020 10:18:02: 9000000 INFO @ Wed, 22 Apr 2020 10:18:04: 14000000 INFO @ Wed, 22 Apr 2020 10:18:06: 22000000 INFO @ Wed, 22 Apr 2020 10:18:09: 10000000 INFO @ Wed, 22 Apr 2020 10:18:10: 15000000 INFO @ Wed, 22 Apr 2020 10:18:12: 23000000 INFO @ Wed, 22 Apr 2020 10:18:15: 11000000 INFO @ Wed, 22 Apr 2020 10:18:17: 16000000 INFO @ Wed, 22 Apr 2020 10:18:18: 24000000 INFO @ Wed, 22 Apr 2020 10:18:21: 12000000 INFO @ Wed, 22 Apr 2020 10:18:23: 17000000 INFO @ Wed, 22 Apr 2020 10:18:24: 25000000 INFO @ Wed, 22 Apr 2020 10:18:27: 13000000 INFO @ Wed, 22 Apr 2020 10:18:29: 26000000 INFO @ Wed, 22 Apr 2020 10:18:30: 18000000 INFO @ Wed, 22 Apr 2020 10:18:34: 14000000 INFO @ Wed, 22 Apr 2020 10:18:35: 27000000 INFO @ Wed, 22 Apr 2020 10:18:36: 19000000 INFO @ Wed, 22 Apr 2020 10:18:40: 15000000 INFO @ Wed, 22 Apr 2020 10:18:40: 28000000 INFO @ Wed, 22 Apr 2020 10:18:42: 20000000 INFO @ Wed, 22 Apr 2020 10:18:46: 29000000 INFO @ Wed, 22 Apr 2020 10:18:47: 16000000 INFO @ Wed, 22 Apr 2020 10:18:48: 21000000 INFO @ Wed, 22 Apr 2020 10:18:52: 30000000 INFO @ Wed, 22 Apr 2020 10:18:53: 17000000 INFO @ Wed, 22 Apr 2020 10:18:55: 22000000 INFO @ Wed, 22 Apr 2020 10:18:58: 31000000 INFO @ Wed, 22 Apr 2020 10:18:59: 18000000 INFO @ Wed, 22 Apr 2020 10:19:01: 23000000 INFO @ Wed, 22 Apr 2020 10:19:03: 32000000 INFO @ Wed, 22 Apr 2020 10:19:05: 19000000 INFO @ Wed, 22 Apr 2020 10:19:07: 24000000 INFO @ Wed, 22 Apr 2020 10:19:09: 33000000 INFO @ Wed, 22 Apr 2020 10:19:12: 20000000 INFO @ Wed, 22 Apr 2020 10:19:13: 25000000 INFO @ Wed, 22 Apr 2020 10:19:14: 34000000 INFO @ Wed, 22 Apr 2020 10:19:18: 21000000 INFO @ Wed, 22 Apr 2020 10:19:19: 26000000 INFO @ Wed, 22 Apr 2020 10:19:20: 35000000 INFO @ Wed, 22 Apr 2020 10:19:24: 22000000 INFO @ Wed, 22 Apr 2020 10:19:25: 27000000 INFO @ Wed, 22 Apr 2020 10:19:26: 36000000 INFO @ Wed, 22 Apr 2020 10:19:30: 23000000 INFO @ Wed, 22 Apr 2020 10:19:31: 37000000 INFO @ Wed, 22 Apr 2020 10:19:32: 28000000 INFO @ Wed, 22 Apr 2020 10:19:36: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:19:37: 38000000 INFO @ Wed, 22 Apr 2020 10:19:38: 29000000 INFO @ Wed, 22 Apr 2020 10:19:43: 39000000 INFO @ Wed, 22 Apr 2020 10:19:43: 25000000 INFO @ Wed, 22 Apr 2020 10:19:44: 30000000 INFO @ Wed, 22 Apr 2020 10:19:48: 40000000 INFO @ Wed, 22 Apr 2020 10:19:49: 26000000 INFO @ Wed, 22 Apr 2020 10:19:51: 31000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:19:54: 41000000 INFO @ Wed, 22 Apr 2020 10:19:55: 27000000 INFO @ Wed, 22 Apr 2020 10:19:57: 32000000 INFO @ Wed, 22 Apr 2020 10:19:58: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:19:58: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:19:58: #1 total tags in treatment: 20668339 INFO @ Wed, 22 Apr 2020 10:19:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:19:58: #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 10:19:59: #1 tags after filtering in treatment: 12504616 INFO @ Wed, 22 Apr 2020 10:19:59: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Apr 2020 10:19:59: #1 finished! INFO @ Wed, 22 Apr 2020 10:19:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:20:00: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:20:00: 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 10:20:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.05_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/SRX7409568/SRX7409568.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:20:01: 28000000 INFO @ Wed, 22 Apr 2020 10:20:03: 33000000 INFO @ Wed, 22 Apr 2020 10:20:07: 29000000 INFO @ Wed, 22 Apr 2020 10:20:09: 34000000 INFO @ Wed, 22 Apr 2020 10:20:14: 30000000 INFO @ Wed, 22 Apr 2020 10:20:16: 35000000 INFO @ Wed, 22 Apr 2020 10:20:20: 31000000 INFO @ Wed, 22 Apr 2020 10:20:22: 36000000 INFO @ Wed, 22 Apr 2020 10:20:26: 32000000 INFO @ Wed, 22 Apr 2020 10:20:28: 37000000 INFO @ Wed, 22 Apr 2020 10:20:32: 33000000 INFO @ Wed, 22 Apr 2020 10:20:34: 38000000 INFO @ Wed, 22 Apr 2020 10:20:38: 34000000 INFO @ Wed, 22 Apr 2020 10:20:40: 39000000 INFO @ Wed, 22 Apr 2020 10:20:44: 35000000 INFO @ Wed, 22 Apr 2020 10:20:46: 40000000 INFO @ Wed, 22 Apr 2020 10:20:50: 36000000 INFO @ Wed, 22 Apr 2020 10:20:53: 41000000 INFO @ Wed, 22 Apr 2020 10:20:56: 37000000 INFO @ Wed, 22 Apr 2020 10:20:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:20:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:20:57: #1 total tags in treatment: 20668339 INFO @ Wed, 22 Apr 2020 10:20:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:20:57: #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 10:20:58: #1 tags after filtering in treatment: 12504616 INFO @ Wed, 22 Apr 2020 10:20:58: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Apr 2020 10:20:58: #1 finished! INFO @ Wed, 22 Apr 2020 10:20:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:20:59: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:20:59: 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 10:20:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.10_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/SRX7409568/SRX7409568.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:21:02: 38000000 INFO @ Wed, 22 Apr 2020 10:21:08: 39000000 INFO @ Wed, 22 Apr 2020 10:21:14: 40000000 INFO @ Wed, 22 Apr 2020 10:21:19: 41000000 INFO @ Wed, 22 Apr 2020 10:21:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:21:24: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:21:24: #1 total tags in treatment: 20668339 INFO @ Wed, 22 Apr 2020 10:21:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:21:24: #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 10:21:24: #1 tags after filtering in treatment: 12504616 INFO @ Wed, 22 Apr 2020 10:21:24: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 22 Apr 2020 10:21:24: #1 finished! INFO @ Wed, 22 Apr 2020 10:21:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:21:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:21:25: 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 10:21:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.20_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/SRX7409568/SRX7409568.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409568/SRX7409568.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling