Job ID = 5791486 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:35:25 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 ) 2020-04-22T00:35:25 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 ) 2020-04-22T00:35:25 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 ) 2020-04-22T00:36:22 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 ) 2020-04-22T00:41:05 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 ) 2020-04-22T00:42:59 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 ) spots read : 23,702,204 reads read : 47,404,408 reads written : 47,404,408 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: 00:13:41 23702204 reads; of these: 23702204 (100.00%) were paired; of these: 289055 (1.22%) aligned concordantly 0 times 20863466 (88.02%) aligned concordantly exactly 1 time 2549683 (10.76%) aligned concordantly >1 times ---- 289055 pairs aligned concordantly 0 times; of these: 60123 (20.80%) aligned discordantly 1 time ---- 228932 pairs aligned 0 times concordantly or discordantly; of these: 457864 mates make up the pairs; of these: 287093 (62.70%) aligned 0 times 130142 (28.42%) aligned exactly 1 time 40629 (8.87%) aligned >1 times 99.39% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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] 4409092 / 23422884 = 0.1882 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 10:09:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.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 10:09:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:09:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:09:34: 1000000 INFO @ Wed, 22 Apr 2020 10:09:39: 2000000 INFO @ Wed, 22 Apr 2020 10:09:45: 3000000 INFO @ Wed, 22 Apr 2020 10:09:50: 4000000 INFO @ Wed, 22 Apr 2020 10:09:55: 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 10:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.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 10:09:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:09:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:10:00: 6000000 INFO @ Wed, 22 Apr 2020 10:10:05: 1000000 INFO @ Wed, 22 Apr 2020 10:10:06: 7000000 INFO @ Wed, 22 Apr 2020 10:10:10: 2000000 INFO @ Wed, 22 Apr 2020 10:10:12: 8000000 INFO @ Wed, 22 Apr 2020 10:10:16: 3000000 INFO @ Wed, 22 Apr 2020 10:10:17: 9000000 INFO @ Wed, 22 Apr 2020 10:10:21: 4000000 INFO @ Wed, 22 Apr 2020 10:10:23: 10000000 INFO @ Wed, 22 Apr 2020 10:10:27: 5000000 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 10:10:28: 11000000 INFO @ Wed, 22 Apr 2020 10:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.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 10:10:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:10:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:10:32: 6000000 INFO @ Wed, 22 Apr 2020 10:10:34: 12000000 INFO @ Wed, 22 Apr 2020 10:10:35: 1000000 INFO @ Wed, 22 Apr 2020 10:10:38: 7000000 INFO @ Wed, 22 Apr 2020 10:10:39: 13000000 INFO @ Wed, 22 Apr 2020 10:10:40: 2000000 INFO @ Wed, 22 Apr 2020 10:10:44: 8000000 INFO @ Wed, 22 Apr 2020 10:10:45: 14000000 INFO @ Wed, 22 Apr 2020 10:10:46: 3000000 INFO @ Wed, 22 Apr 2020 10:10:49: 9000000 INFO @ Wed, 22 Apr 2020 10:10:51: 15000000 INFO @ Wed, 22 Apr 2020 10:10:52: 4000000 INFO @ Wed, 22 Apr 2020 10:10:55: 10000000 INFO @ Wed, 22 Apr 2020 10:10:57: 16000000 INFO @ Wed, 22 Apr 2020 10:10:57: 5000000 INFO @ Wed, 22 Apr 2020 10:11:01: 11000000 INFO @ Wed, 22 Apr 2020 10:11:02: 17000000 INFO @ Wed, 22 Apr 2020 10:11:03: 6000000 INFO @ Wed, 22 Apr 2020 10:11:06: 12000000 INFO @ Wed, 22 Apr 2020 10:11:08: 18000000 INFO @ Wed, 22 Apr 2020 10:11:08: 7000000 INFO @ Wed, 22 Apr 2020 10:11:12: 13000000 INFO @ Wed, 22 Apr 2020 10:11:13: 19000000 INFO @ Wed, 22 Apr 2020 10:11:14: 8000000 INFO @ Wed, 22 Apr 2020 10:11:17: 14000000 INFO @ Wed, 22 Apr 2020 10:11:18: 20000000 INFO @ Wed, 22 Apr 2020 10:11:19: 9000000 INFO @ Wed, 22 Apr 2020 10:11:22: 15000000 INFO @ Wed, 22 Apr 2020 10:11:24: 21000000 INFO @ Wed, 22 Apr 2020 10:11:24: 10000000 INFO @ Wed, 22 Apr 2020 10:11:28: 16000000 INFO @ Wed, 22 Apr 2020 10:11:29: 22000000 INFO @ Wed, 22 Apr 2020 10:11:29: 11000000 INFO @ Wed, 22 Apr 2020 10:11:33: 17000000 INFO @ Wed, 22 Apr 2020 10:11:34: 23000000 INFO @ Wed, 22 Apr 2020 10:11:35: 12000000 INFO @ Wed, 22 Apr 2020 10:11:39: 18000000 INFO @ Wed, 22 Apr 2020 10:11:39: 24000000 INFO @ Wed, 22 Apr 2020 10:11:40: 13000000 INFO @ Wed, 22 Apr 2020 10:11:44: 19000000 INFO @ Wed, 22 Apr 2020 10:11:44: 25000000 INFO @ Wed, 22 Apr 2020 10:11:45: 14000000 INFO @ Wed, 22 Apr 2020 10:11:49: 20000000 INFO @ Wed, 22 Apr 2020 10:11:50: 26000000 INFO @ Wed, 22 Apr 2020 10:11:50: 15000000 INFO @ Wed, 22 Apr 2020 10:11:55: 21000000 INFO @ Wed, 22 Apr 2020 10:11:55: 27000000 INFO @ Wed, 22 Apr 2020 10:11:56: 16000000 INFO @ Wed, 22 Apr 2020 10:12:00: 22000000 INFO @ Wed, 22 Apr 2020 10:12:00: 28000000 INFO @ Wed, 22 Apr 2020 10:12:01: 17000000 INFO @ Wed, 22 Apr 2020 10:12:05: 23000000 INFO @ Wed, 22 Apr 2020 10:12:05: 29000000 INFO @ Wed, 22 Apr 2020 10:12:06: 18000000 INFO @ Wed, 22 Apr 2020 10:12:11: 24000000 INFO @ Wed, 22 Apr 2020 10:12:11: 30000000 INFO @ Wed, 22 Apr 2020 10:12:11: 19000000 INFO @ Wed, 22 Apr 2020 10:12:16: 25000000 INFO @ Wed, 22 Apr 2020 10:12:16: 31000000 INFO @ Wed, 22 Apr 2020 10:12:16: 20000000 INFO @ Wed, 22 Apr 2020 10:12:21: 26000000 INFO @ Wed, 22 Apr 2020 10:12:21: 32000000 INFO @ Wed, 22 Apr 2020 10:12:21: 21000000 INFO @ Wed, 22 Apr 2020 10:12:26: 27000000 INFO @ Wed, 22 Apr 2020 10:12:26: 33000000 INFO @ Wed, 22 Apr 2020 10:12:27: 22000000 INFO @ Wed, 22 Apr 2020 10:12:32: 34000000 INFO @ Wed, 22 Apr 2020 10:12:32: 28000000 INFO @ Wed, 22 Apr 2020 10:12:32: 23000000 INFO @ Wed, 22 Apr 2020 10:12:37: 29000000 INFO @ Wed, 22 Apr 2020 10:12:37: 35000000 INFO @ Wed, 22 Apr 2020 10:12:37: 24000000 INFO @ Wed, 22 Apr 2020 10:12:42: 25000000 INFO @ Wed, 22 Apr 2020 10:12:42: 30000000 INFO @ Wed, 22 Apr 2020 10:12:42: 36000000 INFO @ Wed, 22 Apr 2020 10:12:47: 26000000 INFO @ Wed, 22 Apr 2020 10:12:47: 31000000 INFO @ Wed, 22 Apr 2020 10:12:48: 37000000 INFO @ Wed, 22 Apr 2020 10:12:52: 27000000 INFO @ Wed, 22 Apr 2020 10:12:52: 32000000 INFO @ Wed, 22 Apr 2020 10:12:53: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:12:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:12:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:12:55: #1 total tags in treatment: 19005393 INFO @ Wed, 22 Apr 2020 10:12:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:12:55: #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 10:12:55: #1 tags after filtering in treatment: 12205453 INFO @ Wed, 22 Apr 2020 10:12:55: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 10:12:55: #1 finished! INFO @ Wed, 22 Apr 2020 10:12:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:12:56: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:12:56: 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 10:12:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.05_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/SRX7409573/SRX7409573.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:12:57: 28000000 INFO @ Wed, 22 Apr 2020 10:12:58: 33000000 INFO @ Wed, 22 Apr 2020 10:13:03: 29000000 INFO @ Wed, 22 Apr 2020 10:13:03: 34000000 INFO @ Wed, 22 Apr 2020 10:13:08: 30000000 INFO @ Wed, 22 Apr 2020 10:13:08: 35000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:13:13: 31000000 INFO @ Wed, 22 Apr 2020 10:13:13: 36000000 INFO @ Wed, 22 Apr 2020 10:13:18: 32000000 INFO @ Wed, 22 Apr 2020 10:13:18: 37000000 INFO @ Wed, 22 Apr 2020 10:13:23: 38000000 INFO @ Wed, 22 Apr 2020 10:13:23: 33000000 INFO @ Wed, 22 Apr 2020 10:13:25: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:13:25: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:13:25: #1 total tags in treatment: 19005393 INFO @ Wed, 22 Apr 2020 10:13:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:13:25: #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 10:13:25: #1 tags after filtering in treatment: 12205453 INFO @ Wed, 22 Apr 2020 10:13:25: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 10:13:25: #1 finished! INFO @ Wed, 22 Apr 2020 10:13:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:13:26: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:13:26: 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 10:13:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.10_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/SRX7409573/SRX7409573.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:13:28: 34000000 INFO @ Wed, 22 Apr 2020 10:13:33: 35000000 INFO @ Wed, 22 Apr 2020 10:13:38: 36000000 INFO @ Wed, 22 Apr 2020 10:13:43: 37000000 INFO @ Wed, 22 Apr 2020 10:13:47: 38000000 INFO @ Wed, 22 Apr 2020 10:13:49: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:13:49: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:13:49: #1 total tags in treatment: 19005393 INFO @ Wed, 22 Apr 2020 10:13:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:13:49: #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 10:13:49: #1 tags after filtering in treatment: 12205453 INFO @ Wed, 22 Apr 2020 10:13:49: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 10:13:49: #1 finished! INFO @ Wed, 22 Apr 2020 10:13:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:13:50: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:13:50: 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 10:13:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.20_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/SRX7409573/SRX7409573.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409573/SRX7409573.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling