Job ID = 2641003 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 1900-01-00T11:17:07 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 : NET - Reading information from the socket failed ) 2019-08-24T11:17:07 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 : NET - Reading information from the socket failed ) 2019-08-24T11:17:07 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 ) 2019-08-24T11:17:07 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 ) 2019-08-24T11:34:11 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 ) 2019-08-24T11:34:11 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 ) 2019-08-24T11:34:11 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 ) 2019-08-24T11:34:11 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 : 14,576,522 reads read : 29,153,044 reads written : 29,153,044 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: 00:18:56 14576522 reads; of these: 14576522 (100.00%) were paired; of these: 1691258 (11.60%) aligned concordantly 0 times 11046924 (75.79%) aligned concordantly exactly 1 time 1838340 (12.61%) aligned concordantly >1 times ---- 1691258 pairs aligned concordantly 0 times; of these: 1070067 (63.27%) aligned discordantly 1 time ---- 621191 pairs aligned 0 times concordantly or discordantly; of these: 1242382 mates make up the pairs; of these: 681725 (54.87%) aligned 0 times 181224 (14.59%) aligned exactly 1 time 379433 (30.54%) aligned >1 times 97.66% overall alignment rate Time searching: 00:18:56 Overall time: 00:18:56 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] 1444798 / 13952383 = 0.1036 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.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 @ Sat, 24 Aug 2019 21:15:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:15:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:30: 1000000 INFO @ Sat, 24 Aug 2019 21:15:39: 2000000 INFO @ Sat, 24 Aug 2019 21:15:47: 3000000 INFO @ Sat, 24 Aug 2019 21:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.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 @ Sat, 24 Aug 2019 21:15:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:15:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:56: 4000000 INFO @ Sat, 24 Aug 2019 21:16:02: 1000000 INFO @ Sat, 24 Aug 2019 21:16:05: 5000000 INFO @ Sat, 24 Aug 2019 21:16:13: 2000000 INFO @ Sat, 24 Aug 2019 21:16:14: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.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 @ Sat, 24 Aug 2019 21:16:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:23: 7000000 INFO @ Sat, 24 Aug 2019 21:16:23: 3000000 INFO @ Sat, 24 Aug 2019 21:16:32: 1000000 INFO @ Sat, 24 Aug 2019 21:16:32: 8000000 INFO @ Sat, 24 Aug 2019 21:16:34: 4000000 INFO @ Sat, 24 Aug 2019 21:16:41: 9000000 INFO @ Sat, 24 Aug 2019 21:16:43: 2000000 INFO @ Sat, 24 Aug 2019 21:16:45: 5000000 INFO @ Sat, 24 Aug 2019 21:16:50: 10000000 INFO @ Sat, 24 Aug 2019 21:16:54: 3000000 INFO @ Sat, 24 Aug 2019 21:16:56: 6000000 INFO @ Sat, 24 Aug 2019 21:17:00: 11000000 INFO @ Sat, 24 Aug 2019 21:17:05: 4000000 INFO @ Sat, 24 Aug 2019 21:17:06: 7000000 INFO @ Sat, 24 Aug 2019 21:17:09: 12000000 INFO @ Sat, 24 Aug 2019 21:17:15: 5000000 INFO @ Sat, 24 Aug 2019 21:17:17: 8000000 INFO @ Sat, 24 Aug 2019 21:17:18: 13000000 INFO @ Sat, 24 Aug 2019 21:17:26: 6000000 INFO @ Sat, 24 Aug 2019 21:17:27: 14000000 INFO @ Sat, 24 Aug 2019 21:17:28: 9000000 INFO @ Sat, 24 Aug 2019 21:17:36: 7000000 INFO @ Sat, 24 Aug 2019 21:17:37: 15000000 INFO @ Sat, 24 Aug 2019 21:17:38: 10000000 INFO @ Sat, 24 Aug 2019 21:17:46: 16000000 INFO @ Sat, 24 Aug 2019 21:17:47: 8000000 INFO @ Sat, 24 Aug 2019 21:17:49: 11000000 INFO @ Sat, 24 Aug 2019 21:17:56: 17000000 INFO @ Sat, 24 Aug 2019 21:17:58: 9000000 INFO @ Sat, 24 Aug 2019 21:18:00: 12000000 INFO @ Sat, 24 Aug 2019 21:18:05: 18000000 INFO @ Sat, 24 Aug 2019 21:18:08: 10000000 INFO @ Sat, 24 Aug 2019 21:18:11: 13000000 INFO @ Sat, 24 Aug 2019 21:18:15: 19000000 INFO @ Sat, 24 Aug 2019 21:18:19: 11000000 INFO @ Sat, 24 Aug 2019 21:18:22: 14000000 INFO @ Sat, 24 Aug 2019 21:18:24: 20000000 INFO @ Sat, 24 Aug 2019 21:18:30: 12000000 INFO @ Sat, 24 Aug 2019 21:18:33: 15000000 INFO @ Sat, 24 Aug 2019 21:18:33: 21000000 INFO @ Sat, 24 Aug 2019 21:18:41: 13000000 INFO @ Sat, 24 Aug 2019 21:18:43: 22000000 INFO @ Sat, 24 Aug 2019 21:18:44: 16000000 INFO @ Sat, 24 Aug 2019 21:18:51: 14000000 INFO @ Sat, 24 Aug 2019 21:18:52: 23000000 INFO @ Sat, 24 Aug 2019 21:18:55: 17000000 INFO @ Sat, 24 Aug 2019 21:19:02: 24000000 INFO @ Sat, 24 Aug 2019 21:19:02: 15000000 INFO @ Sat, 24 Aug 2019 21:19:05: 18000000 INFO @ Sat, 24 Aug 2019 21:19:11: 25000000 INFO @ Sat, 24 Aug 2019 21:19:13: 16000000 INFO @ Sat, 24 Aug 2019 21:19:16: 19000000 INFO @ Sat, 24 Aug 2019 21:19:17: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:19:17: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:19:17: #1 total tags in treatment: 11498647 INFO @ Sat, 24 Aug 2019 21:19:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:19:17: #1 tags after filtering in treatment: 8173837 INFO @ Sat, 24 Aug 2019 21:19:17: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:19:17: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:18: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:18: 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 @ Sat, 24 Aug 2019 21:19:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:23: 17000000 INFO @ Sat, 24 Aug 2019 21:19:27: 20000000 INFO @ Sat, 24 Aug 2019 21:19:34: 18000000 INFO @ Sat, 24 Aug 2019 21:19:38: 21000000 INFO @ Sat, 24 Aug 2019 21:19:45: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:19:49: 22000000 INFO @ Sat, 24 Aug 2019 21:19:56: 20000000 INFO @ Sat, 24 Aug 2019 21:20:00: 23000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:20:07: 21000000 INFO @ Sat, 24 Aug 2019 21:20:11: 24000000 INFO @ Sat, 24 Aug 2019 21:20:17: 22000000 INFO @ Sat, 24 Aug 2019 21:20:22: 25000000 INFO @ Sat, 24 Aug 2019 21:20:28: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:20:28: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:20:28: #1 total tags in treatment: 11498647 INFO @ Sat, 24 Aug 2019 21:20:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:20:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:20:28: 23000000 INFO @ Sat, 24 Aug 2019 21:20:28: #1 tags after filtering in treatment: 8173837 INFO @ Sat, 24 Aug 2019 21:20:28: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:20:28: #1 finished! INFO @ Sat, 24 Aug 2019 21:20:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:20:29: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:20:29: 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 @ Sat, 24 Aug 2019 21:20:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.10_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/SRX4936109/SRX4936109.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:20:38: 24000000 INFO @ Sat, 24 Aug 2019 21:20:48: 25000000 INFO @ Sat, 24 Aug 2019 21:20:54: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:20:54: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:20:54: #1 total tags in treatment: 11498647 INFO @ Sat, 24 Aug 2019 21:20:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:20:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:20:54: #1 tags after filtering in treatment: 8173837 INFO @ Sat, 24 Aug 2019 21:20:54: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:20:54: #1 finished! INFO @ Sat, 24 Aug 2019 21:20:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:20:55: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:20:55: 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 @ Sat, 24 Aug 2019 21:20:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936109/SRX4936109.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling