Job ID = 2010741 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:09:49 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T15:11:49 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 ) 2019-07-05T15:12:21 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 ) 2019-07-05T15:21:17 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T15:21:37 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 ) spots read : 13,286,916 reads read : 26,573,832 reads written : 26,573,832 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: 00:12:36 13286916 reads; of these: 13286916 (100.00%) were paired; of these: 2043740 (15.38%) aligned concordantly 0 times 9917579 (74.64%) aligned concordantly exactly 1 time 1325597 (9.98%) aligned concordantly >1 times ---- 2043740 pairs aligned concordantly 0 times; of these: 164363 (8.04%) aligned discordantly 1 time ---- 1879377 pairs aligned 0 times concordantly or discordantly; of these: 3758754 mates make up the pairs; of these: 3188132 (84.82%) aligned 0 times 428797 (11.41%) aligned exactly 1 time 141825 (3.77%) aligned >1 times 88.00% overall alignment rate Time searching: 00:12:36 Overall time: 00:12:36 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] 203036 / 11371214 = 0.0179 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 00:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.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, 06 Jul 2019 00:55:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:55:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.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, 06 Jul 2019 00:55:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:55:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.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, 06 Jul 2019 00:55:13: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:55:13: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:55:22: 1000000 INFO @ Sat, 06 Jul 2019 00:55:22: 1000000 INFO @ Sat, 06 Jul 2019 00:55:24: 1000000 INFO @ Sat, 06 Jul 2019 00:55:33: 2000000 INFO @ Sat, 06 Jul 2019 00:55:33: 2000000 INFO @ Sat, 06 Jul 2019 00:55:34: 2000000 INFO @ Sat, 06 Jul 2019 00:55:44: 3000000 INFO @ Sat, 06 Jul 2019 00:55:44: 3000000 INFO @ Sat, 06 Jul 2019 00:55:44: 3000000 INFO @ Sat, 06 Jul 2019 00:55:54: 4000000 INFO @ Sat, 06 Jul 2019 00:55:55: 4000000 INFO @ Sat, 06 Jul 2019 00:55:55: 4000000 INFO @ Sat, 06 Jul 2019 00:56:05: 5000000 INFO @ Sat, 06 Jul 2019 00:56:05: 5000000 INFO @ Sat, 06 Jul 2019 00:56:06: 5000000 INFO @ Sat, 06 Jul 2019 00:56:16: 6000000 INFO @ Sat, 06 Jul 2019 00:56:16: 6000000 INFO @ Sat, 06 Jul 2019 00:56:16: 6000000 INFO @ Sat, 06 Jul 2019 00:56:27: 7000000 INFO @ Sat, 06 Jul 2019 00:56:27: 7000000 INFO @ Sat, 06 Jul 2019 00:56:27: 7000000 INFO @ Sat, 06 Jul 2019 00:56:37: 8000000 INFO @ Sat, 06 Jul 2019 00:56:37: 8000000 INFO @ Sat, 06 Jul 2019 00:56:37: 8000000 INFO @ Sat, 06 Jul 2019 00:56:47: 9000000 INFO @ Sat, 06 Jul 2019 00:56:48: 9000000 INFO @ Sat, 06 Jul 2019 00:56:48: 9000000 INFO @ Sat, 06 Jul 2019 00:56:57: 10000000 INFO @ Sat, 06 Jul 2019 00:56:59: 10000000 INFO @ Sat, 06 Jul 2019 00:56:59: 10000000 INFO @ Sat, 06 Jul 2019 00:57:08: 11000000 INFO @ Sat, 06 Jul 2019 00:57:09: 11000000 INFO @ Sat, 06 Jul 2019 00:57:09: 11000000 INFO @ Sat, 06 Jul 2019 00:57:18: 12000000 INFO @ Sat, 06 Jul 2019 00:57:20: 12000000 INFO @ Sat, 06 Jul 2019 00:57:20: 12000000 INFO @ Sat, 06 Jul 2019 00:57:28: 13000000 INFO @ Sat, 06 Jul 2019 00:57:30: 13000000 INFO @ Sat, 06 Jul 2019 00:57:30: 13000000 INFO @ Sat, 06 Jul 2019 00:57:38: 14000000 INFO @ Sat, 06 Jul 2019 00:57:41: 14000000 INFO @ Sat, 06 Jul 2019 00:57:41: 14000000 INFO @ Sat, 06 Jul 2019 00:57:49: 15000000 INFO @ Sat, 06 Jul 2019 00:57:52: 15000000 INFO @ Sat, 06 Jul 2019 00:57:53: 15000000 INFO @ Sat, 06 Jul 2019 00:58:01: 16000000 INFO @ Sat, 06 Jul 2019 00:58:03: 16000000 INFO @ Sat, 06 Jul 2019 00:58:04: 16000000 INFO @ Sat, 06 Jul 2019 00:58:12: 17000000 INFO @ Sat, 06 Jul 2019 00:58:15: 17000000 INFO @ Sat, 06 Jul 2019 00:58:15: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:58:23: 18000000 INFO @ Sat, 06 Jul 2019 00:58:26: 18000000 INFO @ Sat, 06 Jul 2019 00:58:26: 18000000 INFO @ Sat, 06 Jul 2019 00:58:33: 19000000 INFO @ Sat, 06 Jul 2019 00:58:35: 19000000 INFO @ Sat, 06 Jul 2019 00:58:36: 19000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:58:43: 20000000 INFO @ Sat, 06 Jul 2019 00:58:44: 20000000 INFO @ Sat, 06 Jul 2019 00:58:46: 20000000 INFO @ Sat, 06 Jul 2019 00:58:52: 21000000 INFO @ Sat, 06 Jul 2019 00:58:53: 21000000 INFO @ Sat, 06 Jul 2019 00:58:56: 21000000 INFO @ Sat, 06 Jul 2019 00:59:01: 22000000 INFO @ Sat, 06 Jul 2019 00:59:03: 22000000 INFO @ Sat, 06 Jul 2019 00:59:06: 22000000 INFO @ Sat, 06 Jul 2019 00:59:10: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:59:10: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:59:10: #1 total tags in treatment: 11041492 INFO @ Sat, 06 Jul 2019 00:59:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:59:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:59:10: #1 tags after filtering in treatment: 8177679 INFO @ Sat, 06 Jul 2019 00:59:10: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:59:10: #1 finished! INFO @ Sat, 06 Jul 2019 00:59:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:59:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:59:11: 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 @ Sat, 06 Jul 2019 00:59:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.20_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/SRX386921/SRX386921.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:59:13: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:59:13: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:59:13: #1 total tags in treatment: 11041492 INFO @ Sat, 06 Jul 2019 00:59:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:59:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:59:13: #1 tags after filtering in treatment: 8177679 INFO @ Sat, 06 Jul 2019 00:59:13: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:59:13: #1 finished! INFO @ Sat, 06 Jul 2019 00:59:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:59:14: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:59:14: 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, 06 Jul 2019 00:59:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.05_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/SRX386921/SRX386921.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:59:16: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:59:16: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:59:16: #1 total tags in treatment: 11041492 INFO @ Sat, 06 Jul 2019 00:59:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:59:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:59:16: #1 tags after filtering in treatment: 8177679 INFO @ Sat, 06 Jul 2019 00:59:16: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:59:16: #1 finished! INFO @ Sat, 06 Jul 2019 00:59:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:59:17: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:59:17: 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, 06 Jul 2019 00:59:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.10_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/SRX386921/SRX386921.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386921/SRX386921.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling