Job ID = 2589959 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:52:00 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 ) 2019-08-12T09:52:14 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 ) 2019-08-12T09:52:14 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 ) 2019-08-12T09:52:23 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 : 31,312,856 reads read : 31,312,856 reads written : 31,312,856 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163556.sra.cache’: 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: 00:08:12 31312856 reads; of these: 31312856 (100.00%) were unpaired; of these: 663104 (2.12%) aligned 0 times 27563629 (88.03%) aligned exactly 1 time 3086123 (9.86%) aligned >1 times 97.88% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 9420975 / 30649752 = 0.3074 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 @ Mon, 12 Aug 2019 19:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:10:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:10:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:10:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:58: 1000000 INFO @ Mon, 12 Aug 2019 19:10:59: 1000000 INFO @ Mon, 12 Aug 2019 19:11:00: 1000000 INFO @ Mon, 12 Aug 2019 19:11:06: 2000000 INFO @ Mon, 12 Aug 2019 19:11:07: 2000000 INFO @ Mon, 12 Aug 2019 19:11:09: 2000000 INFO @ Mon, 12 Aug 2019 19:11:14: 3000000 INFO @ Mon, 12 Aug 2019 19:11:14: 3000000 INFO @ Mon, 12 Aug 2019 19:11:19: 3000000 INFO @ Mon, 12 Aug 2019 19:11:21: 4000000 INFO @ Mon, 12 Aug 2019 19:11:22: 4000000 INFO @ Mon, 12 Aug 2019 19:11:28: 4000000 INFO @ Mon, 12 Aug 2019 19:11:29: 5000000 INFO @ Mon, 12 Aug 2019 19:11:29: 5000000 INFO @ Mon, 12 Aug 2019 19:11:37: 6000000 INFO @ Mon, 12 Aug 2019 19:11:37: 6000000 INFO @ Mon, 12 Aug 2019 19:11:38: 5000000 INFO @ Mon, 12 Aug 2019 19:11:44: 7000000 INFO @ Mon, 12 Aug 2019 19:11:44: 7000000 INFO @ Mon, 12 Aug 2019 19:11:47: 6000000 INFO @ Mon, 12 Aug 2019 19:11:52: 8000000 INFO @ Mon, 12 Aug 2019 19:11:52: 8000000 INFO @ Mon, 12 Aug 2019 19:11:56: 7000000 INFO @ Mon, 12 Aug 2019 19:11:59: 9000000 INFO @ Mon, 12 Aug 2019 19:12:00: 9000000 INFO @ Mon, 12 Aug 2019 19:12:06: 8000000 INFO @ Mon, 12 Aug 2019 19:12:07: 10000000 INFO @ Mon, 12 Aug 2019 19:12:07: 10000000 INFO @ Mon, 12 Aug 2019 19:12:14: 11000000 INFO @ Mon, 12 Aug 2019 19:12:15: 11000000 INFO @ Mon, 12 Aug 2019 19:12:15: 9000000 INFO @ Mon, 12 Aug 2019 19:12:22: 12000000 INFO @ Mon, 12 Aug 2019 19:12:23: 12000000 INFO @ Mon, 12 Aug 2019 19:12:24: 10000000 INFO @ Mon, 12 Aug 2019 19:12:29: 13000000 INFO @ Mon, 12 Aug 2019 19:12:30: 13000000 INFO @ Mon, 12 Aug 2019 19:12:34: 11000000 INFO @ Mon, 12 Aug 2019 19:12:37: 14000000 INFO @ Mon, 12 Aug 2019 19:12:38: 14000000 INFO @ Mon, 12 Aug 2019 19:12:43: 12000000 INFO @ Mon, 12 Aug 2019 19:12:44: 15000000 INFO @ Mon, 12 Aug 2019 19:12:45: 15000000 INFO @ Mon, 12 Aug 2019 19:12:52: 13000000 INFO @ Mon, 12 Aug 2019 19:12:53: 16000000 INFO @ Mon, 12 Aug 2019 19:12:53: 16000000 INFO @ Mon, 12 Aug 2019 19:13:01: 17000000 INFO @ Mon, 12 Aug 2019 19:13:01: 17000000 INFO @ Mon, 12 Aug 2019 19:13:02: 14000000 INFO @ Mon, 12 Aug 2019 19:13:09: 18000000 INFO @ Mon, 12 Aug 2019 19:13:10: 18000000 INFO @ Mon, 12 Aug 2019 19:13:11: 15000000 INFO @ Mon, 12 Aug 2019 19:13:17: 19000000 INFO @ Mon, 12 Aug 2019 19:13:18: 19000000 INFO @ Mon, 12 Aug 2019 19:13:21: 16000000 INFO @ Mon, 12 Aug 2019 19:13:25: 20000000 INFO @ Mon, 12 Aug 2019 19:13:26: 20000000 INFO @ Mon, 12 Aug 2019 19:13:30: 17000000 INFO @ Mon, 12 Aug 2019 19:13:33: 21000000 INFO @ Mon, 12 Aug 2019 19:13:34: 21000000 INFO @ Mon, 12 Aug 2019 19:13:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:13:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:13:35: #1 total tags in treatment: 21228777 INFO @ Mon, 12 Aug 2019 19:13:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:13:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:13:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:13:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:13:36: #1 total tags in treatment: 21228777 INFO @ Mon, 12 Aug 2019 19:13:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:13:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:13:36: #1 tags after filtering in treatment: 21228777 INFO @ Mon, 12 Aug 2019 19:13:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:13:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:13:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:13:36: #1 tags after filtering in treatment: 21228777 INFO @ Mon, 12 Aug 2019 19:13:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:13:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:13:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:13:37: #2 number of paired peaks: 21 WARNING @ Mon, 12 Aug 2019 19:13:37: Too few paired peaks (21) 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 @ Mon, 12 Aug 2019 19:13:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.20_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/ce10/SRX466490/SRX466490.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:13:38: #2 number of paired peaks: 21 WARNING @ Mon, 12 Aug 2019 19:13:38: Too few paired peaks (21) 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 @ Mon, 12 Aug 2019 19:13:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.10_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/ce10/SRX466490/SRX466490.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:13:40: 18000000 INFO @ Mon, 12 Aug 2019 19:13:49: 19000000 INFO @ Mon, 12 Aug 2019 19:13:58: 20000000 INFO @ Mon, 12 Aug 2019 19:14:07: 21000000 INFO @ Mon, 12 Aug 2019 19:14:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:14:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:14:09: #1 total tags in treatment: 21228777 INFO @ Mon, 12 Aug 2019 19:14:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:14:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:14:10: #1 tags after filtering in treatment: 21228777 INFO @ Mon, 12 Aug 2019 19:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:14:10: #1 finished! INFO @ Mon, 12 Aug 2019 19:14:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:14:12: #2 number of paired peaks: 21 WARNING @ Mon, 12 Aug 2019 19:14:12: Too few paired peaks (21) 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 @ Mon, 12 Aug 2019 19:14:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.05_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/ce10/SRX466490/SRX466490.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX466490/SRX466490.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。