Job ID = 2011748 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T17:19:22 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 ) 2019-07-05T17:19:41 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 ) 2019-07-05T17:21:38 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 : 18,807,847 reads read : 18,807,847 reads written : 18,807,847 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: 00:02:36 18807847 reads; of these: 18807847 (100.00%) were unpaired; of these: 1855698 (9.87%) aligned 0 times 12676536 (67.40%) aligned exactly 1 time 4275613 (22.73%) aligned >1 times 90.13% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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 8 files... [bam_rmdupse_core] 10438169 / 16952149 = 0.6157 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 02:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.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 02:31:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:31:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.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 02:31:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:31:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.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 02:31:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:31:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:31:09: 1000000 INFO @ Sat, 06 Jul 2019 02:31:11: 1000000 INFO @ Sat, 06 Jul 2019 02:31:12: 1000000 INFO @ Sat, 06 Jul 2019 02:31:19: 2000000 INFO @ Sat, 06 Jul 2019 02:31:20: 2000000 INFO @ Sat, 06 Jul 2019 02:31:22: 2000000 INFO @ Sat, 06 Jul 2019 02:31:29: 3000000 INFO @ Sat, 06 Jul 2019 02:31:31: 3000000 INFO @ Sat, 06 Jul 2019 02:31:31: 3000000 INFO @ Sat, 06 Jul 2019 02:31:39: 4000000 INFO @ Sat, 06 Jul 2019 02:31:40: 4000000 INFO @ Sat, 06 Jul 2019 02:31:41: 4000000 INFO @ Sat, 06 Jul 2019 02:31:50: 5000000 INFO @ Sat, 06 Jul 2019 02:31:50: 5000000 INFO @ Sat, 06 Jul 2019 02:31:52: 5000000 INFO @ Sat, 06 Jul 2019 02:31:59: 6000000 INFO @ Sat, 06 Jul 2019 02:32:01: 6000000 INFO @ Sat, 06 Jul 2019 02:32:02: 6000000 INFO @ Sat, 06 Jul 2019 02:32:03: #1 tag size is determined as 43 bps INFO @ Sat, 06 Jul 2019 02:32:03: #1 tag size = 43 INFO @ Sat, 06 Jul 2019 02:32:03: #1 total tags in treatment: 6513980 INFO @ Sat, 06 Jul 2019 02:32:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:32:03: #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 02:32:03: #1 tags after filtering in treatment: 6513980 INFO @ Sat, 06 Jul 2019 02:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:32:03: #1 finished! INFO @ Sat, 06 Jul 2019 02:32:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:32:04: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:32:04: 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 02:32:04: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:32:06: #1 tag size is determined as 43 bps INFO @ Sat, 06 Jul 2019 02:32:06: #1 tag size = 43 INFO @ Sat, 06 Jul 2019 02:32:06: #1 total tags in treatment: 6513980 INFO @ Sat, 06 Jul 2019 02:32:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:32:06: #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 02:32:06: #1 tags after filtering in treatment: 6513980 INFO @ Sat, 06 Jul 2019 02:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:32:06: #1 finished! INFO @ Sat, 06 Jul 2019 02:32:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:32:06: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:32:06: 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 02:32:06: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:32:07: #1 tag size is determined as 43 bps INFO @ Sat, 06 Jul 2019 02:32:07: #1 tag size = 43 INFO @ Sat, 06 Jul 2019 02:32:07: #1 total tags in treatment: 6513980 INFO @ Sat, 06 Jul 2019 02:32:07: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:32:07: #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 02:32:07: #1 tags after filtering in treatment: 6513980 INFO @ Sat, 06 Jul 2019 02:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:32:07: #1 finished! INFO @ Sat, 06 Jul 2019 02:32:07: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:32:08: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:32:08: 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 02:32:08: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.10_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4967953/SRX4967953.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。