Job ID = 2641036 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T11:53:40 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 ) 2019-08-24T11:53:40 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 ) 2019-08-24T11:54:14 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T11:54:14 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.232' from '172.19.7.14' 2019-08-24T11:54:14 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (165.112.9.232) from '172.19.7.14' 2019-08-24T11:54:14 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T11:54:14 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.232' from '172.19.7.14' 2019-08-24T11:54:14 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (165.112.9.232) from '172.19.7.14' spots read : 20,307,482 reads read : 40,614,964 reads written : 20,307,482 reads 0-length : 20,307,482 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: 00:03:19 20307482 reads; of these: 20307482 (100.00%) were unpaired; of these: 1300915 (6.41%) aligned 0 times 16848973 (82.97%) aligned exactly 1 time 2157594 (10.62%) aligned >1 times 93.59% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 10686913 / 19006567 = 0.5623 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.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 21:01:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:01:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:01:59: 1000000 INFO @ Sat, 24 Aug 2019 21:02:07: 2000000 INFO @ Sat, 24 Aug 2019 21:02:15: 3000000 INFO @ Sat, 24 Aug 2019 21:02:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.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 21:02:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:23: 4000000 INFO @ Sat, 24 Aug 2019 21:02:29: 1000000 INFO @ Sat, 24 Aug 2019 21:02:31: 5000000 INFO @ Sat, 24 Aug 2019 21:02:36: 2000000 INFO @ Sat, 24 Aug 2019 21:02:39: 6000000 INFO @ Sat, 24 Aug 2019 21:02:43: 3000000 INFO @ Sat, 24 Aug 2019 21:02:47: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:02:50: 4000000 INFO @ Sat, 24 Aug 2019 21:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.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 21:02:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:55: 8000000 INFO @ Sat, 24 Aug 2019 21:02:57: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:02:57: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:02:57: #1 total tags in treatment: 8319654 INFO @ Sat, 24 Aug 2019 21:02:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:02:57: #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 21:02:57: 5000000 INFO @ Sat, 24 Aug 2019 21:02:57: #1 tags after filtering in treatment: 8319654 INFO @ Sat, 24 Aug 2019 21:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:02:57: #1 finished! INFO @ Sat, 24 Aug 2019 21:02:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:02:58: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:02:58: 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 21:02:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.05_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/SRX5257233/SRX5257233.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:02:59: 1000000 INFO @ Sat, 24 Aug 2019 21:03:04: 6000000 INFO @ Sat, 24 Aug 2019 21:03:06: 2000000 INFO @ Sat, 24 Aug 2019 21:03:11: 7000000 INFO @ Sat, 24 Aug 2019 21:03:13: 3000000 INFO @ Sat, 24 Aug 2019 21:03:18: 8000000 INFO @ Sat, 24 Aug 2019 21:03:20: 4000000 INFO @ Sat, 24 Aug 2019 21:03:21: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:03:21: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:03:21: #1 total tags in treatment: 8319654 INFO @ Sat, 24 Aug 2019 21:03:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:21: #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 21:03:21: #1 tags after filtering in treatment: 8319654 INFO @ Sat, 24 Aug 2019 21:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:03:21: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:21: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:21: 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 21:03:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.10_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/SRX5257233/SRX5257233.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:03:27: 5000000 INFO @ Sat, 24 Aug 2019 21:03:34: 6000000 INFO @ Sat, 24 Aug 2019 21:03:41: 7000000 INFO @ Sat, 24 Aug 2019 21:03:48: 8000000 INFO @ Sat, 24 Aug 2019 21:03:50: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:03:50: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:03:50: #1 total tags in treatment: 8319654 INFO @ Sat, 24 Aug 2019 21:03:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:50: #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 21:03:50: #1 tags after filtering in treatment: 8319654 INFO @ Sat, 24 Aug 2019 21:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:03:50: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:51: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:51: 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 21:03:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.20_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/SRX5257233/SRX5257233.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257233/SRX5257233.20_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。