Job ID = 2640983 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:17:03 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 ) 2019-08-24T11:17:20 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 ) 2019-08-24T11:17:20 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 ) 2019-08-24T11:17:20 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 ) 2019-08-24T11:18:26 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 ) 2019-08-24T11:18:26 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 : 9,776,791 reads read : 19,553,582 reads written : 19,553,582 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: 00:11:44 9776791 reads; of these: 9776791 (100.00%) were paired; of these: 817372 (8.36%) aligned concordantly 0 times 8207093 (83.94%) aligned concordantly exactly 1 time 752326 (7.70%) aligned concordantly >1 times ---- 817372 pairs aligned concordantly 0 times; of these: 67704 (8.28%) aligned discordantly 1 time ---- 749668 pairs aligned 0 times concordantly or discordantly; of these: 1499336 mates make up the pairs; of these: 1449651 (96.69%) aligned 0 times 31695 (2.11%) aligned exactly 1 time 17990 (1.20%) aligned >1 times 92.59% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:44 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_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] 131838 / 9024908 = 0.0146 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.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 20:51:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:51:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:52:07: 1000000 INFO @ Sat, 24 Aug 2019 20:52:18: 2000000 INFO @ Sat, 24 Aug 2019 20:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.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 20:52:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:52:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:52:29: 3000000 INFO @ Sat, 24 Aug 2019 20:52:38: 1000000 INFO @ Sat, 24 Aug 2019 20:52:41: 4000000 INFO @ Sat, 24 Aug 2019 20:52:49: 2000000 INFO @ Sat, 24 Aug 2019 20:52:52: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.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 20:52:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:52:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:53:00: 3000000 INFO @ Sat, 24 Aug 2019 20:53:03: 6000000 INFO @ Sat, 24 Aug 2019 20:53:06: 1000000 INFO @ Sat, 24 Aug 2019 20:53:12: 4000000 INFO @ Sat, 24 Aug 2019 20:53:15: 7000000 INFO @ Sat, 24 Aug 2019 20:53:16: 2000000 INFO @ Sat, 24 Aug 2019 20:53:23: 5000000 INFO @ Sat, 24 Aug 2019 20:53:26: 3000000 INFO @ Sat, 24 Aug 2019 20:53:26: 8000000 INFO @ Sat, 24 Aug 2019 20:53:35: 6000000 INFO @ Sat, 24 Aug 2019 20:53:35: 4000000 INFO @ Sat, 24 Aug 2019 20:53:37: 9000000 INFO @ Sat, 24 Aug 2019 20:53:45: 5000000 INFO @ Sat, 24 Aug 2019 20:53:46: 7000000 INFO @ Sat, 24 Aug 2019 20:53:49: 10000000 INFO @ Sat, 24 Aug 2019 20:53:54: 6000000 INFO @ Sat, 24 Aug 2019 20:53:58: 8000000 INFO @ Sat, 24 Aug 2019 20:54:00: 11000000 INFO @ Sat, 24 Aug 2019 20:54:04: 7000000 INFO @ Sat, 24 Aug 2019 20:54:09: 9000000 INFO @ Sat, 24 Aug 2019 20:54:11: 12000000 INFO @ Sat, 24 Aug 2019 20:54:14: 8000000 INFO @ Sat, 24 Aug 2019 20:54:20: 10000000 INFO @ Sat, 24 Aug 2019 20:54:23: 13000000 INFO @ Sat, 24 Aug 2019 20:54:23: 9000000 INFO @ Sat, 24 Aug 2019 20:54:32: 11000000 INFO @ Sat, 24 Aug 2019 20:54:33: 10000000 INFO @ Sat, 24 Aug 2019 20:54:34: 14000000 INFO @ Sat, 24 Aug 2019 20:54:42: 11000000 INFO @ Sat, 24 Aug 2019 20:54:43: 12000000 INFO @ Sat, 24 Aug 2019 20:54:45: 15000000 INFO @ Sat, 24 Aug 2019 20:54:52: 12000000 INFO @ Sat, 24 Aug 2019 20:54:54: 13000000 INFO @ Sat, 24 Aug 2019 20:54:57: 16000000 INFO @ Sat, 24 Aug 2019 20:55:01: 13000000 INFO @ Sat, 24 Aug 2019 20:55:06: 14000000 INFO @ Sat, 24 Aug 2019 20:55:08: 17000000 INFO @ Sat, 24 Aug 2019 20:55:11: 14000000 INFO @ Sat, 24 Aug 2019 20:55:17: 15000000 INFO @ Sat, 24 Aug 2019 20:55:18: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:55:18: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:55:18: #1 total tags in treatment: 8828383 INFO @ Sat, 24 Aug 2019 20:55:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:55:18: #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 20:55:18: #1 tags after filtering in treatment: 7015328 INFO @ Sat, 24 Aug 2019 20:55:18: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 20:55:18: #1 finished! INFO @ Sat, 24 Aug 2019 20:55:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:55:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:55:19: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:55:19: 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 20:55:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.05_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/SRX4936089/SRX4936089.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:55:20: 15000000 INFO @ Sat, 24 Aug 2019 20:55:28: 16000000 INFO @ Sat, 24 Aug 2019 20:55:30: 16000000 INFO @ Sat, 24 Aug 2019 20:55:40: 17000000 INFO @ Sat, 24 Aug 2019 20:55:40: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:55:48: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:55:48: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:55:48: #1 total tags in treatment: 8828383 INFO @ Sat, 24 Aug 2019 20:55:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:55:48: #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 20:55:48: #1 tags after filtering in treatment: 7015328 INFO @ Sat, 24 Aug 2019 20:55:48: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 20:55:48: #1 finished! INFO @ Sat, 24 Aug 2019 20:55:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:55:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:55:48: 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 20:55:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.20_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/SRX4936089/SRX4936089.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:55:49: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:55:49: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:55:49: #1 total tags in treatment: 8828383 INFO @ Sat, 24 Aug 2019 20:55:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:55:49: #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 20:55:50: #1 tags after filtering in treatment: 7015328 INFO @ Sat, 24 Aug 2019 20:55:50: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 20:55:50: #1 finished! INFO @ Sat, 24 Aug 2019 20:55:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:55:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:55:50: 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 20:55:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.10_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/SRX4936089/SRX4936089.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936089/SRX4936089.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。