Job ID = 2011831 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:51:54 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 ) 2019-07-05T17:51:54 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 ) 2019-07-05T17:51:54 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 ) 2019-07-05T17:51:54 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 ) 2019-07-05T17:54:16 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 : 19,303,332 reads read : 38,606,664 reads written : 38,606,663 reads 0-length : 1 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 Warning: skipping mate #1 of read 'SRR8313281.3260927 3260927 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313281.3260927 3260927 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313281.6146477 6146477 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313281.6146477 6146477 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313281.9993882 9993882 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313281.9993882 9993882 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313281.12138357 12138357 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313281.12138357 12138357 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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 16 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] 4679677 / 18606305 = 0.2515 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted 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 03:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.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 03:39:22: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:39:22: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.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 03:39:23: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:39:23: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.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 03:39:24: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:39:24: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:31: 1000000 INFO @ Sat, 06 Jul 2019 03:39:32: 1000000 INFO @ Sat, 06 Jul 2019 03:39:32: 1000000 INFO @ Sat, 06 Jul 2019 03:39:38: 2000000 INFO @ Sat, 06 Jul 2019 03:39:40: 2000000 INFO @ Sat, 06 Jul 2019 03:39:42: 2000000 INFO @ Sat, 06 Jul 2019 03:39:46: 3000000 INFO @ Sat, 06 Jul 2019 03:39:48: 3000000 INFO @ Sat, 06 Jul 2019 03:39:51: 3000000 INFO @ Sat, 06 Jul 2019 03:39:53: 4000000 INFO @ Sat, 06 Jul 2019 03:39:56: 4000000 INFO @ Sat, 06 Jul 2019 03:40:00: 4000000 INFO @ Sat, 06 Jul 2019 03:40:01: 5000000 INFO @ Sat, 06 Jul 2019 03:40:04: 5000000 INFO @ Sat, 06 Jul 2019 03:40:09: 6000000 INFO @ Sat, 06 Jul 2019 03:40:09: 5000000 INFO @ Sat, 06 Jul 2019 03:40:12: 6000000 INFO @ Sat, 06 Jul 2019 03:40:16: 7000000 INFO @ Sat, 06 Jul 2019 03:40:18: 6000000 INFO @ Sat, 06 Jul 2019 03:40:20: 7000000 INFO @ Sat, 06 Jul 2019 03:40:24: 8000000 INFO @ Sat, 06 Jul 2019 03:40:26: 7000000 INFO @ Sat, 06 Jul 2019 03:40:28: 8000000 INFO @ Sat, 06 Jul 2019 03:40:31: 9000000 INFO @ Sat, 06 Jul 2019 03:40:35: 8000000 INFO @ Sat, 06 Jul 2019 03:40:36: 9000000 INFO @ Sat, 06 Jul 2019 03:40:39: 10000000 INFO @ Sat, 06 Jul 2019 03:40:44: 10000000 INFO @ Sat, 06 Jul 2019 03:40:44: 9000000 INFO @ Sat, 06 Jul 2019 03:40:46: 11000000 INFO @ Sat, 06 Jul 2019 03:40:51: 11000000 INFO @ Sat, 06 Jul 2019 03:40:53: 10000000 INFO @ Sat, 06 Jul 2019 03:40:54: 12000000 INFO @ Sat, 06 Jul 2019 03:40:59: 12000000 INFO @ Sat, 06 Jul 2019 03:41:01: 13000000 INFO @ Sat, 06 Jul 2019 03:41:02: 11000000 INFO @ Sat, 06 Jul 2019 03:41:07: 13000000 INFO @ Sat, 06 Jul 2019 03:41:09: 14000000 INFO @ Sat, 06 Jul 2019 03:41:10: 12000000 INFO @ Sat, 06 Jul 2019 03:41:14: 14000000 INFO @ Sat, 06 Jul 2019 03:41:16: 15000000 INFO @ Sat, 06 Jul 2019 03:41:19: 13000000 INFO @ Sat, 06 Jul 2019 03:41:22: 15000000 INFO @ Sat, 06 Jul 2019 03:41:24: 16000000 INFO @ Sat, 06 Jul 2019 03:41:28: 14000000 INFO @ Sat, 06 Jul 2019 03:41:29: 16000000 INFO @ Sat, 06 Jul 2019 03:41:31: 17000000 INFO @ Sat, 06 Jul 2019 03:41:36: 17000000 INFO @ Sat, 06 Jul 2019 03:41:37: 15000000 INFO @ Sat, 06 Jul 2019 03:41:38: 18000000 INFO @ Sat, 06 Jul 2019 03:41:43: 18000000 INFO @ Sat, 06 Jul 2019 03:41:45: 19000000 INFO @ Sat, 06 Jul 2019 03:41:46: 16000000 INFO @ Sat, 06 Jul 2019 03:41:50: 19000000 INFO @ Sat, 06 Jul 2019 03:41:53: 20000000 INFO @ Sat, 06 Jul 2019 03:41:54: 17000000 INFO @ Sat, 06 Jul 2019 03:41:58: 20000000 INFO @ Sat, 06 Jul 2019 03:42:00: 21000000 INFO @ Sat, 06 Jul 2019 03:42:02: 18000000 INFO @ Sat, 06 Jul 2019 03:42:05: 21000000 INFO @ Sat, 06 Jul 2019 03:42:07: 22000000 INFO @ Sat, 06 Jul 2019 03:42:11: 19000000 INFO @ Sat, 06 Jul 2019 03:42:12: 22000000 INFO @ Sat, 06 Jul 2019 03:42:14: 23000000 INFO @ Sat, 06 Jul 2019 03:42:19: 20000000 INFO @ Sat, 06 Jul 2019 03:42:20: 23000000 INFO @ Sat, 06 Jul 2019 03:42:21: 24000000 INFO @ Sat, 06 Jul 2019 03:42:27: 24000000 INFO @ Sat, 06 Jul 2019 03:42:27: 21000000 INFO @ Sat, 06 Jul 2019 03:42:28: 25000000 INFO @ Sat, 06 Jul 2019 03:42:34: 25000000 INFO @ Sat, 06 Jul 2019 03:42:35: 22000000 INFO @ Sat, 06 Jul 2019 03:42:35: 26000000 INFO @ Sat, 06 Jul 2019 03:42:41: 26000000 INFO @ Sat, 06 Jul 2019 03:42:43: 27000000 INFO @ Sat, 06 Jul 2019 03:42:44: 23000000 INFO @ Sat, 06 Jul 2019 03:42:48: 27000000 INFO @ Sat, 06 Jul 2019 03:42:50: 28000000 INFO @ Sat, 06 Jul 2019 03:42:52: 24000000 INFO @ Sat, 06 Jul 2019 03:42:52: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:42:52: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:42:52: #1 total tags in treatment: 13919310 INFO @ Sat, 06 Jul 2019 03:42:52: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:42:52: #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 03:42:52: #1 tags after filtering in treatment: 8079142 INFO @ Sat, 06 Jul 2019 03:42:52: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:42:52: #1 finished! INFO @ Sat, 06 Jul 2019 03:42:52: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:42:53: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:42:53: 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 03:42:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.10_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/SRX5126589/SRX5126589.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:42:55: 28000000 INFO @ Sat, 06 Jul 2019 03:42:57: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:42:57: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:42:57: #1 total tags in treatment: 13919310 INFO @ Sat, 06 Jul 2019 03:42:57: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:42:57: #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 03:42:57: #1 tags after filtering in treatment: 8079142 INFO @ Sat, 06 Jul 2019 03:42:57: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:42:57: #1 finished! INFO @ Sat, 06 Jul 2019 03:42:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:42:58: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:42:58: 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, 06 Jul 2019 03:42:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.20_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/SRX5126589/SRX5126589.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:43:00: 25000000 INFO @ Sat, 06 Jul 2019 03:43:09: 26000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:43:18: 27000000 INFO @ Sat, 06 Jul 2019 03:43:27: 28000000 INFO @ Sat, 06 Jul 2019 03:43:30: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:43:30: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:43:30: #1 total tags in treatment: 13919310 INFO @ Sat, 06 Jul 2019 03:43:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:43:30: #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 03:43:30: #1 tags after filtering in treatment: 8079142 INFO @ Sat, 06 Jul 2019 03:43:30: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:43:30: #1 finished! INFO @ Sat, 06 Jul 2019 03:43:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:43:31: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:43:31: 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 03:43:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.05_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/SRX5126589/SRX5126589.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126589/SRX5126589.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling