Job ID = 2011842 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:54:52 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 ) 2019-07-05T17:54:52 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 : 17,153,933 reads read : 34,307,866 reads written : 34,307,847 reads 0-length : 19 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 'SRR8313290.863158 863158 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.863158 863158 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.1415613 1415613 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.1415613 1415613 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.1739616 1739616 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.1739616 1739616 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.2367599 2367599 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.2367599 2367599 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.3525329 3525329 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.3525329 3525329 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.4403450 4403450 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.4403450 4403450 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.5568114 5568114 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.5568114 5568114 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.5990857 5990857 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.5990857 5990857 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.7144637 7144637 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.7144637 7144637 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.7316518 7316518 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.7316518 7316518 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.7523542 7523542 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.7523542 7523542 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.9435058 9435058 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.9435058 9435058 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.10531629 10531629 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.10531629 10531629 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.10696747 10696747 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.10696747 10696747 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.11168920 11168920 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.11168920 11168920 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.11474857 11474857 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.11474857 11474857 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.12689032 12689032 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.12689032 12689032 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.13182581 13182581 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.13182581 13182581 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.13210041 13210041 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.13210041 13210041 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.13384575 13384575 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.13384575 13384575 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313290.16807698 16807698 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313290.16807698 16807698 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] 2091152 / 16353066 = 0.1279 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 03:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.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 03:35:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:35:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.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 03:35:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:35:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.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 03:35:33: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:35:33: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:35:39: 1000000 INFO @ Sat, 06 Jul 2019 03:35:41: 1000000 INFO @ Sat, 06 Jul 2019 03:35:41: 1000000 INFO @ Sat, 06 Jul 2019 03:35:46: 2000000 INFO @ Sat, 06 Jul 2019 03:35:49: 2000000 INFO @ Sat, 06 Jul 2019 03:35:51: 2000000 INFO @ Sat, 06 Jul 2019 03:35:54: 3000000 INFO @ Sat, 06 Jul 2019 03:35:56: 3000000 INFO @ Sat, 06 Jul 2019 03:35:59: 3000000 INFO @ Sat, 06 Jul 2019 03:36:01: 4000000 INFO @ Sat, 06 Jul 2019 03:36:04: 4000000 INFO @ Sat, 06 Jul 2019 03:36:08: 4000000 INFO @ Sat, 06 Jul 2019 03:36:08: 5000000 INFO @ Sat, 06 Jul 2019 03:36:11: 5000000 INFO @ Sat, 06 Jul 2019 03:36:16: 6000000 INFO @ Sat, 06 Jul 2019 03:36:17: 5000000 INFO @ Sat, 06 Jul 2019 03:36:18: 6000000 INFO @ Sat, 06 Jul 2019 03:36:23: 7000000 INFO @ Sat, 06 Jul 2019 03:36:25: 6000000 INFO @ Sat, 06 Jul 2019 03:36:26: 7000000 INFO @ Sat, 06 Jul 2019 03:36:31: 8000000 INFO @ Sat, 06 Jul 2019 03:36:33: 8000000 INFO @ Sat, 06 Jul 2019 03:36:34: 7000000 INFO @ Sat, 06 Jul 2019 03:36:38: 9000000 INFO @ Sat, 06 Jul 2019 03:36:41: 9000000 INFO @ Sat, 06 Jul 2019 03:36:43: 8000000 INFO @ Sat, 06 Jul 2019 03:36:45: 10000000 INFO @ Sat, 06 Jul 2019 03:36:48: 10000000 INFO @ Sat, 06 Jul 2019 03:36:52: 9000000 INFO @ Sat, 06 Jul 2019 03:36:53: 11000000 INFO @ Sat, 06 Jul 2019 03:36:55: 11000000 INFO @ Sat, 06 Jul 2019 03:37:00: 12000000 INFO @ Sat, 06 Jul 2019 03:37:00: 10000000 INFO @ Sat, 06 Jul 2019 03:37:03: 12000000 INFO @ Sat, 06 Jul 2019 03:37:07: 13000000 INFO @ Sat, 06 Jul 2019 03:37:09: 11000000 INFO @ Sat, 06 Jul 2019 03:37:10: 13000000 INFO @ Sat, 06 Jul 2019 03:37:15: 14000000 INFO @ Sat, 06 Jul 2019 03:37:17: 14000000 INFO @ Sat, 06 Jul 2019 03:37:18: 12000000 INFO @ Sat, 06 Jul 2019 03:37:22: 15000000 INFO @ Sat, 06 Jul 2019 03:37:25: 15000000 INFO @ Sat, 06 Jul 2019 03:37:27: 13000000 INFO @ Sat, 06 Jul 2019 03:37:30: 16000000 INFO @ Sat, 06 Jul 2019 03:37:32: 16000000 INFO @ Sat, 06 Jul 2019 03:37:35: 14000000 INFO @ Sat, 06 Jul 2019 03:37:37: 17000000 INFO @ Sat, 06 Jul 2019 03:37:39: 17000000 INFO @ Sat, 06 Jul 2019 03:37:44: 18000000 INFO @ Sat, 06 Jul 2019 03:37:44: 15000000 INFO @ Sat, 06 Jul 2019 03:37:47: 18000000 INFO @ Sat, 06 Jul 2019 03:37:51: 19000000 INFO @ Sat, 06 Jul 2019 03:37:53: 16000000 INFO @ Sat, 06 Jul 2019 03:37:54: 19000000 INFO @ Sat, 06 Jul 2019 03:37:58: 20000000 INFO @ Sat, 06 Jul 2019 03:38:01: 20000000 INFO @ Sat, 06 Jul 2019 03:38:01: 17000000 INFO @ Sat, 06 Jul 2019 03:38:05: 21000000 INFO @ Sat, 06 Jul 2019 03:38:08: 21000000 INFO @ Sat, 06 Jul 2019 03:38:10: 18000000 INFO @ Sat, 06 Jul 2019 03:38:13: 22000000 INFO @ Sat, 06 Jul 2019 03:38:15: 22000000 INFO @ Sat, 06 Jul 2019 03:38:18: 19000000 INFO @ Sat, 06 Jul 2019 03:38:20: 23000000 INFO @ Sat, 06 Jul 2019 03:38:23: 23000000 INFO @ Sat, 06 Jul 2019 03:38:26: 20000000 INFO @ Sat, 06 Jul 2019 03:38:27: 24000000 INFO @ Sat, 06 Jul 2019 03:38:30: 24000000 INFO @ Sat, 06 Jul 2019 03:38:35: 25000000 INFO @ Sat, 06 Jul 2019 03:38:35: 21000000 INFO @ Sat, 06 Jul 2019 03:38:37: 25000000 INFO @ Sat, 06 Jul 2019 03:38:42: 26000000 INFO @ Sat, 06 Jul 2019 03:38:43: 22000000 INFO @ Sat, 06 Jul 2019 03:38:45: 26000000 INFO @ Sat, 06 Jul 2019 03:38:49: 27000000 INFO @ Sat, 06 Jul 2019 03:38:52: 27000000 INFO @ Sat, 06 Jul 2019 03:38:52: 23000000 INFO @ Sat, 06 Jul 2019 03:38:57: 28000000 INFO @ Sat, 06 Jul 2019 03:38:59: 28000000 INFO @ Sat, 06 Jul 2019 03:39:01: 24000000 INFO @ Sat, 06 Jul 2019 03:39:04: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:39:04: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:39:04: #1 total tags in treatment: 14199638 INFO @ Sat, 06 Jul 2019 03:39:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:39:04: #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 03:39:04: #1 tags after filtering in treatment: 8258277 INFO @ Sat, 06 Jul 2019 03:39:04: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:39:04: #1 finished! INFO @ Sat, 06 Jul 2019 03:39:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:39:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:39:05: 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 03:39:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.05_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/SRX5126598/SRX5126598.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:39:06: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:39:06: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:39:06: #1 total tags in treatment: 14199638 INFO @ Sat, 06 Jul 2019 03:39:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:39:06: #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 03:39:06: #1 tags after filtering in treatment: 8258277 INFO @ Sat, 06 Jul 2019 03:39:06: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:39:06: #1 finished! INFO @ Sat, 06 Jul 2019 03:39:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:39:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:39:07: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:39:07: 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 03:39:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.20_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/SRX5126598/SRX5126598.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:39:09: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:39:18: 26000000 INFO @ Sat, 06 Jul 2019 03:39:27: 27000000 INFO @ Sat, 06 Jul 2019 03:39:36: 28000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:39:45: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:39:45: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:39:45: #1 total tags in treatment: 14199638 INFO @ Sat, 06 Jul 2019 03:39:45: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:39:45: #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 03:39:45: #1 tags after filtering in treatment: 8258277 INFO @ Sat, 06 Jul 2019 03:39:45: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:39:45: #1 finished! INFO @ Sat, 06 Jul 2019 03:39:45: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:39:46: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:39:46: 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 03:39:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.10_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/SRX5126598/SRX5126598.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126598/SRX5126598.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling