Job ID = 2011853 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:50:10 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 ) 2019-07-05T17:50:39 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 : 18,495,204 reads read : 36,990,408 reads written : 36,990,057 reads 0-length : 351 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 'SRR8313300.173880 173880 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.173880 173880 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.275209 275209 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.275209 275209 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.1468253 1468253 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.1468253 1468253 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.1665482 1665482 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.1665482 1665482 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.1678326 1678326 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.1678326 1678326 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.3130699 3130699 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.3130699 3130699 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.3685572 3685572 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.3685572 3685572 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.3774864 3774864 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.3774864 3774864 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.7238786 7238786 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.7238786 7238786 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.7417303 7417303 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.7417303 7417303 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.7863506 7863506 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.7863506 7863506 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.7921611 7921611 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.7921611 7921611 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.9978247 9978247 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.9978247 9978247 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.10472820 10472820 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.10472820 10472820 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.10889289 10889289 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.10889289 10889289 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.12679871 12679871 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.12679871 12679871 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.12798761 12798761 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.12798761 12798761 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.13503610 13503610 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.13503610 13503610 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.16934942 16934942 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.16934942 16934942 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.17299736 17299736 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.17299736 17299736 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.17755490 17755490 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.17755490 17755490 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.17782768 17782768 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.17782768 17782768 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.17861073 17861073 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.17861073 17861073 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313300.18098124 18098124 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313300.18098124 18098124 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] 5786896 / 17579657 = 0.3292 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 03:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.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 03:39:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:39:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.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 03:39:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:39:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.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 03:39:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:39:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:39:47: 1000000 INFO @ Sat, 06 Jul 2019 03:39:48: 1000000 INFO @ Sat, 06 Jul 2019 03:39:49: 1000000 INFO @ Sat, 06 Jul 2019 03:39:56: 2000000 INFO @ Sat, 06 Jul 2019 03:40:00: 2000000 INFO @ Sat, 06 Jul 2019 03:40:00: 2000000 INFO @ Sat, 06 Jul 2019 03:40:06: 3000000 INFO @ Sat, 06 Jul 2019 03:40:12: 3000000 INFO @ Sat, 06 Jul 2019 03:40:13: 3000000 INFO @ Sat, 06 Jul 2019 03:40:16: 4000000 INFO @ Sat, 06 Jul 2019 03:40:23: 4000000 INFO @ Sat, 06 Jul 2019 03:40:25: 4000000 INFO @ Sat, 06 Jul 2019 03:40:26: 5000000 INFO @ Sat, 06 Jul 2019 03:40:34: 5000000 INFO @ Sat, 06 Jul 2019 03:40:35: 6000000 INFO @ Sat, 06 Jul 2019 03:40:36: 5000000 INFO @ Sat, 06 Jul 2019 03:40:45: 7000000 INFO @ Sat, 06 Jul 2019 03:40:45: 6000000 INFO @ Sat, 06 Jul 2019 03:40:50: 6000000 INFO @ Sat, 06 Jul 2019 03:40:54: 8000000 INFO @ Sat, 06 Jul 2019 03:40:56: 7000000 INFO @ Sat, 06 Jul 2019 03:41:01: 7000000 INFO @ Sat, 06 Jul 2019 03:41:04: 9000000 INFO @ Sat, 06 Jul 2019 03:41:06: 8000000 INFO @ Sat, 06 Jul 2019 03:41:13: 8000000 INFO @ Sat, 06 Jul 2019 03:41:13: 10000000 INFO @ Sat, 06 Jul 2019 03:41:17: 9000000 INFO @ Sat, 06 Jul 2019 03:41:23: 11000000 INFO @ Sat, 06 Jul 2019 03:41:24: 9000000 INFO @ Sat, 06 Jul 2019 03:41:28: 10000000 INFO @ Sat, 06 Jul 2019 03:41:32: 12000000 INFO @ Sat, 06 Jul 2019 03:41:36: 10000000 INFO @ Sat, 06 Jul 2019 03:41:39: 11000000 INFO @ Sat, 06 Jul 2019 03:41:42: 13000000 INFO @ Sat, 06 Jul 2019 03:41:48: 11000000 INFO @ Sat, 06 Jul 2019 03:41:50: 12000000 INFO @ Sat, 06 Jul 2019 03:41:51: 14000000 INFO @ Sat, 06 Jul 2019 03:41:59: 12000000 INFO @ Sat, 06 Jul 2019 03:42:00: 15000000 INFO @ Sat, 06 Jul 2019 03:42:00: 13000000 INFO @ Sat, 06 Jul 2019 03:42:09: 16000000 INFO @ Sat, 06 Jul 2019 03:42:11: 14000000 INFO @ Sat, 06 Jul 2019 03:42:11: 13000000 INFO @ Sat, 06 Jul 2019 03:42:18: 17000000 INFO @ Sat, 06 Jul 2019 03:42:21: 15000000 INFO @ Sat, 06 Jul 2019 03:42:22: 14000000 INFO @ Sat, 06 Jul 2019 03:42:27: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:42:31: 16000000 INFO @ Sat, 06 Jul 2019 03:42:33: 15000000 INFO @ Sat, 06 Jul 2019 03:42:36: 19000000 INFO @ Sat, 06 Jul 2019 03:42:41: 17000000 INFO @ Sat, 06 Jul 2019 03:42:43: 16000000 INFO @ Sat, 06 Jul 2019 03:42:45: 20000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:42:51: 18000000 INFO @ Sat, 06 Jul 2019 03:42:54: 17000000 INFO @ Sat, 06 Jul 2019 03:42:54: 21000000 INFO @ Sat, 06 Jul 2019 03:43:02: 19000000 INFO @ Sat, 06 Jul 2019 03:43:04: 22000000 INFO @ Sat, 06 Jul 2019 03:43:05: 18000000 INFO @ Sat, 06 Jul 2019 03:43:12: 20000000 INFO @ Sat, 06 Jul 2019 03:43:13: 23000000 INFO @ Sat, 06 Jul 2019 03:43:16: 19000000 INFO @ Sat, 06 Jul 2019 03:43:22: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:43:22: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:43:22: #1 total tags in treatment: 11785237 INFO @ Sat, 06 Jul 2019 03:43:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:43:22: #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 03:43:22: #1 tags after filtering in treatment: 7495663 INFO @ Sat, 06 Jul 2019 03:43:22: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:43:22: #1 finished! INFO @ Sat, 06 Jul 2019 03:43:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:43:22: 21000000 INFO @ Sat, 06 Jul 2019 03:43:23: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:43:23: 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 03:43:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.10_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/SRX5126608/SRX5126608.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:43:27: 20000000 INFO @ Sat, 06 Jul 2019 03:43:33: 22000000 INFO @ Sat, 06 Jul 2019 03:43:38: 21000000 INFO @ Sat, 06 Jul 2019 03:43:43: 23000000 INFO @ Sat, 06 Jul 2019 03:43:48: 22000000 INFO @ Sat, 06 Jul 2019 03:43:53: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:43:53: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:43:53: #1 total tags in treatment: 11785237 INFO @ Sat, 06 Jul 2019 03:43:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:43:53: #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 03:43:53: #1 tags after filtering in treatment: 7495663 INFO @ Sat, 06 Jul 2019 03:43:53: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:43:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:43:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:43:54: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:43:54: 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 03:43:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.20_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/SRX5126608/SRX5126608.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:43:59: 23000000 INFO @ Sat, 06 Jul 2019 03:44:08: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:44:08: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:44:08: #1 total tags in treatment: 11785237 INFO @ Sat, 06 Jul 2019 03:44:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:44:08: #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 03:44:09: #1 tags after filtering in treatment: 7495663 INFO @ Sat, 06 Jul 2019 03:44:09: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:44:09: #1 finished! INFO @ Sat, 06 Jul 2019 03:44:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:44:09: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:44:09: 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 03:44:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.05_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/SRX5126608/SRX5126608.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126608/SRX5126608.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling