Job ID = 2011841 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:48:52 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 : 13,847,795 reads read : 27,695,590 reads written : 27,695,590 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 'SRR8313289.47317 47317 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.47317 47317 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.258037 258037 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.258037 258037 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.1035153 1035153 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.1035153 1035153 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.2381720 2381720 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.2381720 2381720 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.6002765 6002765 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.6002765 6002765 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.9165563 9165563 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.9165563 9165563 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.10202011 10202011 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.10202011 10202011 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.11669609 11669609 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.11669609 11669609 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313289.13152307 13152307 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313289.13152307 13152307 length=1' because it was < 2 characters long Multiseed full-index search: 00:14:47 13847795 reads; of these: 13847795 (100.00%) were paired; of these: 554180 (4.00%) aligned concordantly 0 times 10855218 (78.39%) aligned concordantly exactly 1 time 2438397 (17.61%) aligned concordantly >1 times ---- 554180 pairs aligned concordantly 0 times; of these: 36443 (6.58%) aligned discordantly 1 time ---- 517737 pairs aligned 0 times concordantly or discordantly; of these: 1035474 mates make up the pairs; of these: 836196 (80.75%) aligned 0 times 125606 (12.13%) aligned exactly 1 time 73672 (7.11%) aligned >1 times 96.98% overall alignment rate Time searching: 00:14:47 Overall time: 00:14:47 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 12 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] 1783844 / 13327491 = 0.1338 in library ' ' 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 03:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.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 03:27:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:27:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.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 03:27:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:27:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.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 03:27:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:27:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:27:27: 1000000 INFO @ Sat, 06 Jul 2019 03:27:27: 1000000 INFO @ Sat, 06 Jul 2019 03:27:28: 1000000 INFO @ Sat, 06 Jul 2019 03:27:35: 2000000 INFO @ Sat, 06 Jul 2019 03:27:36: 2000000 INFO @ Sat, 06 Jul 2019 03:27:37: 2000000 INFO @ Sat, 06 Jul 2019 03:27:43: 3000000 INFO @ Sat, 06 Jul 2019 03:27:44: 3000000 INFO @ Sat, 06 Jul 2019 03:27:47: 3000000 INFO @ Sat, 06 Jul 2019 03:27:51: 4000000 INFO @ Sat, 06 Jul 2019 03:27:52: 4000000 INFO @ Sat, 06 Jul 2019 03:27:56: 4000000 INFO @ Sat, 06 Jul 2019 03:27:58: 5000000 INFO @ Sat, 06 Jul 2019 03:28:00: 5000000 INFO @ Sat, 06 Jul 2019 03:28:05: 6000000 INFO @ Sat, 06 Jul 2019 03:28:06: 5000000 INFO @ Sat, 06 Jul 2019 03:28:08: 6000000 INFO @ Sat, 06 Jul 2019 03:28:13: 7000000 INFO @ Sat, 06 Jul 2019 03:28:16: 6000000 INFO @ Sat, 06 Jul 2019 03:28:16: 7000000 INFO @ Sat, 06 Jul 2019 03:28:22: 8000000 INFO @ Sat, 06 Jul 2019 03:28:24: 8000000 INFO @ Sat, 06 Jul 2019 03:28:25: 7000000 INFO @ Sat, 06 Jul 2019 03:28:30: 9000000 INFO @ Sat, 06 Jul 2019 03:28:33: 9000000 INFO @ Sat, 06 Jul 2019 03:28:35: 8000000 INFO @ Sat, 06 Jul 2019 03:28:38: 10000000 INFO @ Sat, 06 Jul 2019 03:28:40: 10000000 INFO @ Sat, 06 Jul 2019 03:28:45: 9000000 INFO @ Sat, 06 Jul 2019 03:28:46: 11000000 INFO @ Sat, 06 Jul 2019 03:28:49: 11000000 INFO @ Sat, 06 Jul 2019 03:28:54: 10000000 INFO @ Sat, 06 Jul 2019 03:28:54: 12000000 INFO @ Sat, 06 Jul 2019 03:28:57: 12000000 INFO @ Sat, 06 Jul 2019 03:29:03: 13000000 INFO @ Sat, 06 Jul 2019 03:29:04: 11000000 INFO @ Sat, 06 Jul 2019 03:29:05: 13000000 INFO @ Sat, 06 Jul 2019 03:29:10: 14000000 INFO @ Sat, 06 Jul 2019 03:29:12: 14000000 INFO @ Sat, 06 Jul 2019 03:29:13: 12000000 INFO @ Sat, 06 Jul 2019 03:29:18: 15000000 INFO @ Sat, 06 Jul 2019 03:29:19: 15000000 INFO @ Sat, 06 Jul 2019 03:29:24: 13000000 INFO @ Sat, 06 Jul 2019 03:29:26: 16000000 INFO @ Sat, 06 Jul 2019 03:29:28: 16000000 INFO @ Sat, 06 Jul 2019 03:29:33: 17000000 INFO @ Sat, 06 Jul 2019 03:29:34: 14000000 INFO @ Sat, 06 Jul 2019 03:29:36: 17000000 INFO @ Sat, 06 Jul 2019 03:29:41: 18000000 INFO @ Sat, 06 Jul 2019 03:29:44: 18000000 INFO @ Sat, 06 Jul 2019 03:29:44: 15000000 INFO @ Sat, 06 Jul 2019 03:29:51: 19000000 INFO @ Sat, 06 Jul 2019 03:29:52: 19000000 INFO @ Sat, 06 Jul 2019 03:29:54: 16000000 INFO @ Sat, 06 Jul 2019 03:30:00: 20000000 INFO @ Sat, 06 Jul 2019 03:30:01: 20000000 INFO @ Sat, 06 Jul 2019 03:30:04: 17000000 INFO @ Sat, 06 Jul 2019 03:30:08: 21000000 INFO @ Sat, 06 Jul 2019 03:30:09: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:30:14: 18000000 INFO @ Sat, 06 Jul 2019 03:30:17: 22000000 INFO @ Sat, 06 Jul 2019 03:30:18: 22000000 INFO @ Sat, 06 Jul 2019 03:30:24: 19000000 INFO @ Sat, 06 Jul 2019 03:30:26: 23000000 INFO @ Sat, 06 Jul 2019 03:30:26: 23000000 INFO @ Sat, 06 Jul 2019 03:30:28: #1 tag size is determined as 72 bps INFO @ Sat, 06 Jul 2019 03:30:28: #1 tag size = 72 INFO @ Sat, 06 Jul 2019 03:30:28: #1 total tags in treatment: 11511454 INFO @ Sat, 06 Jul 2019 03:30:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:28: #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 03:30:28: #1 tags after filtering in treatment: 7263459 INFO @ Sat, 06 Jul 2019 03:30:28: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:30:28: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:30:29: #1 tag size is determined as 72 bps INFO @ Sat, 06 Jul 2019 03:30:29: #1 tag size = 72 INFO @ Sat, 06 Jul 2019 03:30:29: #1 total tags in treatment: 11511454 INFO @ Sat, 06 Jul 2019 03:30:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:29: #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 03:30:29: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:30:29: 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 03:30:29: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:30:29: #1 tags after filtering in treatment: 7263459 INFO @ Sat, 06 Jul 2019 03:30:29: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:30:29: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:29: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.20_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/SRX5126597/SRX5126597.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:30:30: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:30:30: 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 03:30:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.10_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/SRX5126597/SRX5126597.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:30:33: 20000000 INFO @ Sat, 06 Jul 2019 03:30:43: 21000000 INFO @ Sat, 06 Jul 2019 03:30:52: 22000000 INFO @ Sat, 06 Jul 2019 03:31:01: 23000000 INFO @ Sat, 06 Jul 2019 03:31:04: #1 tag size is determined as 72 bps INFO @ Sat, 06 Jul 2019 03:31:04: #1 tag size = 72 INFO @ Sat, 06 Jul 2019 03:31:04: #1 total tags in treatment: 11511454 INFO @ Sat, 06 Jul 2019 03:31:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:31:04: #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 03:31:05: #1 tags after filtering in treatment: 7263459 INFO @ Sat, 06 Jul 2019 03:31:05: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 06 Jul 2019 03:31:05: #1 finished! INFO @ Sat, 06 Jul 2019 03:31:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:31:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:31:05: 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 03:31:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.05_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/SRX5126597/SRX5126597.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126597/SRX5126597.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling