Job ID = 2011838 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:47:24 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T17:47:24 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.92' 2019-07-05T17:47:24 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.26) from '172.19.7.92' 2019-07-05T17:52:02 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 : 20,274,838 reads read : 40,549,676 reads written : 40,549,676 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 'SRR8313286.10694740 10694740 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313286.10694740 10694740 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313286.13092255 13092255 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313286.13092255 13092255 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313286.15415783 15415783 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313286.15415783 15415783 length=1' because it was < 2 characters long Multiseed full-index search: 00:21:39 20274838 reads; of these: 20274838 (100.00%) were paired; of these: 757470 (3.74%) aligned concordantly 0 times 13586296 (67.01%) aligned concordantly exactly 1 time 5931072 (29.25%) aligned concordantly >1 times ---- 757470 pairs aligned concordantly 0 times; of these: 28629 (3.78%) aligned discordantly 1 time ---- 728841 pairs aligned 0 times concordantly or discordantly; of these: 1457682 mates make up the pairs; of these: 1045648 (71.73%) aligned 0 times 260188 (17.85%) aligned exactly 1 time 151846 (10.42%) aligned >1 times 97.42% overall alignment rate Time searching: 00:21:39 Overall time: 00:21:39 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 20 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] 5056142 / 19525607 = 0.2589 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 03:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.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 03:43:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.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 03:43:08: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:08: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.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 03:43:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:17: 1000000 INFO @ Sat, 06 Jul 2019 03:43:18: 1000000 INFO @ Sat, 06 Jul 2019 03:43:19: 1000000 INFO @ Sat, 06 Jul 2019 03:43:27: 2000000 INFO @ Sat, 06 Jul 2019 03:43:28: 2000000 INFO @ Sat, 06 Jul 2019 03:43:30: 2000000 INFO @ Sat, 06 Jul 2019 03:43:35: 3000000 INFO @ Sat, 06 Jul 2019 03:43:36: 3000000 INFO @ Sat, 06 Jul 2019 03:43:42: 3000000 INFO @ Sat, 06 Jul 2019 03:43:43: 4000000 INFO @ Sat, 06 Jul 2019 03:43:44: 4000000 INFO @ Sat, 06 Jul 2019 03:43:51: 5000000 INFO @ Sat, 06 Jul 2019 03:43:52: 5000000 INFO @ Sat, 06 Jul 2019 03:43:53: 4000000 INFO @ Sat, 06 Jul 2019 03:43:59: 6000000 INFO @ Sat, 06 Jul 2019 03:44:01: 6000000 INFO @ Sat, 06 Jul 2019 03:44:05: 5000000 INFO @ Sat, 06 Jul 2019 03:44:08: 7000000 INFO @ Sat, 06 Jul 2019 03:44:09: 7000000 INFO @ Sat, 06 Jul 2019 03:44:16: 8000000 INFO @ Sat, 06 Jul 2019 03:44:16: 6000000 INFO @ Sat, 06 Jul 2019 03:44:17: 8000000 INFO @ Sat, 06 Jul 2019 03:44:24: 9000000 INFO @ Sat, 06 Jul 2019 03:44:25: 9000000 INFO @ Sat, 06 Jul 2019 03:44:28: 7000000 INFO @ Sat, 06 Jul 2019 03:44:32: 10000000 INFO @ Sat, 06 Jul 2019 03:44:33: 10000000 INFO @ Sat, 06 Jul 2019 03:44:39: 8000000 INFO @ Sat, 06 Jul 2019 03:44:40: 11000000 INFO @ Sat, 06 Jul 2019 03:44:41: 11000000 INFO @ Sat, 06 Jul 2019 03:44:48: 12000000 INFO @ Sat, 06 Jul 2019 03:44:49: 12000000 INFO @ Sat, 06 Jul 2019 03:44:50: 9000000 INFO @ Sat, 06 Jul 2019 03:44:57: 13000000 INFO @ Sat, 06 Jul 2019 03:44:58: 13000000 INFO @ Sat, 06 Jul 2019 03:45:02: 10000000 INFO @ Sat, 06 Jul 2019 03:45:05: 14000000 INFO @ Sat, 06 Jul 2019 03:45:06: 14000000 INFO @ Sat, 06 Jul 2019 03:45:13: 15000000 INFO @ Sat, 06 Jul 2019 03:45:13: 11000000 INFO @ Sat, 06 Jul 2019 03:45:14: 15000000 INFO @ Sat, 06 Jul 2019 03:45:21: 16000000 INFO @ Sat, 06 Jul 2019 03:45:22: 16000000 INFO @ Sat, 06 Jul 2019 03:45:25: 12000000 INFO @ Sat, 06 Jul 2019 03:45:29: 17000000 INFO @ Sat, 06 Jul 2019 03:45:30: 17000000 INFO @ Sat, 06 Jul 2019 03:45:36: 13000000 INFO @ Sat, 06 Jul 2019 03:45:37: 18000000 INFO @ Sat, 06 Jul 2019 03:45:38: 18000000 INFO @ Sat, 06 Jul 2019 03:45:45: 19000000 INFO @ Sat, 06 Jul 2019 03:45:46: 19000000 INFO @ Sat, 06 Jul 2019 03:45:47: 14000000 INFO @ Sat, 06 Jul 2019 03:45:53: 20000000 INFO @ Sat, 06 Jul 2019 03:45:54: 20000000 INFO @ Sat, 06 Jul 2019 03:45:59: 15000000 INFO @ Sat, 06 Jul 2019 03:46:01: 21000000 INFO @ Sat, 06 Jul 2019 03:46:02: 21000000 INFO @ Sat, 06 Jul 2019 03:46:09: 22000000 INFO @ Sat, 06 Jul 2019 03:46:10: 22000000 INFO @ Sat, 06 Jul 2019 03:46:10: 16000000 INFO @ Sat, 06 Jul 2019 03:46:17: 23000000 INFO @ Sat, 06 Jul 2019 03:46:18: 23000000 INFO @ Sat, 06 Jul 2019 03:46:22: 17000000 INFO @ Sat, 06 Jul 2019 03:46:25: 24000000 INFO @ Sat, 06 Jul 2019 03:46:26: 24000000 INFO @ Sat, 06 Jul 2019 03:46:33: 25000000 INFO @ Sat, 06 Jul 2019 03:46:33: 18000000 INFO @ Sat, 06 Jul 2019 03:46:34: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:46:41: 26000000 INFO @ Sat, 06 Jul 2019 03:46:42: 26000000 INFO @ Sat, 06 Jul 2019 03:46:44: 19000000 INFO @ Sat, 06 Jul 2019 03:46:48: 27000000 INFO @ Sat, 06 Jul 2019 03:46:49: 27000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:46:56: 20000000 INFO @ Sat, 06 Jul 2019 03:46:56: 28000000 INFO @ Sat, 06 Jul 2019 03:46:57: 28000000 INFO @ Sat, 06 Jul 2019 03:47:04: 29000000 INFO @ Sat, 06 Jul 2019 03:47:05: 29000000 INFO @ Sat, 06 Jul 2019 03:47:07: 21000000 INFO @ Sat, 06 Jul 2019 03:47:08: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:47:08: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:47:08: #1 total tags in treatment: 14461888 INFO @ Sat, 06 Jul 2019 03:47:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:47:08: #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 03:47:08: #1 tags after filtering in treatment: 8374316 INFO @ Sat, 06 Jul 2019 03:47:08: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:47:08: #1 finished! INFO @ Sat, 06 Jul 2019 03:47:08: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:47:08: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:47:08: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:47:08: #1 total tags in treatment: 14461888 INFO @ Sat, 06 Jul 2019 03:47:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:47:08: #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 03:47:09: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:47:09: 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 03:47:09: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:47:09: #1 tags after filtering in treatment: 8374316 INFO @ Sat, 06 Jul 2019 03:47:09: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:47:09: #1 finished! INFO @ Sat, 06 Jul 2019 03:47:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:47:09: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:47:09: 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 03:47:09: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:47:17: 22000000 INFO @ Sat, 06 Jul 2019 03:47:27: 23000000 INFO @ Sat, 06 Jul 2019 03:47:38: 24000000 INFO @ Sat, 06 Jul 2019 03:47:48: 25000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.10_model.r’: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.10_*.xls’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.20_model.r’: No such file or directory : No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.10_peaks.narrowPeak’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.20_*.xls’: No such file or directory: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:47:58: 26000000 INFO @ Sat, 06 Jul 2019 03:48:09: 27000000 INFO @ Sat, 06 Jul 2019 03:48:19: 28000000 INFO @ Sat, 06 Jul 2019 03:48:29: 29000000 INFO @ Sat, 06 Jul 2019 03:48:33: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 03:48:33: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 03:48:33: #1 total tags in treatment: 14461888 INFO @ Sat, 06 Jul 2019 03:48:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:48:33: #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 03:48:34: #1 tags after filtering in treatment: 8374316 INFO @ Sat, 06 Jul 2019 03:48:34: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:48:34: #1 finished! INFO @ Sat, 06 Jul 2019 03:48:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:48:34: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:48:34: 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 03:48:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.05_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/SRX5126594/SRX5126594.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126594/SRX5126594.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling