Job ID = 2011743 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:19:15 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 : 15,127,660 reads read : 30,255,320 reads written : 30,255,320 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 Multiseed full-index search: 00:10:52 15127660 reads; of these: 15127660 (100.00%) were paired; of these: 1486888 (9.83%) aligned concordantly 0 times 11977844 (79.18%) aligned concordantly exactly 1 time 1662928 (10.99%) aligned concordantly >1 times ---- 1486888 pairs aligned concordantly 0 times; of these: 376337 (25.31%) aligned discordantly 1 time ---- 1110551 pairs aligned 0 times concordantly or discordantly; of these: 2221102 mates make up the pairs; of these: 1650362 (74.30%) aligned 0 times 341129 (15.36%) aligned exactly 1 time 229611 (10.34%) aligned >1 times 94.55% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 622721 / 14013027 = 0.0444 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 02:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.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 02:44:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.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 02:44:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:10: 1000000 INFO @ Sat, 06 Jul 2019 02:44:11: 1000000 INFO @ Sat, 06 Jul 2019 02:44:19: 2000000 INFO @ Sat, 06 Jul 2019 02:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.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 02:44:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:21: 2000000 INFO @ Sat, 06 Jul 2019 02:44:28: 1000000 INFO @ Sat, 06 Jul 2019 02:44:28: 3000000 INFO @ Sat, 06 Jul 2019 02:44:30: 3000000 INFO @ Sat, 06 Jul 2019 02:44:34: 2000000 INFO @ Sat, 06 Jul 2019 02:44:37: 4000000 INFO @ Sat, 06 Jul 2019 02:44:39: 4000000 INFO @ Sat, 06 Jul 2019 02:44:41: 3000000 INFO @ Sat, 06 Jul 2019 02:44:44: 5000000 INFO @ Sat, 06 Jul 2019 02:44:47: 5000000 INFO @ Sat, 06 Jul 2019 02:44:48: 4000000 INFO @ Sat, 06 Jul 2019 02:44:53: 6000000 INFO @ Sat, 06 Jul 2019 02:44:55: 5000000 INFO @ Sat, 06 Jul 2019 02:44:56: 6000000 INFO @ Sat, 06 Jul 2019 02:45:01: 7000000 INFO @ Sat, 06 Jul 2019 02:45:02: 6000000 INFO @ Sat, 06 Jul 2019 02:45:05: 7000000 INFO @ Sat, 06 Jul 2019 02:45:08: 7000000 INFO @ Sat, 06 Jul 2019 02:45:09: 8000000 INFO @ Sat, 06 Jul 2019 02:45:13: 8000000 INFO @ Sat, 06 Jul 2019 02:45:14: 8000000 INFO @ Sat, 06 Jul 2019 02:45:17: 9000000 INFO @ Sat, 06 Jul 2019 02:45:21: 9000000 INFO @ Sat, 06 Jul 2019 02:45:22: 9000000 INFO @ Sat, 06 Jul 2019 02:45:24: 10000000 INFO @ Sat, 06 Jul 2019 02:45:27: 10000000 INFO @ Sat, 06 Jul 2019 02:45:31: 10000000 INFO @ Sat, 06 Jul 2019 02:45:32: 11000000 INFO @ Sat, 06 Jul 2019 02:45:33: 11000000 INFO @ Sat, 06 Jul 2019 02:45:38: 11000000 INFO @ Sat, 06 Jul 2019 02:45:40: 12000000 INFO @ Sat, 06 Jul 2019 02:45:40: 12000000 INFO @ Sat, 06 Jul 2019 02:45:46: 13000000 INFO @ Sat, 06 Jul 2019 02:45:46: 12000000 INFO @ Sat, 06 Jul 2019 02:45:48: 13000000 INFO @ Sat, 06 Jul 2019 02:45:52: 14000000 INFO @ Sat, 06 Jul 2019 02:45:54: 13000000 INFO @ Sat, 06 Jul 2019 02:45:56: 14000000 INFO @ Sat, 06 Jul 2019 02:45:58: 15000000 INFO @ Sat, 06 Jul 2019 02:46:03: 14000000 INFO @ Sat, 06 Jul 2019 02:46:05: 16000000 INFO @ Sat, 06 Jul 2019 02:46:05: 15000000 INFO @ Sat, 06 Jul 2019 02:46:11: 17000000 INFO @ Sat, 06 Jul 2019 02:46:12: 15000000 INFO @ Sat, 06 Jul 2019 02:46:13: 16000000 INFO @ Sat, 06 Jul 2019 02:46:17: 18000000 INFO @ Sat, 06 Jul 2019 02:46:20: 16000000 INFO @ Sat, 06 Jul 2019 02:46:21: 17000000 INFO @ Sat, 06 Jul 2019 02:46:23: 19000000 INFO @ Sat, 06 Jul 2019 02:46:27: 17000000 INFO @ Sat, 06 Jul 2019 02:46:28: 18000000 INFO @ Sat, 06 Jul 2019 02:46:29: 20000000 INFO @ Sat, 06 Jul 2019 02:46:35: 21000000 INFO @ Sat, 06 Jul 2019 02:46:35: 18000000 INFO @ Sat, 06 Jul 2019 02:46:36: 19000000 INFO @ Sat, 06 Jul 2019 02:46:41: 22000000 INFO @ Sat, 06 Jul 2019 02:46:43: 19000000 INFO @ Sat, 06 Jul 2019 02:46:44: 20000000 INFO @ Sat, 06 Jul 2019 02:46:47: 23000000 INFO @ Sat, 06 Jul 2019 02:46:50: 20000000 INFO @ Sat, 06 Jul 2019 02:46:52: 21000000 INFO @ Sat, 06 Jul 2019 02:46:53: 24000000 INFO @ Sat, 06 Jul 2019 02:46:58: 21000000 INFO @ Sat, 06 Jul 2019 02:46:59: 22000000 INFO @ Sat, 06 Jul 2019 02:47:00: 25000000 INFO @ Sat, 06 Jul 2019 02:47:05: 22000000 INFO @ Sat, 06 Jul 2019 02:47:06: 26000000 INFO @ Sat, 06 Jul 2019 02:47:07: 23000000 INFO @ Sat, 06 Jul 2019 02:47:13: 23000000 INFO @ Sat, 06 Jul 2019 02:47:13: 27000000 INFO @ Sat, 06 Jul 2019 02:47:14: 24000000 INFO @ Sat, 06 Jul 2019 02:47:16: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:47:16: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:47:16: #1 total tags in treatment: 13028831 INFO @ Sat, 06 Jul 2019 02:47:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:47:16: #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 02:47:16: #1 tags after filtering in treatment: 8341116 INFO @ Sat, 06 Jul 2019 02:47:16: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 02:47:16: #1 finished! INFO @ Sat, 06 Jul 2019 02:47:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:47:17: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:47:17: 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 02:47:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.20_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/SRX4915183/SRX4915183.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:47:20: 24000000 INFO @ Sat, 06 Jul 2019 02:47:22: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:47:28: 25000000 INFO @ Sat, 06 Jul 2019 02:47:29: 26000000 INFO @ Sat, 06 Jul 2019 02:47:36: 26000000 INFO @ Sat, 06 Jul 2019 02:47:37: 27000000 INFO @ Sat, 06 Jul 2019 02:47:40: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:47:40: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:47:40: #1 total tags in treatment: 13028831 INFO @ Sat, 06 Jul 2019 02:47:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:47:40: #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 02:47:40: #1 tags after filtering in treatment: 8341116 INFO @ Sat, 06 Jul 2019 02:47:40: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 02:47:40: #1 finished! INFO @ Sat, 06 Jul 2019 02:47:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:47:41: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:47:41: 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 02:47:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.05_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/SRX4915183/SRX4915183.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:47:43: 27000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:47:46: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:47:46: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:47:46: #1 total tags in treatment: 13028831 INFO @ Sat, 06 Jul 2019 02:47:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:47:46: #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 02:47:47: #1 tags after filtering in treatment: 8341116 INFO @ Sat, 06 Jul 2019 02:47:47: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 02:47:47: #1 finished! INFO @ Sat, 06 Jul 2019 02:47:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:47:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:47:47: 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 02:47:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.10_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/SRX4915183/SRX4915183.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915183/SRX4915183.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling