Job ID = 2010996 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T16:35:41 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 : 7,271,117 reads read : 14,542,234 reads written : 14,542,234 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: 00:04:02 7271117 reads; of these: 7271117 (100.00%) were paired; of these: 3400841 (46.77%) aligned concordantly 0 times 3718705 (51.14%) aligned concordantly exactly 1 time 151571 (2.08%) aligned concordantly >1 times ---- 3400841 pairs aligned concordantly 0 times; of these: 45332 (1.33%) aligned discordantly 1 time ---- 3355509 pairs aligned 0 times concordantly or discordantly; of these: 6711018 mates make up the pairs; of these: 3710778 (55.29%) aligned 0 times 2860328 (42.62%) aligned exactly 1 time 139912 (2.08%) aligned >1 times 74.48% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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_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] 122248 / 3914953 = 0.0312 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 01:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.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 01:45:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:45:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.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 01:45:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:45:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.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 01:45:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:45:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:45:46: 1000000 INFO @ Sat, 06 Jul 2019 01:45:48: 1000000 INFO @ Sat, 06 Jul 2019 01:45:50: 1000000 INFO @ Sat, 06 Jul 2019 01:45:53: 2000000 INFO @ Sat, 06 Jul 2019 01:45:54: 2000000 INFO @ Sat, 06 Jul 2019 01:45:58: 2000000 INFO @ Sat, 06 Jul 2019 01:45:59: 3000000 INFO @ Sat, 06 Jul 2019 01:46:00: 3000000 INFO @ Sat, 06 Jul 2019 01:46:05: 4000000 INFO @ Sat, 06 Jul 2019 01:46:06: 4000000 INFO @ Sat, 06 Jul 2019 01:46:07: 3000000 INFO @ Sat, 06 Jul 2019 01:46:11: 5000000 INFO @ Sat, 06 Jul 2019 01:46:12: 5000000 INFO @ Sat, 06 Jul 2019 01:46:16: 4000000 INFO @ Sat, 06 Jul 2019 01:46:17: 6000000 INFO @ Sat, 06 Jul 2019 01:46:18: 6000000 INFO @ Sat, 06 Jul 2019 01:46:23: 7000000 INFO @ Sat, 06 Jul 2019 01:46:24: 5000000 INFO @ Sat, 06 Jul 2019 01:46:24: 7000000 INFO @ Sat, 06 Jul 2019 01:46:28: 8000000 INFO @ Sat, 06 Jul 2019 01:46:31: 8000000 INFO @ Sat, 06 Jul 2019 01:46:33: 6000000 INFO @ Sat, 06 Jul 2019 01:46:34: 9000000 INFO @ Sat, 06 Jul 2019 01:46:37: 9000000 INFO @ Sat, 06 Jul 2019 01:46:40: 10000000 INFO @ Sat, 06 Jul 2019 01:46:41: 7000000 INFO @ Sat, 06 Jul 2019 01:46:43: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:46:43: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:46:43: #1 total tags in treatment: 3748415 INFO @ Sat, 06 Jul 2019 01:46:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:46:43: #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 01:46:43: #1 tags after filtering in treatment: 2482443 INFO @ Sat, 06 Jul 2019 01:46:43: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 01:46:43: #1 finished! INFO @ Sat, 06 Jul 2019 01:46:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:46:43: 10000000 INFO @ Sat, 06 Jul 2019 01:46:43: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:46:43: 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 01:46:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.20_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/SRX4342942/SRX4342942.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:46:47: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:46:47: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:46:47: #1 total tags in treatment: 3748415 INFO @ Sat, 06 Jul 2019 01:46:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:46:47: #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 01:46:47: #1 tags after filtering in treatment: 2482443 INFO @ Sat, 06 Jul 2019 01:46:47: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 01:46:47: #1 finished! INFO @ Sat, 06 Jul 2019 01:46:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:46:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:46:47: 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 01:46:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.05_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/SRX4342942/SRX4342942.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:46:50: 8000000 INFO @ Sat, 06 Jul 2019 01:46:58: 9000000 INFO @ Sat, 06 Jul 2019 01:47:07: 10000000 INFO @ Sat, 06 Jul 2019 01:47:11: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:47:11: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:47:11: #1 total tags in treatment: 3748415 INFO @ Sat, 06 Jul 2019 01:47:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:47:11: #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 01:47:12: #1 tags after filtering in treatment: 2482443 INFO @ Sat, 06 Jul 2019 01:47:12: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 01:47:12: #1 finished! INFO @ Sat, 06 Jul 2019 01:47:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:47:12: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:47:12: 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 01:47:12: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.10_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342942/SRX4342942.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。