Job ID = 4289512 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-10T05:38:14 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 ) 2019-12-10T05:38:14 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 : 16,303,794 reads read : 32,607,588 reads written : 32,607,588 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: 00:12:20 16303794 reads; of these: 16303794 (100.00%) were paired; of these: 1937524 (11.88%) aligned concordantly 0 times 12496446 (76.65%) aligned concordantly exactly 1 time 1869824 (11.47%) aligned concordantly >1 times ---- 1937524 pairs aligned concordantly 0 times; of these: 361599 (18.66%) aligned discordantly 1 time ---- 1575925 pairs aligned 0 times concordantly or discordantly; of these: 3151850 mates make up the pairs; of these: 2745130 (87.10%) aligned 0 times 247253 (7.84%) aligned exactly 1 time 159467 (5.06%) aligned >1 times 91.58% overall alignment rate Time searching: 00:12:20 Overall time: 00:12:20 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] 663516 / 14612757 = 0.0454 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 15:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.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 @ Tue, 10 Dec 2019 15:01:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:01:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:01:24: 1000000 INFO @ Tue, 10 Dec 2019 15:01:31: 2000000 INFO @ Tue, 10 Dec 2019 15:01:37: 3000000 INFO @ Tue, 10 Dec 2019 15:01:43: 4000000 INFO @ Tue, 10 Dec 2019 15:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.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 @ Tue, 10 Dec 2019 15:01:48: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:01:48: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:01:49: 5000000 INFO @ Tue, 10 Dec 2019 15:01:54: 1000000 INFO @ Tue, 10 Dec 2019 15:01:56: 6000000 INFO @ Tue, 10 Dec 2019 15:02:01: 2000000 INFO @ Tue, 10 Dec 2019 15:02:02: 7000000 INFO @ Tue, 10 Dec 2019 15:02:07: 3000000 INFO @ Tue, 10 Dec 2019 15:02:08: 8000000 INFO @ Tue, 10 Dec 2019 15:02:13: 4000000 INFO @ Tue, 10 Dec 2019 15:02:15: 9000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.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 @ Tue, 10 Dec 2019 15:02:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:02:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:02:19: 5000000 INFO @ Tue, 10 Dec 2019 15:02:21: 10000000 INFO @ Tue, 10 Dec 2019 15:02:24: 1000000 INFO @ Tue, 10 Dec 2019 15:02:25: 6000000 INFO @ Tue, 10 Dec 2019 15:02:28: 11000000 INFO @ Tue, 10 Dec 2019 15:02:30: 2000000 INFO @ Tue, 10 Dec 2019 15:02:32: 7000000 INFO @ Tue, 10 Dec 2019 15:02:34: 12000000 INFO @ Tue, 10 Dec 2019 15:02:35: 3000000 INFO @ Tue, 10 Dec 2019 15:02:38: 8000000 INFO @ Tue, 10 Dec 2019 15:02:40: 13000000 INFO @ Tue, 10 Dec 2019 15:02:41: 4000000 INFO @ Tue, 10 Dec 2019 15:02:44: 9000000 INFO @ Tue, 10 Dec 2019 15:02:47: 14000000 INFO @ Tue, 10 Dec 2019 15:02:47: 5000000 INFO @ Tue, 10 Dec 2019 15:02:51: 10000000 INFO @ Tue, 10 Dec 2019 15:02:52: 6000000 INFO @ Tue, 10 Dec 2019 15:02:53: 15000000 INFO @ Tue, 10 Dec 2019 15:02:57: 11000000 INFO @ Tue, 10 Dec 2019 15:02:58: 7000000 INFO @ Tue, 10 Dec 2019 15:02:59: 16000000 INFO @ Tue, 10 Dec 2019 15:03:03: 12000000 INFO @ Tue, 10 Dec 2019 15:03:04: 8000000 INFO @ Tue, 10 Dec 2019 15:03:06: 17000000 INFO @ Tue, 10 Dec 2019 15:03:09: 13000000 INFO @ Tue, 10 Dec 2019 15:03:10: 9000000 INFO @ Tue, 10 Dec 2019 15:03:12: 18000000 INFO @ Tue, 10 Dec 2019 15:03:15: 14000000 INFO @ Tue, 10 Dec 2019 15:03:16: 10000000 INFO @ Tue, 10 Dec 2019 15:03:18: 19000000 INFO @ Tue, 10 Dec 2019 15:03:21: 11000000 INFO @ Tue, 10 Dec 2019 15:03:22: 15000000 INFO @ Tue, 10 Dec 2019 15:03:25: 20000000 INFO @ Tue, 10 Dec 2019 15:03:27: 12000000 INFO @ Tue, 10 Dec 2019 15:03:28: 16000000 INFO @ Tue, 10 Dec 2019 15:03:31: 21000000 INFO @ Tue, 10 Dec 2019 15:03:33: 13000000 INFO @ Tue, 10 Dec 2019 15:03:34: 17000000 INFO @ Tue, 10 Dec 2019 15:03:37: 22000000 INFO @ Tue, 10 Dec 2019 15:03:38: 14000000 INFO @ Tue, 10 Dec 2019 15:03:40: 18000000 INFO @ Tue, 10 Dec 2019 15:03:44: 23000000 INFO @ Tue, 10 Dec 2019 15:03:44: 15000000 INFO @ Tue, 10 Dec 2019 15:03:46: 19000000 INFO @ Tue, 10 Dec 2019 15:03:50: 24000000 INFO @ Tue, 10 Dec 2019 15:03:50: 16000000 INFO @ Tue, 10 Dec 2019 15:03:53: 20000000 INFO @ Tue, 10 Dec 2019 15:03:56: 17000000 INFO @ Tue, 10 Dec 2019 15:03:56: 25000000 INFO @ Tue, 10 Dec 2019 15:03:59: 21000000 INFO @ Tue, 10 Dec 2019 15:04:02: 18000000 INFO @ Tue, 10 Dec 2019 15:04:03: 26000000 INFO @ Tue, 10 Dec 2019 15:04:05: 22000000 INFO @ Tue, 10 Dec 2019 15:04:07: 19000000 INFO @ Tue, 10 Dec 2019 15:04:09: 27000000 INFO @ Tue, 10 Dec 2019 15:04:11: 23000000 INFO @ Tue, 10 Dec 2019 15:04:13: 20000000 INFO @ Tue, 10 Dec 2019 15:04:16: 28000000 INFO @ Tue, 10 Dec 2019 15:04:17: 24000000 INFO @ Tue, 10 Dec 2019 15:04:19: 21000000 INFO @ Tue, 10 Dec 2019 15:04:19: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:04:19: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:04:19: #1 total tags in treatment: 13710625 INFO @ Tue, 10 Dec 2019 15:04:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:04:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 15:04:19: #1 tags after filtering in treatment: 7970811 INFO @ Tue, 10 Dec 2019 15:04:19: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 10 Dec 2019 15:04:19: #1 finished! INFO @ Tue, 10 Dec 2019 15:04:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:04:20: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:04:20: 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 @ Tue, 10 Dec 2019 15:04:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.05_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/SRX6742721/SRX6742721.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:04:24: 25000000 INFO @ Tue, 10 Dec 2019 15:04:24: 22000000 INFO @ Tue, 10 Dec 2019 15:04:30: 26000000 INFO @ Tue, 10 Dec 2019 15:04:30: 23000000 INFO @ Tue, 10 Dec 2019 15:04:36: 24000000 INFO @ Tue, 10 Dec 2019 15:04:36: 27000000 INFO @ Tue, 10 Dec 2019 15:04:41: 25000000 INFO @ Tue, 10 Dec 2019 15:04:42: 28000000 INFO @ Tue, 10 Dec 2019 15:04:45: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:04:45: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:04:45: #1 total tags in treatment: 13710625 INFO @ Tue, 10 Dec 2019 15:04:45: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:04:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 15:04:46: #1 tags after filtering in treatment: 7970811 INFO @ Tue, 10 Dec 2019 15:04:46: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 10 Dec 2019 15:04:46: #1 finished! INFO @ Tue, 10 Dec 2019 15:04:46: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:04:46: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:04:46: 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 @ Tue, 10 Dec 2019 15:04:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.10_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/SRX6742721/SRX6742721.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:04:47: 26000000 INFO @ Tue, 10 Dec 2019 15:04:53: 27000000 INFO @ Tue, 10 Dec 2019 15:04:58: 28000000 INFO @ Tue, 10 Dec 2019 15:05:01: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:05:01: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:05:01: #1 total tags in treatment: 13710625 INFO @ Tue, 10 Dec 2019 15:05:01: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:05:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 15:05:02: #1 tags after filtering in treatment: 7970811 INFO @ Tue, 10 Dec 2019 15:05:02: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 10 Dec 2019 15:05:02: #1 finished! INFO @ Tue, 10 Dec 2019 15:05:02: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:05:02: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:05:02: 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 @ Tue, 10 Dec 2019 15:05:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.20_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/SRX6742721/SRX6742721.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742721/SRX6742721.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。