Job ID = 2640771 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T10:04:16 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 ) 2019-08-24T10:07:48 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 ) 2019-08-24T10:08:11 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 : 8,756,758 reads read : 17,513,516 reads written : 17,513,516 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: 00:06:28 8756758 reads; of these: 8756758 (100.00%) were paired; of these: 609341 (6.96%) aligned concordantly 0 times 7341355 (83.84%) aligned concordantly exactly 1 time 806062 (9.21%) aligned concordantly >1 times ---- 609341 pairs aligned concordantly 0 times; of these: 14880 (2.44%) aligned discordantly 1 time ---- 594461 pairs aligned 0 times concordantly or discordantly; of these: 1188922 mates make up the pairs; of these: 1130489 (95.09%) aligned 0 times 43926 (3.69%) aligned exactly 1 time 14507 (1.22%) aligned >1 times 93.55% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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 8 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] 352660 / 8157108 = 0.0432 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.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, 24 Aug 2019 19:20:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:40: 1000000 INFO @ Sat, 24 Aug 2019 19:20:47: 2000000 INFO @ Sat, 24 Aug 2019 19:20:54: 3000000 INFO @ Sat, 24 Aug 2019 19:21:02: 4000000 INFO @ Sat, 24 Aug 2019 19:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.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, 24 Aug 2019 19:21:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:10: 5000000 INFO @ Sat, 24 Aug 2019 19:21:10: 1000000 INFO @ Sat, 24 Aug 2019 19:21:17: 2000000 INFO @ Sat, 24 Aug 2019 19:21:17: 6000000 INFO @ Sat, 24 Aug 2019 19:21:23: 3000000 INFO @ Sat, 24 Aug 2019 19:21:25: 7000000 INFO @ Sat, 24 Aug 2019 19:21:29: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:21:33: 8000000 INFO @ Sat, 24 Aug 2019 19:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.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, 24 Aug 2019 19:21:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:36: 5000000 INFO @ Sat, 24 Aug 2019 19:21:40: 9000000 INFO @ Sat, 24 Aug 2019 19:21:42: 1000000 INFO @ Sat, 24 Aug 2019 19:21:42: 6000000 INFO @ Sat, 24 Aug 2019 19:21:48: 10000000 INFO @ Sat, 24 Aug 2019 19:21:49: 7000000 INFO @ Sat, 24 Aug 2019 19:21:51: 2000000 INFO @ Sat, 24 Aug 2019 19:21:56: 11000000 INFO @ Sat, 24 Aug 2019 19:21:56: 8000000 INFO @ Sat, 24 Aug 2019 19:22:00: 3000000 INFO @ Sat, 24 Aug 2019 19:22:03: 9000000 INFO @ Sat, 24 Aug 2019 19:22:04: 12000000 INFO @ Sat, 24 Aug 2019 19:22:09: 4000000 INFO @ Sat, 24 Aug 2019 19:22:09: 10000000 INFO @ Sat, 24 Aug 2019 19:22:12: 13000000 INFO @ Sat, 24 Aug 2019 19:22:16: 11000000 INFO @ Sat, 24 Aug 2019 19:22:19: 5000000 INFO @ Sat, 24 Aug 2019 19:22:20: 14000000 INFO @ Sat, 24 Aug 2019 19:22:23: 12000000 INFO @ Sat, 24 Aug 2019 19:22:27: 15000000 INFO @ Sat, 24 Aug 2019 19:22:28: 6000000 INFO @ Sat, 24 Aug 2019 19:22:30: 13000000 INFO @ Sat, 24 Aug 2019 19:22:33: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:22:33: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:22:33: #1 total tags in treatment: 7794955 INFO @ Sat, 24 Aug 2019 19:22:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:33: #1 tags after filtering in treatment: 5758254 INFO @ Sat, 24 Aug 2019 19:22:33: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 19:22:33: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:33: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:22:33: 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, 24 Aug 2019 19:22:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.05_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/ERX2732456/ERX2732456.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:36: 7000000 INFO @ Sat, 24 Aug 2019 19:22:37: 14000000 INFO @ Sat, 24 Aug 2019 19:22:44: 15000000 INFO @ Sat, 24 Aug 2019 19:22:45: 8000000 INFO @ Sat, 24 Aug 2019 19:22:49: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:22:49: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:22:49: #1 total tags in treatment: 7794955 INFO @ Sat, 24 Aug 2019 19:22:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:49: #1 tags after filtering in treatment: 5758254 INFO @ Sat, 24 Aug 2019 19:22:49: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 19:22:49: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:22:50: 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, 24 Aug 2019 19:22:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.10_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/ERX2732456/ERX2732456.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:53: 9000000 INFO @ Sat, 24 Aug 2019 19:23:02: 10000000 INFO @ Sat, 24 Aug 2019 19:23:10: 11000000 INFO @ Sat, 24 Aug 2019 19:23:18: 12000000 INFO @ Sat, 24 Aug 2019 19:23:27: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:23:35: 14000000 INFO @ Sat, 24 Aug 2019 19:23:44: 15000000 INFO @ Sat, 24 Aug 2019 19:23:50: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:23:50: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:23:50: #1 total tags in treatment: 7794955 INFO @ Sat, 24 Aug 2019 19:23:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:23:50: #1 tags after filtering in treatment: 5758254 INFO @ Sat, 24 Aug 2019 19:23:50: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 19:23:50: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:50: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 19:23:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:23:50: 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, 24 Aug 2019 19:23:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.20_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/ERX2732456/ERX2732456.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732456/ERX2732456.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling