Job ID = 2640989 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:14:48 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 ) 2019-08-24T11:19:09 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 : 10,773,237 reads read : 21,546,474 reads written : 21,546,474 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: 00:12:50 10773237 reads; of these: 10773237 (100.00%) were paired; of these: 1088955 (10.11%) aligned concordantly 0 times 8886363 (82.49%) aligned concordantly exactly 1 time 797919 (7.41%) aligned concordantly >1 times ---- 1088955 pairs aligned concordantly 0 times; of these: 155949 (14.32%) aligned discordantly 1 time ---- 933006 pairs aligned 0 times concordantly or discordantly; of these: 1866012 mates make up the pairs; of these: 1790401 (95.95%) aligned 0 times 39637 (2.12%) aligned exactly 1 time 35974 (1.93%) aligned >1 times 91.69% overall alignment rate Time searching: 00:12:50 Overall time: 00:12:50 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] 127193 / 9837692 = 0.0129 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:59:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.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 20:59:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:59:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:59:13: 1000000 INFO @ Sat, 24 Aug 2019 20:59:22: 2000000 INFO @ Sat, 24 Aug 2019 20:59:31: 3000000 INFO @ Sat, 24 Aug 2019 20:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.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 20:59:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:59:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:59:40: 4000000 INFO @ Sat, 24 Aug 2019 20:59:46: 1000000 INFO @ Sat, 24 Aug 2019 20:59:50: 5000000 INFO @ Sat, 24 Aug 2019 20:59:57: 2000000 INFO @ Sat, 24 Aug 2019 20:59:59: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.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 21:00:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:00:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:00:08: 3000000 INFO @ Sat, 24 Aug 2019 21:00:08: 7000000 INFO @ Sat, 24 Aug 2019 21:00:18: 1000000 INFO @ Sat, 24 Aug 2019 21:00:18: 8000000 INFO @ Sat, 24 Aug 2019 21:00:20: 4000000 INFO @ Sat, 24 Aug 2019 21:00:28: 9000000 INFO @ Sat, 24 Aug 2019 21:00:32: 5000000 INFO @ Sat, 24 Aug 2019 21:00:32: 2000000 INFO @ Sat, 24 Aug 2019 21:00:37: 10000000 INFO @ Sat, 24 Aug 2019 21:00:43: 6000000 INFO @ Sat, 24 Aug 2019 21:00:45: 3000000 INFO @ Sat, 24 Aug 2019 21:00:47: 11000000 INFO @ Sat, 24 Aug 2019 21:00:55: 7000000 INFO @ Sat, 24 Aug 2019 21:00:56: 12000000 INFO @ Sat, 24 Aug 2019 21:00:59: 4000000 INFO @ Sat, 24 Aug 2019 21:01:06: 13000000 INFO @ Sat, 24 Aug 2019 21:01:06: 8000000 INFO @ Sat, 24 Aug 2019 21:01:13: 5000000 INFO @ Sat, 24 Aug 2019 21:01:16: 14000000 INFO @ Sat, 24 Aug 2019 21:01:18: 9000000 INFO @ Sat, 24 Aug 2019 21:01:25: 15000000 INFO @ Sat, 24 Aug 2019 21:01:27: 6000000 INFO @ Sat, 24 Aug 2019 21:01:29: 10000000 INFO @ Sat, 24 Aug 2019 21:01:35: 16000000 INFO @ Sat, 24 Aug 2019 21:01:40: 7000000 INFO @ Sat, 24 Aug 2019 21:01:41: 11000000 INFO @ Sat, 24 Aug 2019 21:01:44: 17000000 INFO @ Sat, 24 Aug 2019 21:01:52: 12000000 INFO @ Sat, 24 Aug 2019 21:01:54: 18000000 INFO @ Sat, 24 Aug 2019 21:01:54: 8000000 INFO @ Sat, 24 Aug 2019 21:02:03: 19000000 INFO @ Sat, 24 Aug 2019 21:02:04: 13000000 INFO @ Sat, 24 Aug 2019 21:02:08: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:02:08: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:02:08: #1 total tags in treatment: 9558916 INFO @ Sat, 24 Aug 2019 21:02:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:02:08: #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 21:02:08: 9000000 INFO @ Sat, 24 Aug 2019 21:02:08: #1 tags after filtering in treatment: 7469693 INFO @ Sat, 24 Aug 2019 21:02:08: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 21:02:08: #1 finished! INFO @ Sat, 24 Aug 2019 21:02:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:02:09: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:02:09: 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, 24 Aug 2019 21:02:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:02:15: 14000000 INFO @ Sat, 24 Aug 2019 21:02:22: 10000000 INFO @ Sat, 24 Aug 2019 21:02:27: 15000000 INFO @ Sat, 24 Aug 2019 21:02:35: 11000000 INFO @ Sat, 24 Aug 2019 21:02:38: 16000000 INFO @ Sat, 24 Aug 2019 21:02:49: 12000000 INFO @ Sat, 24 Aug 2019 21:02:50: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:03:01: 18000000 INFO @ Sat, 24 Aug 2019 21:03:02: 13000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:03:13: 19000000 INFO @ Sat, 24 Aug 2019 21:03:16: 14000000 INFO @ Sat, 24 Aug 2019 21:03:19: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:03:19: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:03:19: #1 total tags in treatment: 9558916 INFO @ Sat, 24 Aug 2019 21:03:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:19: #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 21:03:19: #1 tags after filtering in treatment: 7469693 INFO @ Sat, 24 Aug 2019 21:03:19: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 21:03:19: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:20: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:20: 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 @ Sat, 24 Aug 2019 21:03:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.10_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/SRX4936095/SRX4936095.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:03:29: 15000000 INFO @ Sat, 24 Aug 2019 21:03:42: 16000000 INFO @ Sat, 24 Aug 2019 21:03:54: 17000000 INFO @ Sat, 24 Aug 2019 21:04:07: 18000000 INFO @ Sat, 24 Aug 2019 21:04:20: 19000000 INFO @ Sat, 24 Aug 2019 21:04:26: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:04:26: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:04:26: #1 total tags in treatment: 9558916 INFO @ Sat, 24 Aug 2019 21:04:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:04:26: #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 21:04:26: #1 tags after filtering in treatment: 7469693 INFO @ Sat, 24 Aug 2019 21:04:26: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 24 Aug 2019 21:04:26: #1 finished! INFO @ Sat, 24 Aug 2019 21:04:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:04:27: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:04:27: 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 21:04:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.20_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/SRX4936095/SRX4936095.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936095/SRX4936095.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling