Job ID = 2010000 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T11:45:16 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T11:45:16 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/004891/SRR5008422' 2019-07-05T11:45:16 fasterq-dump.2.9.6 err: invalid accession 'SRR5008422' 2019-07-05T11:45:31 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T11:45:31 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/004891/SRR5008422' 2019-07-05T11:45:31 fasterq-dump.2.9.6 err: invalid accession 'SRR5008422' spots read : 8,821,602 reads read : 17,643,204 reads written : 17,643,204 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: 00:07:18 8821602 reads; of these: 8821602 (100.00%) were paired; of these: 598419 (6.78%) aligned concordantly 0 times 6488170 (73.55%) aligned concordantly exactly 1 time 1735013 (19.67%) aligned concordantly >1 times ---- 598419 pairs aligned concordantly 0 times; of these: 67688 (11.31%) aligned discordantly 1 time ---- 530731 pairs aligned 0 times concordantly or discordantly; of these: 1061462 mates make up the pairs; of these: 809330 (76.25%) aligned 0 times 168030 (15.83%) aligned exactly 1 time 84102 (7.92%) aligned >1 times 95.41% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 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] 446335 / 8284102 = 0.0539 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 @ Fri, 05 Jul 2019 21:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.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 @ Fri, 05 Jul 2019 21:13:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:13:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.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 @ Fri, 05 Jul 2019 21:13:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:13:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.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 @ Fri, 05 Jul 2019 21:13:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:13:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:13:12: 1000000 INFO @ Fri, 05 Jul 2019 21:13:13: 1000000 INFO @ Fri, 05 Jul 2019 21:13:13: 1000000 INFO @ Fri, 05 Jul 2019 21:13:21: 2000000 INFO @ Fri, 05 Jul 2019 21:13:22: 2000000 INFO @ Fri, 05 Jul 2019 21:13:23: 2000000 INFO @ Fri, 05 Jul 2019 21:13:29: 3000000 INFO @ Fri, 05 Jul 2019 21:13:30: 3000000 INFO @ Fri, 05 Jul 2019 21:13:33: 3000000 INFO @ Fri, 05 Jul 2019 21:13:37: 4000000 INFO @ Fri, 05 Jul 2019 21:13:38: 4000000 INFO @ Fri, 05 Jul 2019 21:13:43: 4000000 INFO @ Fri, 05 Jul 2019 21:13:45: 5000000 INFO @ Fri, 05 Jul 2019 21:13:46: 5000000 INFO @ Fri, 05 Jul 2019 21:13:53: 5000000 INFO @ Fri, 05 Jul 2019 21:13:53: 6000000 INFO @ Fri, 05 Jul 2019 21:13:54: 6000000 INFO @ Fri, 05 Jul 2019 21:14:02: 7000000 INFO @ Fri, 05 Jul 2019 21:14:02: 7000000 INFO @ Fri, 05 Jul 2019 21:14:03: 6000000 INFO @ Fri, 05 Jul 2019 21:14:10: 8000000 INFO @ Fri, 05 Jul 2019 21:14:10: 8000000 INFO @ Fri, 05 Jul 2019 21:14:13: 7000000 INFO @ Fri, 05 Jul 2019 21:14:18: 9000000 INFO @ Fri, 05 Jul 2019 21:14:18: 9000000 INFO @ Fri, 05 Jul 2019 21:14:22: 8000000 INFO @ Fri, 05 Jul 2019 21:14:26: 10000000 INFO @ Fri, 05 Jul 2019 21:14:27: 10000000 INFO @ Fri, 05 Jul 2019 21:14:32: 9000000 INFO @ Fri, 05 Jul 2019 21:14:35: 11000000 INFO @ Fri, 05 Jul 2019 21:14:35: 11000000 INFO @ Fri, 05 Jul 2019 21:14:42: 10000000 INFO @ Fri, 05 Jul 2019 21:14:43: 12000000 INFO @ Fri, 05 Jul 2019 21:14:43: 12000000 INFO @ Fri, 05 Jul 2019 21:14:51: 13000000 INFO @ Fri, 05 Jul 2019 21:14:51: 13000000 INFO @ Fri, 05 Jul 2019 21:14:52: 11000000 INFO @ Fri, 05 Jul 2019 21:14:59: 14000000 INFO @ Fri, 05 Jul 2019 21:14:59: 14000000 INFO @ Fri, 05 Jul 2019 21:15:02: 12000000 INFO @ Fri, 05 Jul 2019 21:15:07: 15000000 INFO @ Fri, 05 Jul 2019 21:15:07: 15000000 INFO @ Fri, 05 Jul 2019 21:15:11: 13000000 INFO @ Fri, 05 Jul 2019 21:15:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:15:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:15:15: #1 total tags in treatment: 7777860 INFO @ Fri, 05 Jul 2019 21:15:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:15:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:15:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:15:15: #1 total tags in treatment: 7777860 INFO @ Fri, 05 Jul 2019 21:15:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:15:15: #1 tags after filtering in treatment: 5248357 INFO @ Fri, 05 Jul 2019 21:15:15: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 21:15:15: #1 finished! INFO @ Fri, 05 Jul 2019 21:15:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:15:15: #1 tags after filtering in treatment: 5248357 INFO @ Fri, 05 Jul 2019 21:15:15: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 21:15:15: #1 finished! INFO @ Fri, 05 Jul 2019 21:15:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:15:16: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:15:16: 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 @ Fri, 05 Jul 2019 21:15:16: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 21:15:16: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:15:16: 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 @ Fri, 05 Jul 2019 21:15:16: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 21:15:21: 14000000 BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 21:15:30: 15000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.10_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis pass1 - making usageList (0 chroms)needLargeMem: trying to allocate 0 bytes (limit: 17179869184): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:15:39: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:15:39: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:15:39: #1 total tags in treatment: 7777860 INFO @ Fri, 05 Jul 2019 21:15:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:15:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:15:39: #1 tags after filtering in treatment: 5248357 INFO @ Fri, 05 Jul 2019 21:15:39: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 21:15:39: #1 finished! INFO @ Fri, 05 Jul 2019 21:15:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:15:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:15:39: 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 @ Fri, 05 Jul 2019 21:15:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.05_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/SRX2339863/SRX2339863.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2339863/SRX2339863.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。