Job ID = 4289012 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-10T04:33:59 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 6,188,474 reads read : 12,376,948 reads written : 12,376,948 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: 00:06:14 6188474 reads; of these: 6188474 (100.00%) were paired; of these: 1030616 (16.65%) aligned concordantly 0 times 4601759 (74.36%) aligned concordantly exactly 1 time 556099 (8.99%) aligned concordantly >1 times ---- 1030616 pairs aligned concordantly 0 times; of these: 265380 (25.75%) aligned discordantly 1 time ---- 765236 pairs aligned 0 times concordantly or discordantly; of these: 1530472 mates make up the pairs; of these: 1212674 (79.24%) aligned 0 times 237487 (15.52%) aligned exactly 1 time 80311 (5.25%) aligned >1 times 90.20% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:29 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] 396112 / 5416582 = 0.0731 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.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 13:56:24: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:56:24: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:56:32: 1000000 INFO @ Tue, 10 Dec 2019 13:56:41: 2000000 INFO @ Tue, 10 Dec 2019 13:56:49: 3000000 INFO @ Tue, 10 Dec 2019 13:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.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 13:56:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:56:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:56:57: 4000000 INFO @ Tue, 10 Dec 2019 13:57:02: 1000000 INFO @ Tue, 10 Dec 2019 13:57:05: 5000000 INFO @ Tue, 10 Dec 2019 13:57:12: 2000000 INFO @ Tue, 10 Dec 2019 13:57:13: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:57:22: 3000000 INFO @ Tue, 10 Dec 2019 13:57:22: 7000000 INFO @ Tue, 10 Dec 2019 13:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.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 13:57:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:57:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:57:30: 8000000 INFO @ Tue, 10 Dec 2019 13:57:31: 4000000 INFO @ Tue, 10 Dec 2019 13:57:33: 1000000 INFO @ Tue, 10 Dec 2019 13:57:39: 9000000 INFO @ Tue, 10 Dec 2019 13:57:41: 5000000 INFO @ Tue, 10 Dec 2019 13:57:43: 2000000 INFO @ Tue, 10 Dec 2019 13:57:47: 10000000 INFO @ Tue, 10 Dec 2019 13:57:50: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:57:50: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:57:50: #1 total tags in treatment: 4765757 INFO @ Tue, 10 Dec 2019 13:57:50: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:57:50: #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 13:57:50: #1 tags after filtering in treatment: 3989885 INFO @ Tue, 10 Dec 2019 13:57:50: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 10 Dec 2019 13:57:50: #1 finished! INFO @ Tue, 10 Dec 2019 13:57:50: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:57:50: #2 number of paired peaks: 27 WARNING @ Tue, 10 Dec 2019 13:57:50: Too few paired peaks (27) 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 13:57:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.05_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/SRX3205548/SRX3205548.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:57:51: 6000000 INFO @ Tue, 10 Dec 2019 13:57:53: 3000000 INFO @ Tue, 10 Dec 2019 13:58:00: 7000000 INFO @ Tue, 10 Dec 2019 13:58:03: 4000000 INFO @ Tue, 10 Dec 2019 13:58:10: 8000000 INFO @ Tue, 10 Dec 2019 13:58:13: 5000000 INFO @ Tue, 10 Dec 2019 13:58:20: 9000000 INFO @ Tue, 10 Dec 2019 13:58:23: 6000000 INFO @ Tue, 10 Dec 2019 13:58:29: 10000000 INFO @ Tue, 10 Dec 2019 13:58:32: 7000000 INFO @ Tue, 10 Dec 2019 13:58:33: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:58:33: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:58:33: #1 total tags in treatment: 4765757 INFO @ Tue, 10 Dec 2019 13:58:33: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:58:33: #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 13:58:33: #1 tags after filtering in treatment: 3989885 INFO @ Tue, 10 Dec 2019 13:58:33: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 10 Dec 2019 13:58:33: #1 finished! INFO @ Tue, 10 Dec 2019 13:58:33: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:58:33: #2 number of paired peaks: 27 WARNING @ Tue, 10 Dec 2019 13:58:33: Too few paired peaks (27) 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 13:58:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.10_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/SRX3205548/SRX3205548.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:58:42: 8000000 INFO @ Tue, 10 Dec 2019 13:58:51: 9000000 INFO @ Tue, 10 Dec 2019 13:59:01: 10000000 INFO @ Tue, 10 Dec 2019 13:59:04: #1 tag size is determined as 75 bps INFO @ Tue, 10 Dec 2019 13:59:04: #1 tag size = 75 INFO @ Tue, 10 Dec 2019 13:59:04: #1 total tags in treatment: 4765757 INFO @ Tue, 10 Dec 2019 13:59:04: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:59:04: #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 13:59:04: #1 tags after filtering in treatment: 3989885 INFO @ Tue, 10 Dec 2019 13:59:04: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 10 Dec 2019 13:59:04: #1 finished! INFO @ Tue, 10 Dec 2019 13:59:04: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:59:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:59:05: #2 number of paired peaks: 27 WARNING @ Tue, 10 Dec 2019 13:59:05: Too few paired peaks (27) 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 13:59:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.20_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/SRX3205548/SRX3205548.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3205548/SRX3205548.20_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。