Job ID = 2011943 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T18:36:25 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 : 9,646,401 reads read : 19,292,802 reads written : 19,292,802 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: 00:07:41 9646401 reads; of these: 9646401 (100.00%) were paired; of these: 6302683 (65.34%) aligned concordantly 0 times 2795220 (28.98%) aligned concordantly exactly 1 time 548498 (5.69%) aligned concordantly >1 times ---- 6302683 pairs aligned concordantly 0 times; of these: 1563483 (24.81%) aligned discordantly 1 time ---- 4739200 pairs aligned 0 times concordantly or discordantly; of these: 9478400 mates make up the pairs; of these: 8518668 (89.87%) aligned 0 times 315265 (3.33%) aligned exactly 1 time 644467 (6.80%) aligned >1 times 55.85% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 683427 / 4803551 = 0.1423 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 @ Sat, 06 Jul 2019 03:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.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, 06 Jul 2019 03:48:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:48:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.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, 06 Jul 2019 03:48:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:48:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:48:50: 1000000 INFO @ Sat, 06 Jul 2019 03:48:51: 1000000 INFO @ Sat, 06 Jul 2019 03:49:01: 2000000 INFO @ Sat, 06 Jul 2019 03:49:02: 2000000 INFO @ Sat, 06 Jul 2019 03:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.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, 06 Jul 2019 03:49:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:49:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:49:12: 3000000 INFO @ Sat, 06 Jul 2019 03:49:15: 3000000 INFO @ Sat, 06 Jul 2019 03:49:20: 1000000 INFO @ Sat, 06 Jul 2019 03:49:24: 4000000 INFO @ Sat, 06 Jul 2019 03:49:29: 4000000 INFO @ Sat, 06 Jul 2019 03:49:33: 2000000 INFO @ Sat, 06 Jul 2019 03:49:35: 5000000 INFO @ Sat, 06 Jul 2019 03:49:43: 5000000 INFO @ Sat, 06 Jul 2019 03:49:46: 6000000 INFO @ Sat, 06 Jul 2019 03:49:47: 3000000 INFO @ Sat, 06 Jul 2019 03:49:56: 6000000 INFO @ Sat, 06 Jul 2019 03:49:57: 7000000 INFO @ Sat, 06 Jul 2019 03:50:00: 4000000 INFO @ Sat, 06 Jul 2019 03:50:08: 8000000 INFO @ Sat, 06 Jul 2019 03:50:09: 7000000 INFO @ Sat, 06 Jul 2019 03:50:14: 5000000 INFO @ Sat, 06 Jul 2019 03:50:20: 9000000 INFO @ Sat, 06 Jul 2019 03:50:22: 8000000 INFO @ Sat, 06 Jul 2019 03:50:24: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:50:24: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:50:24: #1 total tags in treatment: 2882669 INFO @ Sat, 06 Jul 2019 03:50:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:50:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:50:24: #1 tags after filtering in treatment: 2135381 INFO @ Sat, 06 Jul 2019 03:50:24: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:50:24: #1 finished! INFO @ Sat, 06 Jul 2019 03:50:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:50:24: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:50:24: Too few paired peaks (28) 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, 06 Jul 2019 03:50:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.05_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/SRX5624302/SRX5624302.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:50:26: 6000000 INFO @ Sat, 06 Jul 2019 03:50:34: 9000000 INFO @ Sat, 06 Jul 2019 03:50:38: 7000000 INFO @ Sat, 06 Jul 2019 03:50:39: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:50:39: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:50:39: #1 total tags in treatment: 2882669 INFO @ Sat, 06 Jul 2019 03:50:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:50:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:50:39: #1 tags after filtering in treatment: 2135381 INFO @ Sat, 06 Jul 2019 03:50:39: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:50:39: #1 finished! INFO @ Sat, 06 Jul 2019 03:50:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:50:40: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:50:40: Too few paired peaks (28) 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, 06 Jul 2019 03:50:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.10_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/SRX5624302/SRX5624302.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:50:49: 8000000 INFO @ Sat, 06 Jul 2019 03:51:00: 9000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:51:04: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:51:04: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:51:04: #1 total tags in treatment: 2882669 INFO @ Sat, 06 Jul 2019 03:51:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:51:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:51:04: #1 tags after filtering in treatment: 2135381 INFO @ Sat, 06 Jul 2019 03:51:04: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:51:04: #1 finished! INFO @ Sat, 06 Jul 2019 03:51:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:51:04: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 03:51:04: Too few paired peaks (28) 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, 06 Jul 2019 03:51:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.20_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/SRX5624302/SRX5624302.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5624302/SRX5624302.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling