Job ID = 2011738 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:19:15 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 : 11,341,741 reads read : 22,683,482 reads written : 22,683,482 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: 00:07:16 11341741 reads; of these: 11341741 (100.00%) were paired; of these: 2496333 (22.01%) aligned concordantly 0 times 7377773 (65.05%) aligned concordantly exactly 1 time 1467635 (12.94%) aligned concordantly >1 times ---- 2496333 pairs aligned concordantly 0 times; of these: 330996 (13.26%) aligned discordantly 1 time ---- 2165337 pairs aligned 0 times concordantly or discordantly; of these: 4330674 mates make up the pairs; of these: 3926791 (90.67%) aligned 0 times 178806 (4.13%) aligned exactly 1 time 225077 (5.20%) aligned >1 times 82.69% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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] 965285 / 9174117 = 0.1052 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 02:34:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.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 02:34:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:34:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.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 02:34:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:34:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.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 02:34:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:34:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:34:12: 1000000 INFO @ Sat, 06 Jul 2019 02:34:14: 1000000 INFO @ Sat, 06 Jul 2019 02:34:14: 1000000 INFO @ Sat, 06 Jul 2019 02:34:18: 2000000 INFO @ Sat, 06 Jul 2019 02:34:22: 2000000 INFO @ Sat, 06 Jul 2019 02:34:23: 2000000 INFO @ Sat, 06 Jul 2019 02:34:25: 3000000 INFO @ Sat, 06 Jul 2019 02:34:29: 3000000 INFO @ Sat, 06 Jul 2019 02:34:31: 4000000 INFO @ Sat, 06 Jul 2019 02:34:32: 3000000 INFO @ Sat, 06 Jul 2019 02:34:37: 4000000 INFO @ Sat, 06 Jul 2019 02:34:38: 5000000 INFO @ Sat, 06 Jul 2019 02:34:40: 4000000 INFO @ Sat, 06 Jul 2019 02:34:44: 5000000 INFO @ Sat, 06 Jul 2019 02:34:44: 6000000 INFO @ Sat, 06 Jul 2019 02:34:49: 5000000 INFO @ Sat, 06 Jul 2019 02:34:51: 7000000 INFO @ Sat, 06 Jul 2019 02:34:52: 6000000 INFO @ Sat, 06 Jul 2019 02:34:57: 6000000 INFO @ Sat, 06 Jul 2019 02:34:58: 8000000 INFO @ Sat, 06 Jul 2019 02:34:59: 7000000 INFO @ Sat, 06 Jul 2019 02:35:04: 9000000 INFO @ Sat, 06 Jul 2019 02:35:06: 7000000 INFO @ Sat, 06 Jul 2019 02:35:07: 8000000 INFO @ Sat, 06 Jul 2019 02:35:11: 10000000 INFO @ Sat, 06 Jul 2019 02:35:14: 9000000 INFO @ Sat, 06 Jul 2019 02:35:15: 8000000 INFO @ Sat, 06 Jul 2019 02:35:17: 11000000 INFO @ Sat, 06 Jul 2019 02:35:21: 10000000 INFO @ Sat, 06 Jul 2019 02:35:23: 9000000 INFO @ Sat, 06 Jul 2019 02:35:24: 12000000 INFO @ Sat, 06 Jul 2019 02:35:29: 11000000 INFO @ Sat, 06 Jul 2019 02:35:30: 13000000 INFO @ Sat, 06 Jul 2019 02:35:32: 10000000 INFO @ Sat, 06 Jul 2019 02:35:36: 12000000 INFO @ Sat, 06 Jul 2019 02:35:37: 14000000 INFO @ Sat, 06 Jul 2019 02:35:40: 11000000 INFO @ Sat, 06 Jul 2019 02:35:44: 13000000 INFO @ Sat, 06 Jul 2019 02:35:44: 15000000 INFO @ Sat, 06 Jul 2019 02:35:50: 12000000 INFO @ Sat, 06 Jul 2019 02:35:50: 16000000 INFO @ Sat, 06 Jul 2019 02:35:51: 14000000 INFO @ Sat, 06 Jul 2019 02:35:56: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:35:56: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:35:56: #1 total tags in treatment: 7905215 INFO @ Sat, 06 Jul 2019 02:35:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:35:56: #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 02:35:56: #1 tags after filtering in treatment: 5642458 INFO @ Sat, 06 Jul 2019 02:35:56: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 02:35:56: #1 finished! INFO @ Sat, 06 Jul 2019 02:35:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:35:56: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:35:56: 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, 06 Jul 2019 02:35:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.05_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/SRX4915177/SRX4915177.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:35:59: 15000000 INFO @ Sat, 06 Jul 2019 02:35:59: 13000000 INFO @ Sat, 06 Jul 2019 02:36:06: 16000000 INFO @ Sat, 06 Jul 2019 02:36:08: 14000000 INFO @ Sat, 06 Jul 2019 02:36:12: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:36:12: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:36:12: #1 total tags in treatment: 7905215 INFO @ Sat, 06 Jul 2019 02:36:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:36:12: #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 02:36:12: #1 tags after filtering in treatment: 5642458 INFO @ Sat, 06 Jul 2019 02:36:12: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 02:36:12: #1 finished! INFO @ Sat, 06 Jul 2019 02:36:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:36:13: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:36:13: 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, 06 Jul 2019 02:36:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.20_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/SRX4915177/SRX4915177.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:36:18: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:36:27: 16000000 INFO @ Sat, 06 Jul 2019 02:36:34: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:36:34: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:36:34: #1 total tags in treatment: 7905215 INFO @ Sat, 06 Jul 2019 02:36:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:36:34: #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 02:36:34: #1 tags after filtering in treatment: 5642458 INFO @ Sat, 06 Jul 2019 02:36:34: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 06 Jul 2019 02:36:34: #1 finished! INFO @ Sat, 06 Jul 2019 02:36:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:36:34: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:36:34: 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, 06 Jul 2019 02:36:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.10_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/SRX4915177/SRX4915177.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915177/SRX4915177.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。