Job ID = 2011761 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:26:02 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 ) 2019-07-05T17:26:02 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 : 6,902,593 reads read : 13,805,186 reads written : 13,805,186 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: 00:05:24 6902593 reads; of these: 6902593 (100.00%) were paired; of these: 631903 (9.15%) aligned concordantly 0 times 4575080 (66.28%) aligned concordantly exactly 1 time 1695610 (24.56%) aligned concordantly >1 times ---- 631903 pairs aligned concordantly 0 times; of these: 73635 (11.65%) aligned discordantly 1 time ---- 558268 pairs aligned 0 times concordantly or discordantly; of these: 1116536 mates make up the pairs; of these: 991506 (88.80%) aligned 0 times 73771 (6.61%) aligned exactly 1 time 51259 (4.59%) aligned >1 times 92.82% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 845481 / 6338449 = 0.1334 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 02:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.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 02:39:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.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 02:39:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.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 02:39:08: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:08: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:14: 1000000 INFO @ Sat, 06 Jul 2019 02:39:15: 1000000 INFO @ Sat, 06 Jul 2019 02:39:18: 1000000 INFO @ Sat, 06 Jul 2019 02:39:20: 2000000 INFO @ Sat, 06 Jul 2019 02:39:23: 2000000 INFO @ Sat, 06 Jul 2019 02:39:27: 2000000 INFO @ Sat, 06 Jul 2019 02:39:27: 3000000 INFO @ Sat, 06 Jul 2019 02:39:31: 3000000 INFO @ Sat, 06 Jul 2019 02:39:34: 4000000 INFO @ Sat, 06 Jul 2019 02:39:37: 3000000 INFO @ Sat, 06 Jul 2019 02:39:38: 4000000 INFO @ Sat, 06 Jul 2019 02:39:41: 5000000 INFO @ Sat, 06 Jul 2019 02:39:46: 4000000 INFO @ Sat, 06 Jul 2019 02:39:46: 5000000 INFO @ Sat, 06 Jul 2019 02:39:48: 6000000 INFO @ Sat, 06 Jul 2019 02:39:54: 6000000 INFO @ Sat, 06 Jul 2019 02:39:55: 7000000 INFO @ Sat, 06 Jul 2019 02:39:55: 5000000 INFO @ Sat, 06 Jul 2019 02:40:02: 7000000 INFO @ Sat, 06 Jul 2019 02:40:02: 8000000 INFO @ Sat, 06 Jul 2019 02:40:05: 6000000 INFO @ Sat, 06 Jul 2019 02:40:09: 9000000 INFO @ Sat, 06 Jul 2019 02:40:09: 8000000 INFO @ Sat, 06 Jul 2019 02:40:14: 7000000 INFO @ Sat, 06 Jul 2019 02:40:15: 10000000 INFO @ Sat, 06 Jul 2019 02:40:17: 9000000 INFO @ Sat, 06 Jul 2019 02:40:22: 11000000 INFO @ Sat, 06 Jul 2019 02:40:23: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:40:23: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:40:23: #1 total tags in treatment: 5426133 INFO @ Sat, 06 Jul 2019 02:40:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:40:23: #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 02:40:23: 8000000 INFO @ Sat, 06 Jul 2019 02:40:23: #1 tags after filtering in treatment: 3885423 INFO @ Sat, 06 Jul 2019 02:40:23: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 06 Jul 2019 02:40:23: #1 finished! INFO @ Sat, 06 Jul 2019 02:40:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:40:24: #2 number of paired peaks: 45 WARNING @ Sat, 06 Jul 2019 02:40:24: Too few paired peaks (45) 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 02:40:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.05_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/SRX497387/SRX497387.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:40:25: 10000000 INFO @ Sat, 06 Jul 2019 02:40:32: 9000000 INFO @ Sat, 06 Jul 2019 02:40:32: 11000000 INFO @ Sat, 06 Jul 2019 02:40:33: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:40:33: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:40:33: #1 total tags in treatment: 5426133 INFO @ Sat, 06 Jul 2019 02:40:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:40:33: #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 02:40:34: #1 tags after filtering in treatment: 3885423 INFO @ Sat, 06 Jul 2019 02:40:34: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 06 Jul 2019 02:40:34: #1 finished! INFO @ Sat, 06 Jul 2019 02:40:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:40:34: #2 number of paired peaks: 45 WARNING @ Sat, 06 Jul 2019 02:40:34: Too few paired peaks (45) 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 02:40:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.10_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/SRX497387/SRX497387.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:40:41: 10000000 INFO @ Sat, 06 Jul 2019 02:40:50: 11000000 INFO @ Sat, 06 Jul 2019 02:40:51: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:40:51: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:40:51: #1 total tags in treatment: 5426133 INFO @ Sat, 06 Jul 2019 02:40:51: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:40:51: #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 02:40:51: #1 tags after filtering in treatment: 3885423 INFO @ Sat, 06 Jul 2019 02:40:51: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 06 Jul 2019 02:40:51: #1 finished! INFO @ Sat, 06 Jul 2019 02:40:51: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:40:52: #2 number of paired peaks: 45 WARNING @ Sat, 06 Jul 2019 02:40:52: Too few paired peaks (45) 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 02:40:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.20_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/SRX497387/SRX497387.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX497387/SRX497387.20_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。