Job ID = 2010714 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:11:49 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 ) 2019-07-05T15:11:49 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 ) 2019-07-05T15:11:49 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 : 8,895,981 reads read : 17,791,962 reads written : 17,791,962 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: 00:07:53 8895981 reads; of these: 8895981 (100.00%) were paired; of these: 1932608 (21.72%) aligned concordantly 0 times 6140628 (69.03%) aligned concordantly exactly 1 time 822745 (9.25%) aligned concordantly >1 times ---- 1932608 pairs aligned concordantly 0 times; of these: 95132 (4.92%) aligned discordantly 1 time ---- 1837476 pairs aligned 0 times concordantly or discordantly; of these: 3674952 mates make up the pairs; of these: 3250548 (88.45%) aligned 0 times 333287 (9.07%) aligned exactly 1 time 91117 (2.48%) aligned >1 times 81.73% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 100162 / 7038499 = 0.0142 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 00:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.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 00:30:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:30:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:30:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.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 00:30:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:30:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.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 00:30:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:30:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:30:45: 1000000 INFO @ Sat, 06 Jul 2019 00:30:48: 1000000 INFO @ Sat, 06 Jul 2019 00:30:49: 1000000 INFO @ Sat, 06 Jul 2019 00:30:56: 2000000 INFO @ Sat, 06 Jul 2019 00:30:59: 2000000 INFO @ Sat, 06 Jul 2019 00:31:00: 2000000 INFO @ Sat, 06 Jul 2019 00:31:06: 3000000 INFO @ Sat, 06 Jul 2019 00:31:10: 3000000 INFO @ Sat, 06 Jul 2019 00:31:11: 3000000 INFO @ Sat, 06 Jul 2019 00:31:16: 4000000 INFO @ Sat, 06 Jul 2019 00:31:21: 4000000 INFO @ Sat, 06 Jul 2019 00:31:21: 4000000 INFO @ Sat, 06 Jul 2019 00:31:27: 5000000 INFO @ Sat, 06 Jul 2019 00:31:31: 5000000 INFO @ Sat, 06 Jul 2019 00:31:32: 5000000 INFO @ Sat, 06 Jul 2019 00:31:37: 6000000 INFO @ Sat, 06 Jul 2019 00:31:42: 6000000 INFO @ Sat, 06 Jul 2019 00:31:42: 6000000 INFO @ Sat, 06 Jul 2019 00:31:47: 7000000 INFO @ Sat, 06 Jul 2019 00:31:53: 7000000 INFO @ Sat, 06 Jul 2019 00:31:53: 7000000 INFO @ Sat, 06 Jul 2019 00:31:58: 8000000 INFO @ Sat, 06 Jul 2019 00:32:03: 8000000 INFO @ Sat, 06 Jul 2019 00:32:04: 8000000 INFO @ Sat, 06 Jul 2019 00:32:08: 9000000 INFO @ Sat, 06 Jul 2019 00:32:14: 9000000 INFO @ Sat, 06 Jul 2019 00:32:14: 9000000 INFO @ Sat, 06 Jul 2019 00:32:18: 10000000 INFO @ Sat, 06 Jul 2019 00:32:25: 10000000 INFO @ Sat, 06 Jul 2019 00:32:25: 10000000 INFO @ Sat, 06 Jul 2019 00:32:29: 11000000 INFO @ Sat, 06 Jul 2019 00:32:36: 11000000 INFO @ Sat, 06 Jul 2019 00:32:36: 11000000 INFO @ Sat, 06 Jul 2019 00:32:39: 12000000 INFO @ Sat, 06 Jul 2019 00:32:47: 12000000 INFO @ Sat, 06 Jul 2019 00:32:47: 12000000 INFO @ Sat, 06 Jul 2019 00:32:49: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:32:57: 13000000 INFO @ Sat, 06 Jul 2019 00:32:57: 13000000 INFO @ Sat, 06 Jul 2019 00:32:59: 14000000 INFO @ Sat, 06 Jul 2019 00:33:03: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:33:03: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:33:03: #1 total tags in treatment: 6863976 INFO @ Sat, 06 Jul 2019 00:33:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:33:03: #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 00:33:03: #1 tags after filtering in treatment: 5484531 INFO @ Sat, 06 Jul 2019 00:33:03: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:33:03: #1 finished! INFO @ Sat, 06 Jul 2019 00:33:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:33:03: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:33:03: 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 00:33:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.05_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/SRX386897/SRX386897.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:33:08: 14000000 INFO @ Sat, 06 Jul 2019 00:33:08: 14000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:33:12: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:33:12: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:33:12: #1 total tags in treatment: 6863976 INFO @ Sat, 06 Jul 2019 00:33:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:33:12: #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 00:33:12: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:33:12: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:33:12: #1 total tags in treatment: 6863976 INFO @ Sat, 06 Jul 2019 00:33:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:33:12: #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 00:33:12: #1 tags after filtering in treatment: 5484531 INFO @ Sat, 06 Jul 2019 00:33:12: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:33:12: #1 finished! INFO @ Sat, 06 Jul 2019 00:33:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:33:12: #1 tags after filtering in treatment: 5484531 INFO @ Sat, 06 Jul 2019 00:33:12: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:33:12: #1 finished! INFO @ Sat, 06 Jul 2019 00:33:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:33:12: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:33:12: 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 00:33:12: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:33:12: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:33:12: 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 00:33:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386897/SRX386897.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling