Job ID = 2010737 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:11:35 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 ) 2019-07-05T15:11:35 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 ) 2019-07-05T15:11:35 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 ) 2019-07-05T15:11:35 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 ) 2019-07-05T15:11:35 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 ) 2019-07-05T15:11:35 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 ) 2019-07-05T15:13:06 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 ) 2019-07-05T15:13:06 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 : 5,681,943 reads read : 11,363,886 reads written : 11,363,886 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: 00:05:14 5681943 reads; of these: 5681943 (100.00%) were paired; of these: 995477 (17.52%) aligned concordantly 0 times 4081459 (71.83%) aligned concordantly exactly 1 time 605007 (10.65%) aligned concordantly >1 times ---- 995477 pairs aligned concordantly 0 times; of these: 73032 (7.34%) aligned discordantly 1 time ---- 922445 pairs aligned 0 times concordantly or discordantly; of these: 1844890 mates make up the pairs; of these: 1659693 (89.96%) aligned 0 times 120958 (6.56%) aligned exactly 1 time 64239 (3.48%) aligned >1 times 85.40% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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_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] 60376 / 4744733 = 0.0127 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 00:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.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 00:30:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:30:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.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 00:30:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:30:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.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 00:30:57: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:30:57: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:31:05: 1000000 INFO @ Sat, 06 Jul 2019 00:31:06: 1000000 INFO @ Sat, 06 Jul 2019 00:31:10: 1000000 INFO @ Sat, 06 Jul 2019 00:31:14: 2000000 INFO @ Sat, 06 Jul 2019 00:31:15: 2000000 INFO @ Sat, 06 Jul 2019 00:31:21: 2000000 INFO @ Sat, 06 Jul 2019 00:31:22: 3000000 INFO @ Sat, 06 Jul 2019 00:31:25: 3000000 INFO @ Sat, 06 Jul 2019 00:31:30: 4000000 INFO @ Sat, 06 Jul 2019 00:31:33: 3000000 INFO @ Sat, 06 Jul 2019 00:31:35: 4000000 INFO @ Sat, 06 Jul 2019 00:31:39: 5000000 INFO @ Sat, 06 Jul 2019 00:31:44: 5000000 INFO @ Sat, 06 Jul 2019 00:31:45: 4000000 INFO @ Sat, 06 Jul 2019 00:31:47: 6000000 INFO @ Sat, 06 Jul 2019 00:31:54: 6000000 INFO @ Sat, 06 Jul 2019 00:31:55: 7000000 INFO @ Sat, 06 Jul 2019 00:31:57: 5000000 INFO @ Sat, 06 Jul 2019 00:32:03: 7000000 INFO @ Sat, 06 Jul 2019 00:32:04: 8000000 INFO @ Sat, 06 Jul 2019 00:32:09: 6000000 INFO @ Sat, 06 Jul 2019 00:32:12: 9000000 INFO @ Sat, 06 Jul 2019 00:32:13: 8000000 INFO @ Sat, 06 Jul 2019 00:32:17: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:17: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:17: #1 total tags in treatment: 4626561 INFO @ Sat, 06 Jul 2019 00:32:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:17: #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 00:32:17: #1 tags after filtering in treatment: 3890480 INFO @ Sat, 06 Jul 2019 00:32:17: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 00:32:17: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:17: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 00:32:17: Too few paired peaks (29) 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 00:32:17: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:32:20: 7000000 INFO @ Sat, 06 Jul 2019 00:32:23: 9000000 INFO @ Sat, 06 Jul 2019 00:32:29: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:29: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:29: #1 total tags in treatment: 4626561 INFO @ Sat, 06 Jul 2019 00:32:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:29: #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 00:32:29: #1 tags after filtering in treatment: 3890480 INFO @ Sat, 06 Jul 2019 00:32:29: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 00:32:29: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:29: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 00:32:29: Too few paired peaks (29) 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 00:32:29: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:32:32: 8000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.05_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/SRX386918/SRX386918.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:32:43: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:32:49: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:49: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:49: #1 total tags in treatment: 4626561 INFO @ Sat, 06 Jul 2019 00:32:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:49: #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 00:32:49: #1 tags after filtering in treatment: 3890480 INFO @ Sat, 06 Jul 2019 00:32:49: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 00:32:49: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:49: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:50: #2 number of paired peaks: 29 WARNING @ Sat, 06 Jul 2019 00:32:50: Too few paired peaks (29) 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 00:32:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.20_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/SRX386918/SRX386918.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386918/SRX386918.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。