Job ID = 2010668 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:48:39 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 ) 2019-07-05T14:50:22 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 ) 2019-07-05T14:50:22 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 ) 2019-07-05T14:51:33 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 ) 2019-07-05T14:51:33 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 ) 2019-07-05T14:52:06 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 : 7,952,041 reads read : 15,904,082 reads written : 15,904,082 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: 00:03:50 7952041 reads; of these: 7952041 (100.00%) were paired; of these: 2788099 (35.06%) aligned concordantly 0 times 4070186 (51.18%) aligned concordantly exactly 1 time 1093756 (13.75%) aligned concordantly >1 times ---- 2788099 pairs aligned concordantly 0 times; of these: 66010 (2.37%) aligned discordantly 1 time ---- 2722089 pairs aligned 0 times concordantly or discordantly; of these: 5444178 mates make up the pairs; of these: 5105821 (93.78%) aligned 0 times 231261 (4.25%) aligned exactly 1 time 107096 (1.97%) aligned >1 times 67.90% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 583893 / 5213296 = 0.1120 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 00:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.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 00:00:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:00:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.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 00:00:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:00:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.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 00:00:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:00:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:00:08: 1000000 INFO @ Sat, 06 Jul 2019 00:00:09: 1000000 INFO @ Sat, 06 Jul 2019 00:00:10: 1000000 INFO @ Sat, 06 Jul 2019 00:00:14: 2000000 INFO @ Sat, 06 Jul 2019 00:00:16: 2000000 INFO @ Sat, 06 Jul 2019 00:00:19: 2000000 INFO @ Sat, 06 Jul 2019 00:00:22: 3000000 INFO @ Sat, 06 Jul 2019 00:00:23: 3000000 INFO @ Sat, 06 Jul 2019 00:00:27: 3000000 INFO @ Sat, 06 Jul 2019 00:00:29: 4000000 INFO @ Sat, 06 Jul 2019 00:00:30: 4000000 INFO @ Sat, 06 Jul 2019 00:00:35: 4000000 INFO @ Sat, 06 Jul 2019 00:00:36: 5000000 INFO @ Sat, 06 Jul 2019 00:00:38: 5000000 INFO @ Sat, 06 Jul 2019 00:00:43: 6000000 INFO @ Sat, 06 Jul 2019 00:00:44: 5000000 INFO @ Sat, 06 Jul 2019 00:00:45: 6000000 INFO @ Sat, 06 Jul 2019 00:00:50: 7000000 INFO @ Sat, 06 Jul 2019 00:00:51: 6000000 INFO @ Sat, 06 Jul 2019 00:00:53: 7000000 INFO @ Sat, 06 Jul 2019 00:00:58: 8000000 INFO @ Sat, 06 Jul 2019 00:01:00: 7000000 INFO @ Sat, 06 Jul 2019 00:01:00: 8000000 INFO @ Sat, 06 Jul 2019 00:01:06: 9000000 INFO @ Sat, 06 Jul 2019 00:01:08: 8000000 INFO @ Sat, 06 Jul 2019 00:01:08: 9000000 INFO @ Sat, 06 Jul 2019 00:01:10: #1 tag size is determined as 36 bps INFO @ Sat, 06 Jul 2019 00:01:10: #1 tag size = 36 INFO @ Sat, 06 Jul 2019 00:01:10: #1 total tags in treatment: 4581687 INFO @ Sat, 06 Jul 2019 00:01:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:01:10: #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 00:01:10: #1 tags after filtering in treatment: 2857304 INFO @ Sat, 06 Jul 2019 00:01:10: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 00:01:10: #1 finished! INFO @ Sat, 06 Jul 2019 00:01:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:01:11: #2 number of paired peaks: 38 WARNING @ Sat, 06 Jul 2019 00:01:11: Too few paired peaks (38) 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 00:01:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.05_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/SRX3865871/SRX3865871.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:01:13: #1 tag size is determined as 36 bps INFO @ Sat, 06 Jul 2019 00:01:13: #1 tag size = 36 INFO @ Sat, 06 Jul 2019 00:01:13: #1 total tags in treatment: 4581687 INFO @ Sat, 06 Jul 2019 00:01:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:01:13: #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 00:01:13: #1 tags after filtering in treatment: 2857304 INFO @ Sat, 06 Jul 2019 00:01:13: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 00:01:13: #1 finished! INFO @ Sat, 06 Jul 2019 00:01:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:01:14: #2 number of paired peaks: 38 WARNING @ Sat, 06 Jul 2019 00:01:14: Too few paired peaks (38) 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 00:01:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.10_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/SRX3865871/SRX3865871.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:01:16: 9000000 INFO @ Sat, 06 Jul 2019 00:01:21: #1 tag size is determined as 36 bps INFO @ Sat, 06 Jul 2019 00:01:21: #1 tag size = 36 INFO @ Sat, 06 Jul 2019 00:01:21: #1 total tags in treatment: 4581687 INFO @ Sat, 06 Jul 2019 00:01:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:01:21: #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 00:01:21: #1 tags after filtering in treatment: 2857304 INFO @ Sat, 06 Jul 2019 00:01:21: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 00:01:21: #1 finished! INFO @ Sat, 06 Jul 2019 00:01:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:01:21: #2 number of paired peaks: 38 WARNING @ Sat, 06 Jul 2019 00:01:21: Too few paired peaks (38) 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 00:01:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.20_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/SRX3865871/SRX3865871.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865871/SRX3865871.20_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。