Job ID = 2010674 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:52:28 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 ) 2019-07-05T14:52:28 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 ) 2019-07-05T14:52:28 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 ) 2019-07-05T14:52:28 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 : 7,277,646 reads read : 14,555,292 reads written : 14,555,292 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: 00:04:07 7277646 reads; of these: 7277646 (100.00%) were paired; of these: 2366339 (32.52%) aligned concordantly 0 times 4694070 (64.50%) aligned concordantly exactly 1 time 217237 (2.98%) aligned concordantly >1 times ---- 2366339 pairs aligned concordantly 0 times; of these: 70068 (2.96%) aligned discordantly 1 time ---- 2296271 pairs aligned 0 times concordantly or discordantly; of these: 4592542 mates make up the pairs; of these: 2527067 (55.03%) aligned 0 times 1949564 (42.45%) aligned exactly 1 time 115911 (2.52%) aligned >1 times 82.64% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 228480 / 4980749 = 0.0459 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 00:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.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 00:02:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:02:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.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 00:02:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:02:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.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 00:03:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:04: 1000000 INFO @ Sat, 06 Jul 2019 00:03:06: 1000000 INFO @ Sat, 06 Jul 2019 00:03:06: 1000000 INFO @ Sat, 06 Jul 2019 00:03:10: 2000000 INFO @ Sat, 06 Jul 2019 00:03:13: 2000000 INFO @ Sat, 06 Jul 2019 00:03:13: 2000000 INFO @ Sat, 06 Jul 2019 00:03:17: 3000000 INFO @ Sat, 06 Jul 2019 00:03:19: 3000000 INFO @ Sat, 06 Jul 2019 00:03:21: 3000000 INFO @ Sat, 06 Jul 2019 00:03:23: 4000000 INFO @ Sat, 06 Jul 2019 00:03:25: 4000000 INFO @ Sat, 06 Jul 2019 00:03:28: 4000000 INFO @ Sat, 06 Jul 2019 00:03:29: 5000000 INFO @ Sat, 06 Jul 2019 00:03:32: 5000000 INFO @ Sat, 06 Jul 2019 00:03:35: 6000000 INFO @ Sat, 06 Jul 2019 00:03:36: 5000000 INFO @ Sat, 06 Jul 2019 00:03:38: 6000000 INFO @ Sat, 06 Jul 2019 00:03:42: 7000000 INFO @ Sat, 06 Jul 2019 00:03:44: 7000000 INFO @ Sat, 06 Jul 2019 00:03:45: 6000000 INFO @ Sat, 06 Jul 2019 00:03:48: 8000000 INFO @ Sat, 06 Jul 2019 00:03:51: 8000000 INFO @ Sat, 06 Jul 2019 00:03:54: 7000000 INFO @ Sat, 06 Jul 2019 00:03:54: 9000000 INFO @ Sat, 06 Jul 2019 00:03:57: 9000000 INFO @ Sat, 06 Jul 2019 00:04:01: 10000000 INFO @ Sat, 06 Jul 2019 00:04:02: 8000000 INFO @ Sat, 06 Jul 2019 00:04:03: 10000000 INFO @ Sat, 06 Jul 2019 00:04:07: 11000000 INFO @ Sat, 06 Jul 2019 00:04:09: 11000000 INFO @ Sat, 06 Jul 2019 00:04:11: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:04:11: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:04:11: #1 total tags in treatment: 4683597 INFO @ Sat, 06 Jul 2019 00:04:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:04:11: #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 00:04:11: #1 tags after filtering in treatment: 2650155 INFO @ Sat, 06 Jul 2019 00:04:11: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 06 Jul 2019 00:04:11: #1 finished! INFO @ Sat, 06 Jul 2019 00:04:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:04:11: 9000000 INFO @ Sat, 06 Jul 2019 00:04:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:04:11: 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 00:04:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.05_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/SRX3865885/SRX3865885.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:04:13: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:04:13: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:04:13: #1 total tags in treatment: 4683597 INFO @ Sat, 06 Jul 2019 00:04:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:04:13: #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 00:04:13: #1 tags after filtering in treatment: 2650155 INFO @ Sat, 06 Jul 2019 00:04:13: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 06 Jul 2019 00:04:13: #1 finished! INFO @ Sat, 06 Jul 2019 00:04:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:04:13: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:04:13: 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 00:04:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.20_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/SRX3865885/SRX3865885.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:04:19: 10000000 INFO @ Sat, 06 Jul 2019 00:04:27: 11000000 INFO @ Sat, 06 Jul 2019 00:04:32: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:04:32: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:04:32: #1 total tags in treatment: 4683597 INFO @ Sat, 06 Jul 2019 00:04:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:04:32: #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 00:04:32: #1 tags after filtering in treatment: 2650155 INFO @ Sat, 06 Jul 2019 00:04:32: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 06 Jul 2019 00:04:32: #1 finished! INFO @ Sat, 06 Jul 2019 00:04:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:04:32: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:04:32: 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 00:04:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.10_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/SRX3865885/SRX3865885.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865885/SRX3865885.10_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。