Job ID = 2010746 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:11:51 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 ) 2019-07-05T15:16:16 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 ) 2019-07-05T15:19:46 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 ) 2019-07-05T15:26:50 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 : 12,441,206 reads read : 24,882,412 reads written : 24,882,412 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: 00:11:15 12441206 reads; of these: 12441206 (100.00%) were paired; of these: 1774637 (14.26%) aligned concordantly 0 times 9307022 (74.81%) aligned concordantly exactly 1 time 1359547 (10.93%) aligned concordantly >1 times ---- 1774637 pairs aligned concordantly 0 times; of these: 159205 (8.97%) aligned discordantly 1 time ---- 1615432 pairs aligned 0 times concordantly or discordantly; of these: 3230864 mates make up the pairs; of these: 2732283 (84.57%) aligned 0 times 359105 (11.11%) aligned exactly 1 time 139476 (4.32%) aligned >1 times 89.02% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 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 12 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] 210415 / 10792221 = 0.0195 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 00:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.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 00:55:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:55:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.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 00:56:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:56:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.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 00:56:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:56:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:56:07: 1000000 INFO @ Sat, 06 Jul 2019 00:56:10: 1000000 INFO @ Sat, 06 Jul 2019 00:56:12: 1000000 INFO @ Sat, 06 Jul 2019 00:56:15: 2000000 INFO @ Sat, 06 Jul 2019 00:56:20: 2000000 INFO @ Sat, 06 Jul 2019 00:56:21: 2000000 INFO @ Sat, 06 Jul 2019 00:56:23: 3000000 INFO @ Sat, 06 Jul 2019 00:56:30: 3000000 INFO @ Sat, 06 Jul 2019 00:56:31: 3000000 INFO @ Sat, 06 Jul 2019 00:56:31: 4000000 INFO @ Sat, 06 Jul 2019 00:56:40: 5000000 INFO @ Sat, 06 Jul 2019 00:56:40: 4000000 INFO @ Sat, 06 Jul 2019 00:56:41: 4000000 INFO @ Sat, 06 Jul 2019 00:56:48: 6000000 INFO @ Sat, 06 Jul 2019 00:56:51: 5000000 INFO @ Sat, 06 Jul 2019 00:56:52: 5000000 INFO @ Sat, 06 Jul 2019 00:56:56: 7000000 INFO @ Sat, 06 Jul 2019 00:57:01: 6000000 INFO @ Sat, 06 Jul 2019 00:57:02: 6000000 INFO @ Sat, 06 Jul 2019 00:57:04: 8000000 INFO @ Sat, 06 Jul 2019 00:57:11: 7000000 INFO @ Sat, 06 Jul 2019 00:57:12: 7000000 INFO @ Sat, 06 Jul 2019 00:57:12: 9000000 INFO @ Sat, 06 Jul 2019 00:57:20: 10000000 INFO @ Sat, 06 Jul 2019 00:57:21: 8000000 INFO @ Sat, 06 Jul 2019 00:57:22: 8000000 INFO @ Sat, 06 Jul 2019 00:57:28: 11000000 INFO @ Sat, 06 Jul 2019 00:57:32: 9000000 INFO @ Sat, 06 Jul 2019 00:57:33: 9000000 INFO @ Sat, 06 Jul 2019 00:57:37: 12000000 INFO @ Sat, 06 Jul 2019 00:57:42: 10000000 INFO @ Sat, 06 Jul 2019 00:57:43: 10000000 INFO @ Sat, 06 Jul 2019 00:57:45: 13000000 INFO @ Sat, 06 Jul 2019 00:57:52: 11000000 INFO @ Sat, 06 Jul 2019 00:57:53: 14000000 INFO @ Sat, 06 Jul 2019 00:57:53: 11000000 INFO @ Sat, 06 Jul 2019 00:58:01: 15000000 INFO @ Sat, 06 Jul 2019 00:58:02: 12000000 INFO @ Sat, 06 Jul 2019 00:58:03: 12000000 INFO @ Sat, 06 Jul 2019 00:58:09: 16000000 INFO @ Sat, 06 Jul 2019 00:58:12: 13000000 INFO @ Sat, 06 Jul 2019 00:58:13: 13000000 INFO @ Sat, 06 Jul 2019 00:58:17: 17000000 INFO @ Sat, 06 Jul 2019 00:58:23: 14000000 INFO @ Sat, 06 Jul 2019 00:58:23: 14000000 INFO @ Sat, 06 Jul 2019 00:58:25: 18000000 INFO @ Sat, 06 Jul 2019 00:58:33: 15000000 INFO @ Sat, 06 Jul 2019 00:58:33: 19000000 INFO @ Sat, 06 Jul 2019 00:58:33: 15000000 INFO @ Sat, 06 Jul 2019 00:58:41: 20000000 INFO @ Sat, 06 Jul 2019 00:58:43: 16000000 INFO @ Sat, 06 Jul 2019 00:58:43: 16000000 INFO @ Sat, 06 Jul 2019 00:58:49: 21000000 INFO @ Sat, 06 Jul 2019 00:58:53: 17000000 INFO @ Sat, 06 Jul 2019 00:58:54: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:58:55: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:58:55: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:58:55: #1 total tags in treatment: 10457333 INFO @ Sat, 06 Jul 2019 00:58:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:58:55: #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 00:58:55: #1 tags after filtering in treatment: 7815449 INFO @ Sat, 06 Jul 2019 00:58:55: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 00:58:55: #1 finished! INFO @ Sat, 06 Jul 2019 00:58:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:58:56: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:58:56: 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 00:58:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.05_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/SRX386926/SRX386926.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:59:02: 18000000 INFO @ Sat, 06 Jul 2019 00:59:03: 18000000 INFO @ Sat, 06 Jul 2019 00:59:11: 19000000 INFO @ Sat, 06 Jul 2019 00:59:12: 19000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:59:20: 20000000 INFO @ Sat, 06 Jul 2019 00:59:21: 20000000 INFO @ Sat, 06 Jul 2019 00:59:30: 21000000 INFO @ Sat, 06 Jul 2019 00:59:31: 21000000 INFO @ Sat, 06 Jul 2019 00:59:36: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:59:36: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:59:36: #1 total tags in treatment: 10457333 INFO @ Sat, 06 Jul 2019 00:59:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:59:36: #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 00:59:36: #1 tags after filtering in treatment: 7815449 INFO @ Sat, 06 Jul 2019 00:59:36: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 00:59:36: #1 finished! INFO @ Sat, 06 Jul 2019 00:59:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:59:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:59:37: 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 00:59:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.10_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/SRX386926/SRX386926.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:59:37: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:59:37: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:59:37: #1 total tags in treatment: 10457333 INFO @ Sat, 06 Jul 2019 00:59:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:59:37: #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 00:59:37: #1 tags after filtering in treatment: 7815449 INFO @ Sat, 06 Jul 2019 00:59:37: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 00:59:37: #1 finished! INFO @ Sat, 06 Jul 2019 00:59:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:59:38: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:59:38: 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 00:59:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.20_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/SRX386926/SRX386926.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386926/SRX386926.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling