Job ID = 2010785 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:41:00 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 ) 2019-07-05T15:41:00 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 ) 2019-07-05T15:43:37 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 ) 2019-07-05T15:50:48 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 ) 2019-07-05T15:50:48 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 : 13,808,287 reads read : 27,616,574 reads written : 27,616,574 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: 00:11:21 13808287 reads; of these: 13808287 (100.00%) were paired; of these: 4363954 (31.60%) aligned concordantly 0 times 5444424 (39.43%) aligned concordantly exactly 1 time 3999909 (28.97%) aligned concordantly >1 times ---- 4363954 pairs aligned concordantly 0 times; of these: 3714 (0.09%) aligned discordantly 1 time ---- 4360240 pairs aligned 0 times concordantly or discordantly; of these: 8720480 mates make up the pairs; of these: 8036485 (92.16%) aligned 0 times 178154 (2.04%) aligned exactly 1 time 505841 (5.80%) aligned >1 times 70.90% overall alignment rate Time searching: 00:11:21 Overall time: 00:11:21 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] 2312728 / 9439455 = 0.2450 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 01:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.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 01:10:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:10:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.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 01:10:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:10:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.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 01:10:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:10:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:11:02: 1000000 INFO @ Sat, 06 Jul 2019 01:11:03: 1000000 INFO @ Sat, 06 Jul 2019 01:11:04: 1000000 INFO @ Sat, 06 Jul 2019 01:11:10: 2000000 INFO @ Sat, 06 Jul 2019 01:11:11: 2000000 INFO @ Sat, 06 Jul 2019 01:11:11: 2000000 INFO @ Sat, 06 Jul 2019 01:11:18: 3000000 INFO @ Sat, 06 Jul 2019 01:11:18: 3000000 INFO @ Sat, 06 Jul 2019 01:11:19: 3000000 INFO @ Sat, 06 Jul 2019 01:11:25: 4000000 INFO @ Sat, 06 Jul 2019 01:11:26: 4000000 INFO @ Sat, 06 Jul 2019 01:11:27: 4000000 INFO @ Sat, 06 Jul 2019 01:11:32: 5000000 INFO @ Sat, 06 Jul 2019 01:11:34: 5000000 INFO @ Sat, 06 Jul 2019 01:11:35: 5000000 INFO @ Sat, 06 Jul 2019 01:11:40: 6000000 INFO @ Sat, 06 Jul 2019 01:11:42: 6000000 INFO @ Sat, 06 Jul 2019 01:11:43: 6000000 INFO @ Sat, 06 Jul 2019 01:11:48: 7000000 INFO @ Sat, 06 Jul 2019 01:11:51: 7000000 INFO @ Sat, 06 Jul 2019 01:11:52: 7000000 INFO @ Sat, 06 Jul 2019 01:11:58: 8000000 INFO @ Sat, 06 Jul 2019 01:11:59: 8000000 INFO @ Sat, 06 Jul 2019 01:12:00: 8000000 INFO @ Sat, 06 Jul 2019 01:12:06: 9000000 INFO @ Sat, 06 Jul 2019 01:12:08: 9000000 INFO @ Sat, 06 Jul 2019 01:12:08: 9000000 INFO @ Sat, 06 Jul 2019 01:12:14: 10000000 INFO @ Sat, 06 Jul 2019 01:12:16: 10000000 INFO @ Sat, 06 Jul 2019 01:12:17: 10000000 INFO @ Sat, 06 Jul 2019 01:12:22: 11000000 INFO @ Sat, 06 Jul 2019 01:12:23: 11000000 INFO @ Sat, 06 Jul 2019 01:12:26: 11000000 INFO @ Sat, 06 Jul 2019 01:12:30: 12000000 INFO @ Sat, 06 Jul 2019 01:12:31: 12000000 INFO @ Sat, 06 Jul 2019 01:12:36: 12000000 INFO @ Sat, 06 Jul 2019 01:12:38: 13000000 INFO @ Sat, 06 Jul 2019 01:12:39: 13000000 INFO @ Sat, 06 Jul 2019 01:12:45: 14000000 INFO @ Sat, 06 Jul 2019 01:12:46: 13000000 INFO @ Sat, 06 Jul 2019 01:12:47: 14000000 INFO @ Sat, 06 Jul 2019 01:12:53: #1 tag size is determined as 45 bps INFO @ Sat, 06 Jul 2019 01:12:53: #1 tag size = 45 INFO @ Sat, 06 Jul 2019 01:12:53: #1 total tags in treatment: 7132037 INFO @ Sat, 06 Jul 2019 01:12:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:12:53: #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 01:12:53: #1 tags after filtering in treatment: 4303524 INFO @ Sat, 06 Jul 2019 01:12:53: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 01:12:53: #1 finished! INFO @ Sat, 06 Jul 2019 01:12:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:12:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:12:53: #2 number of paired peaks: 44 WARNING @ Sat, 06 Jul 2019 01:12:53: Too few paired peaks (44) 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 01:12:53: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:12:54: #1 tag size is determined as 45 bps INFO @ Sat, 06 Jul 2019 01:12:54: #1 tag size = 45 INFO @ Sat, 06 Jul 2019 01:12:54: #1 total tags in treatment: 7132037 INFO @ Sat, 06 Jul 2019 01:12:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:12:54: #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 01:12:54: #1 tags after filtering in treatment: 4303524 INFO @ Sat, 06 Jul 2019 01:12:54: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 01:12:54: #1 finished! INFO @ Sat, 06 Jul 2019 01:12:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:12:55: #2 number of paired peaks: 44 WARNING @ Sat, 06 Jul 2019 01:12:55: Too few paired peaks (44) 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 01:12:55: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:12:55: 14000000 BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 01:13:03: #1 tag size is determined as 45 bps INFO @ Sat, 06 Jul 2019 01:13:03: #1 tag size = 45 INFO @ Sat, 06 Jul 2019 01:13:03: #1 total tags in treatment: 7132037 INFO @ Sat, 06 Jul 2019 01:13:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:13:03: #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 01:13:03: #1 tags after filtering in treatment: 4303524 INFO @ Sat, 06 Jul 2019 01:13:03: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 01:13:03: #1 finished! INFO @ Sat, 06 Jul 2019 01:13:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:13:04: #2 number of paired peaks: 44 WARNING @ Sat, 06 Jul 2019 01:13:04: Too few paired peaks (44) 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 01:13:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.20_peaks.narrowPeak : No such file or directoryBigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.10_model.r’: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.20_model.r’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.10_*.xls’: No such file or directory: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404602/SRX404602.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。