Job ID = 2640984 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:17:03 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 ) 2019-08-24T11:17:03 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 ) 2019-08-24T11:17:03 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 ) 2019-08-24T11:17:03 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 ) 2019-08-24T11:18:50 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 ) 2019-08-24T11:19:12 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 : 12,942,438 reads read : 25,884,876 reads written : 25,884,876 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: 00:15:04 12942438 reads; of these: 12942438 (100.00%) were paired; of these: 910207 (7.03%) aligned concordantly 0 times 11039260 (85.30%) aligned concordantly exactly 1 time 992971 (7.67%) aligned concordantly >1 times ---- 910207 pairs aligned concordantly 0 times; of these: 99485 (10.93%) aligned discordantly 1 time ---- 810722 pairs aligned 0 times concordantly or discordantly; of these: 1621444 mates make up the pairs; of these: 1575544 (97.17%) aligned 0 times 23963 (1.48%) aligned exactly 1 time 21937 (1.35%) aligned >1 times 93.91% overall alignment rate Time searching: 00:15:04 Overall time: 00:15:04 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] 159308 / 12126988 = 0.0131 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.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, 24 Aug 2019 20:58:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:58:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:58:14: 1000000 INFO @ Sat, 24 Aug 2019 20:58:21: 2000000 INFO @ Sat, 24 Aug 2019 20:58:29: 3000000 INFO @ Sat, 24 Aug 2019 20:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.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, 24 Aug 2019 20:58:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:58:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:58:37: 4000000 INFO @ Sat, 24 Aug 2019 20:58:45: 5000000 INFO @ Sat, 24 Aug 2019 20:58:47: 1000000 INFO @ Sat, 24 Aug 2019 20:58:53: 6000000 INFO @ Sat, 24 Aug 2019 20:58:59: 2000000 INFO @ Sat, 24 Aug 2019 20:59:01: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.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, 24 Aug 2019 20:59:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:59:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:59:10: 8000000 INFO @ Sat, 24 Aug 2019 20:59:10: 3000000 INFO @ Sat, 24 Aug 2019 20:59:14: 1000000 INFO @ Sat, 24 Aug 2019 20:59:18: 9000000 INFO @ Sat, 24 Aug 2019 20:59:22: 4000000 INFO @ Sat, 24 Aug 2019 20:59:23: 2000000 INFO @ Sat, 24 Aug 2019 20:59:26: 10000000 INFO @ Sat, 24 Aug 2019 20:59:31: 3000000 INFO @ Sat, 24 Aug 2019 20:59:33: 5000000 INFO @ Sat, 24 Aug 2019 20:59:34: 11000000 INFO @ Sat, 24 Aug 2019 20:59:40: 4000000 INFO @ Sat, 24 Aug 2019 20:59:43: 12000000 INFO @ Sat, 24 Aug 2019 20:59:45: 6000000 INFO @ Sat, 24 Aug 2019 20:59:48: 5000000 INFO @ Sat, 24 Aug 2019 20:59:51: 13000000 INFO @ Sat, 24 Aug 2019 20:59:56: 7000000 INFO @ Sat, 24 Aug 2019 20:59:56: 6000000 INFO @ Sat, 24 Aug 2019 20:59:59: 14000000 INFO @ Sat, 24 Aug 2019 21:00:05: 7000000 INFO @ Sat, 24 Aug 2019 21:00:07: 8000000 INFO @ Sat, 24 Aug 2019 21:00:08: 15000000 INFO @ Sat, 24 Aug 2019 21:00:13: 8000000 INFO @ Sat, 24 Aug 2019 21:00:16: 16000000 INFO @ Sat, 24 Aug 2019 21:00:19: 9000000 INFO @ Sat, 24 Aug 2019 21:00:21: 9000000 INFO @ Sat, 24 Aug 2019 21:00:24: 17000000 INFO @ Sat, 24 Aug 2019 21:00:31: 10000000 INFO @ Sat, 24 Aug 2019 21:00:31: 10000000 INFO @ Sat, 24 Aug 2019 21:00:32: 18000000 INFO @ Sat, 24 Aug 2019 21:00:40: 11000000 INFO @ Sat, 24 Aug 2019 21:00:42: 19000000 INFO @ Sat, 24 Aug 2019 21:00:43: 11000000 INFO @ Sat, 24 Aug 2019 21:00:50: 12000000 INFO @ Sat, 24 Aug 2019 21:00:52: 20000000 INFO @ Sat, 24 Aug 2019 21:00:54: 12000000 INFO @ Sat, 24 Aug 2019 21:01:00: 13000000 INFO @ Sat, 24 Aug 2019 21:01:02: 21000000 INFO @ Sat, 24 Aug 2019 21:01:06: 13000000 INFO @ Sat, 24 Aug 2019 21:01:10: 14000000 INFO @ Sat, 24 Aug 2019 21:01:11: 22000000 INFO @ Sat, 24 Aug 2019 21:01:17: 14000000 INFO @ Sat, 24 Aug 2019 21:01:19: 15000000 INFO @ Sat, 24 Aug 2019 21:01:21: 23000000 INFO @ Sat, 24 Aug 2019 21:01:29: 15000000 INFO @ Sat, 24 Aug 2019 21:01:29: 16000000 INFO @ Sat, 24 Aug 2019 21:01:31: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:01:31: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:01:31: #1 total tags in treatment: 11873650 INFO @ Sat, 24 Aug 2019 21:01:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:01:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:01:31: #1 tags after filtering in treatment: 8372470 INFO @ Sat, 24 Aug 2019 21:01:31: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:01:31: #1 finished! INFO @ Sat, 24 Aug 2019 21:01:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:01:31: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:01:31: 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, 24 Aug 2019 21:01:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.05_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/SRX4936090/SRX4936090.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:01:37: 17000000 INFO @ Sat, 24 Aug 2019 21:01:40: 16000000 INFO @ Sat, 24 Aug 2019 21:01:45: 18000000 INFO @ Sat, 24 Aug 2019 21:01:51: 17000000 INFO @ Sat, 24 Aug 2019 21:01:53: 19000000 INFO @ Sat, 24 Aug 2019 21:02:01: 20000000 INFO @ Sat, 24 Aug 2019 21:02:02: 18000000 INFO @ Sat, 24 Aug 2019 21:02:09: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:02:14: 19000000 INFO @ Sat, 24 Aug 2019 21:02:18: 22000000 INFO @ Sat, 24 Aug 2019 21:02:25: 20000000 INFO @ Sat, 24 Aug 2019 21:02:26: 23000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:02:34: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:02:34: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:02:34: #1 total tags in treatment: 11873650 INFO @ Sat, 24 Aug 2019 21:02:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:02:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:02:34: #1 tags after filtering in treatment: 8372470 INFO @ Sat, 24 Aug 2019 21:02:34: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:02:34: #1 finished! INFO @ Sat, 24 Aug 2019 21:02:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:02:35: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:02:35: 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, 24 Aug 2019 21:02:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.20_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/SRX4936090/SRX4936090.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:02:36: 21000000 INFO @ Sat, 24 Aug 2019 21:02:47: 22000000 INFO @ Sat, 24 Aug 2019 21:02:59: 23000000 INFO @ Sat, 24 Aug 2019 21:03:10: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:03:10: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:03:10: #1 total tags in treatment: 11873650 INFO @ Sat, 24 Aug 2019 21:03:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:03:10: #1 tags after filtering in treatment: 8372470 INFO @ Sat, 24 Aug 2019 21:03:10: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:03:10: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:11: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:11: 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, 24 Aug 2019 21:03:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.10_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/SRX4936090/SRX4936090.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936090/SRX4936090.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling